Last updated: 2021-12-20

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Lost in seagrasses

The GO enrichment does not work well on my laptop so I’m setting this to eval=FALSE and run it on a remote server. The script which writes the input files is a Python script in the scripts/ folder: findClustersUniqueToAquatic.py. This script parses Orthofinder output to pull out genome-specific groups and genes.

# give properly formatted background in format: GO:0005838  GSBRNA2T00088508001;GSBRNA2T00088313001;GSBRNA2T00035842001 
#annAT <- readMappings('BACKGROUND.txt.gz', sep="\t", IDsep=";")
#save(annAT, file='annAtObject.RData')

load('annAtObject.RData')
allgenes <- unique(unlist(annAT))

compare <- function(genelistfile, outname, allgenes, annAT) {
  # give file with your genes of interest, one gene_id per line
  
  mygenes <-scan(genelistfile ,what="")
  geneList <- factor(as.integer(allgenes %in% mygenes))
  names(geneList) <- allgenes
  
  GOdata <-new ("topGOdata", ontology = 'BP', allGenes = geneList, nodeSize = 5, annot=annFUN.GO2genes, GO2genes=annAT)
  # using ClassicCount:
  #test.stat <-new ("classicCount", testStatistic = GOFisherTest, name = "Fisher Test")
  #resultsFisherC <-getSigGroups (GOdata, test.stat)
  # using weight01:
  weight01.fisher <- runTest(GOdata, statistic = "fisher")
  # using ClassicCount:
  # allRes <- GenTable(GOdata, classicFisher= resultsFisherC, topNodes = 30)
  # using weight01:
  allRes <- GenTable(GOdata, classicFisher=weight01.fisher,topNodes=30)#,topNodes=100)
  names(allRes)[length(allRes)] <- "p.value"
  p_values <- score(weight01.fisher)
  adjusted_p <- p.adjust(p_values)
  adjusted_p[adjusted_p < 0.05] %>% enframe() %>% write_csv('data/' + outname)

}

lost in seagrasses, each one uniquely vs all terrestrials

compare('lost_in_amphi_vs_all.txt', 'missing_amphi_vs_all_GO.txt', allgenes, annAT)
compare('lost_in_posi_vs_all.txt', 'missing_posi_vs_all_GO.txt', allgenes, annAT)
compare('lost_in_zmar_vs_all.txt', 'missing_zmar_vs_all_GO.txt', allgenes, annAT)
compare('lost_in_zmuel_vs_all.txt', 'missing_zmuel_vs_all_GO.txt', allgenes, annAT)

lost in seagrasses vs all terrestrials

Here we compare GO terms for seagrasses and aquatics (seagrasses+duckweeds) vs all terrestrials

compare('lost_in_seagrasses.txt', 'missing_seagrasses_GO.txt', allgenes, annAT)
compare('lost_in_aquatics.txt', 'missing_aquatics_GO.txt', allgenes, annAT)
compare('only_in_seagrasses.txt', 'only_seagrasses_GO.txt', allgenes, annAT)

Seagrass only comparisons

Now we compare seagrasses within each other.

For the seagrass-only comparisons, I’m using a Seagrass-only background as that makes more biological sense to me.s

# give properly formatted background in format: GO:0005838  GSBRNA2T00088508001;GSBRNA2T00088313001;GSBRNA2T00035842001 
#sannAT <- readMappings('SEAGRASSBACKGROUND.txt', sep="\t", IDsep=";")
#save(sannAT, file='sannAtObject.RData')

load('annAtObject.RData')
sallgenes <- unique(unlist(sannAT))

compare('lost_in_amphi.txt', 'lost_in_amphi_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('lost_in_posi.txt', 'lost_in_posi_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('lost_in_zmar.txt', 'lost_in_zmar_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('lost_in_zmuel.txt', 'lost_in_zmuel_vs_seagrasses_GO.txt', sallgenes, sannAT)

Present in seagrasses

The opposite - which GO-terms are present only in one of the four species?

compare('only_in_amphi.txt', 'only_in_amphi_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('only_in_posi.txt', 'only_in_posi_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('only_in_zmar.txt', 'only_in_zmar_vs_seagrasses_GO.txt', sallgenes, sannAT)
compare('only_in_zmuel.txt', 'only_in_zmuel_vs_seagrasses_GO.txt', sallgenes, sannAT)

Alright now we have all these different GO terms in all these files - we can send them to revigo for visualiation and some deduplication!

Revigo

This code is based on http://revigo.irb.hr/CodeExamples/revigo.R.txt

results_list <- list()

for (f in list.files('./data/', pattern='GO.txt')){
  filename <- paste('./data/', f, sep='')
  go_and_pvalues <- readChar(filename, file.info(filename)$size)
  go_and_pvalues <- gsub(',', ' ', go_and_pvalues)
  
  httr::POST(
    url = "http://revigo.irb.hr/StartJob.aspx",
    body = list(
      cutoff = "0.7",
      valueType = "pvalue",
     # speciesTaxon = "4577", # zea mays
     #speciesTaxon = '39947', # japonica
     speciesTaxon = '3702', # arabidopsis
      measure = "SIMREL",
      goList = go_and_pvalues
    ),
    # application/x-www-form-urlencoded
    encode = "form"
  ) -> res
  
  dat <- httr::content(res, encoding = "UTF-8")
  
  jobid <- jsonlite::fromJSON(dat,bigint_as_char=TRUE)$jobid
  
  # Check job status
  running <- "1"
  while (running != "0" ) {
      httr::POST(
        url = "http://revigo.irb.hr/QueryJobStatus.aspx",
        query = list( jobid = jobid )
      ) -> res2
      dat2 <- httr::content(res2, encoding = "UTF-8")
      running <- jsonlite::fromJSON(dat2)$running
      Sys.sleep(1)
  }
  
  # Fetch results
  httr::POST(
    url = "http://revigo.irb.hr/ExportJob.aspx",
    query = list(
      jobid = jobid, 
      namespace = "1",
      type = "CSVTable"
    )
  ) -> res3
  
  dat3 <- httr::content(res3, encoding = "UTF-8")
  
  dat3 <- stri_replace_all_fixed(dat3, "\r", "")
  # Now we have a csv table in a string!

  # read_csv does not like the ', ', it wants ','
  dat <- read_csv(gsub(', ', ',', dat3), show_col_types = FALSE) 
  
  # do we even have results?
  if(nrow(dat) == 0){next}
  results_list[[f]] <- dat
  
}

OK we have a list with all results in a big list. Now we can plot!

Making Supplementary Tables for the REVIGO results

Let’s also pull these terms out as tables. Value is the unadjusted p-value (-3.7 = 10 * -3.7)

for( i in names(results_list)) {
  print(i)
  print(knitr::kable(results_list[[i]] %>% filter(Eliminated == FALSE) %>% select(TermID, Name, Value) %>% arrange(Value), caption=i))
  cat("\n")
}

[1] “lost_in_amphi_GO.txt”

lost_in_amphi_GO.txt
TermID Name Value
GO:0006278 RNA-dependent DNA biosynthetic process -154.570365
GO:0032197 transposition,RNA-mediated -153.541147
GO:0090501 RNA phosphodiester bond hydrolysis -99.312749
GO:0006508 proteolysis -79.607924
GO:0071395 cellular response to jasmonic acid stimulus -23.603685
GO:0010726 positive regulation of hydrogen peroxide metabolic process -19.887919
GO:0080181 lateral root branching -17.324362
GO:0090305 nucleic acid phosphodiester bond hydrolysis -16.906247
GO:0010942 positive regulation of cell death -14.685584
GO:0009451 RNA modification -13.803692
GO:0044245 polysaccharide digestion -13.713775
GO:0010337 regulation of salicylic acid metabolic process -10.566727
GO:0045962 positive regulation of development,heterochronic -9.318720
GO:0006182 cGMP biosynthetic process -8.073348
GO:0015709 thiosulfate transport -7.854354
GO:0033259 plastid DNA replication -7.854354
GO:0070562 regulation of vitamin D receptor signaling pathway -6.913688
GO:0048385 regulation of retinoic acid receptor signaling pathway -6.913688
GO:0006032 chitin catabolic process -6.683057
GO:0080021 response to benzoic acid -6.390517
GO:0071465 cellular response to desiccation -6.390517
GO:0072488 ammonium transmembrane transport -6.112218
GO:0015695 organic cation transport -5.943629
GO:0071422 succinate transmembrane transport -5.214207
GO:0000350 generation of catalytic spliceosome for second transesterification step -4.812729
GO:0006264 mitochondrial DNA replication -4.812729
GO:0006334 nucleosome assembly -4.587444
GO:0009737 response to abscisic acid -3.781098
GO:1904580 regulation of intracellular mRNA localization -3.743490
GO:0006275 regulation of DNA replication -3.730017
GO:0002229 defense response to oomycetes -3.722154
GO:1990481 mRNA pseudouridine synthesis -3.677092
GO:0009648 photoperiodism -3.590301
GO:0010951 negative regulation of endopeptidase activity -3.564044
GO:0016101 diterpenoid metabolic process -3.540981
GO:0003094 glomerular filtration -3.506441
GO:0034626 fatty acid elongation,polyunsaturated fatty acid -3.464066
GO:0080153 negative regulation of reductive pentose-phosphate cycle -3.464066
GO:0010555 response to mannitol -3.407172
GO:0042178 xenobiotic catabolic process -3.362176
GO:0090059 protoxylem development -3.236933
GO:0090110 COPII-coated vesicle cargo loading -3.236933
GO:0009629 response to gravity -3.039850
GO:0048657 anther wall tapetum cell differentiation -2.917278
GO:1903335 regulation of vacuolar transport -2.864523
GO:0009089 lysine biosynthetic process via diaminopimelate -2.699278
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I -2.689686
GO:1901333 positive regulation of lateral root development -2.689686
GO:0072756 cellular response to paraquat -2.168010
GO:0035445 borate transmembrane transport -2.035237
GO:0051258 protein polymerization -1.810823
GO:2000032 regulation of secondary shoot formation -1.698816
GO:0006012 galactose metabolic process -1.606369
GO:0009554 megasporogenesis -1.321762
GO:0000495 box H/ACA RNA 3’-end processing -1.315281
GO:2000636 positive regulation of primary miRNA processing -1.315281
GO:0072344 rescue of stalled ribosome -1.315281
GO:2000630 positive regulation of miRNA metabolic process -1.315281
GO:0070126 mitochondrial translational termination -1.315281
GO:0001561 fatty acid alpha-oxidation -1.315281
GO:1902609 (R)-2-hydroxy-alpha-linolenic acid biosynthetic process -1.315281
GO:0043693 monoterpene biosynthetic process -1.315281
GO:0046622 positive regulation of organ growth -1.315281

[1] “lost_in_posi_GO.txt”

lost_in_posi_GO.txt
TermID Name Value
GO:0009451 RNA modification -42.299053
GO:0090305 nucleic acid phosphodiester bond hydrolysis -40.107639
GO:0071602 phytosphingosine biosynthetic process -10.064067
GO:0033485 cyanidin 3-O-glucoside biosynthetic process -9.116936
GO:1902184 negative regulation of shoot apical meristem development -8.322884
GO:0010064 embryonic shoot morphogenesis -6.780537
GO:0018008 N-terminal peptidyl-glycine N-myristoylation -6.780537
GO:1904158 axonemal central apparatus assembly -6.383832
GO:0052472 modulation by host of symbiont transcription -5.743965
GO:0042407 cristae formation -5.459308
GO:0050434 positive regulation of viral transcription -5.148961
GO:0031098 stress-activated protein kinase signaling cascade -4.952222
GO:0033542 fatty acid beta-oxidation,unsaturated,even number -4.842284
GO:0042351 ‘de novo’ GDP-L-fucose biosynthetic process -4.842284
GO:1904837 beta-catenin-TCF complex assembly -4.842284
GO:0046740 transport of virus in host,cell to cell -4.842284
GO:0009833 plant-type primary cell wall biogenesis -4.679683
GO:0043406 positive regulation of MAP kinase activity -4.619586
GO:2000117 negative regulation of cysteine-type endopeptidase activity -4.611786
GO:0019471 4-hydroxyproline metabolic process -4.570910
GO:0018401 peptidyl-proline hydroxylation to 4-hydroxy-L-proline -4.570910
GO:0048660 regulation of smooth muscle cell proliferation -3.111010
GO:0070848 response to growth factor -3.109409
GO:0031333 negative regulation of protein-containing complex assembly -3.096418
GO:0051131 chaperone-mediated protein complex assembly -2.989676
GO:0048658 anther wall tapetum development -2.860563
GO:0060776 simple leaf morphogenesis -2.475052
GO:0034307 regulation of ascospore formation -2.411002
GO:0050728 negative regulation of inflammatory response -2.411002
GO:0071507 pheromone response MAPK cascade -2.411002
GO:0030244 cellulose biosynthetic process -2.313130
GO:1902290 positive regulation of defense response to oomycetes -2.284022
GO:0042450 arginine biosynthetic process via ornithine -2.239011
GO:0002238 response to molecule of fungal origin -2.175661
GO:0010727 negative regulation of hydrogen peroxide metabolic process -1.940740
GO:0042353 fucose biosynthetic process -1.940740
GO:0006488 dolichol-linked oligosaccharide biosynthetic process -1.695773
GO:0009653 anatomical structure morphogenesis -1.681340
GO:0010030 positive regulation of seed germination -1.592823
GO:0002237 response to molecule of bacterial origin -1.494860
GO:0051782 negative regulation of cell division -1.358334

[1] “lost_in_zmar_GO.txt”

lost_in_zmar_GO.txt
TermID Name Value
GO:0009083 branched-chain amino acid catabolic process -23.825644
GO:1902418 (+)-abscisic acid D-glucopyranosyl ester transmembrane transport -16.818712
GO:0015700 arsenite transport -13.260514
GO:1901684 arsenate ion transmembrane transport -13.048999
GO:0043617 cellular response to sucrose starvation -11.063985
GO:1902198 3-methylbut-2-enoyl-CoA(4-) metabolic process -8.703391
GO:1904211 membrane protein proteolysis involved in retrograde protein transport,ER to cytosol -8.703391
GO:0009846 pollen germination -7.057244
GO:0046685 response to arsenic-containing substance -6.914746
GO:1900153 positive regulation of nuclear-transcribed mRNA catabolic process,deadenylation-dependent decay -6.908359
GO:0009556 microsporogenesis -6.737358
GO:0080037 negative regulation of cytokinin-activated signaling pathway -6.440151
GO:1900400 regulation of iron ion import into cell by regulation of transcription from RNA polymerase II promoter -6.440151
GO:0007059 chromosome segregation -5.880062
GO:0040029 regulation of gene expression,epigenetic -5.265680
GO:0043966 histone H3 acetylation -5.141144
GO:0106004 tRNA (guanine-N7)-methylation -5.114010
GO:1900000 regulation of anthocyanin catabolic process -5.114010
GO:0044829 positive regulation by host of viral genome replication -5.002696
GO:0051729 germline cell cycle switching,mitotic to meiotic cell cycle -5.002696
GO:0007018 microtubule-based movement -4.860293
GO:0010104 regulation of ethylene-activated signaling pathway -4.578960
GO:0006293 nucleotide-excision repair,preincision complex stabilization -3.979599
GO:0000454 snoRNA guided rRNA pseudouridine synthesis -3.979599
GO:0006075 (1->3)-beta-D-glucan biosynthetic process -3.716869
GO:0032508 DNA duplex unwinding -3.700286
GO:1903902 positive regulation of viral life cycle -2.883008
GO:0006368 transcription elongation from RNA polymerase II promoter -2.824435
GO:0035194 post-transcriptional gene silencing by RNA -2.797707
GO:0097502 mannosylation -2.726690
GO:0098660 inorganic ion transmembrane transport -2.721593
GO:0034333 adherens junction assembly -2.627603
GO:0061326 renal tubule development -2.627603
GO:0042048 olfactory behavior -2.627603
GO:0048599 oocyte development -2.568839
GO:0070911 global genome nucleotide-excision repair -2.554750
GO:1900150 regulation of defense response to fungus -2.374111
GO:0006396 RNA processing -2.281902
GO:0055047 generative cell mitosis -2.265927
GO:0006337 nucleosome disassembly -2.257923
GO:0010199 organ boundary specification between lateral organs and the meristem -2.173048
GO:0043524 negative regulation of neuron apoptotic process -2.053021
GO:0080092 regulation of pollen tube growth -1.916242
GO:0045948 positive regulation of translational initiation -1.889705
GO:0006294 nucleotide-excision repair,preincision complex assembly -1.668643
GO:0009226 nucleotide-sugar biosynthetic process -1.665611
GO:0033234 negative regulation of protein sumoylation -1.637393
GO:0042631 cellular response to water deprivation -1.383875

[1] “lost_in_zmuel_GO.txt”

lost_in_zmuel_GO.txt
TermID Name Value
GO:0006597 spermine biosynthetic process -7.719845
GO:0006490 oligosaccharide-lipid intermediate biosynthetic process -7.691661
GO:0097502 mannosylation -5.271569
GO:0031037 myosin II filament disassembly -4.228771
GO:0089709 L-histidine transmembrane transport -3.309566
GO:0001841 neural tube formation -2.894824
GO:0033577 protein glycosylation in endoplasmic reticulum -2.894824
GO:0072488 ammonium transmembrane transport -2.416930
GO:0015697 quaternary ammonium group transport -2.047144
GO:0010197 polar nucleus fusion -1.891385
GO:0042372 phylloquinone biosynthetic process -1.854951
GO:0071461 cellular response to redox state -1.547943
GO:0090071 negative regulation of ribosome biogenesis -1.345457
GO:0015847 putrescine transport -1.345457

[1] “missing_amphi_vs_all_GO.txt”

missing_amphi_vs_all_GO.txt
TermID Name Value
GO:0051762 sesquiterpene biosynthetic process -155.412480
GO:0090305 nucleic acid phosphodiester bond hydrolysis -151.260631
GO:0009451 RNA modification -129.609917
GO:0007165 signal transduction -124.739426
GO:0044550 secondary metabolite biosynthetic process -109.732139
GO:0009626 plant-type hypersensitive response -89.199181
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -73.404016
GO:0010082 regulation of root meristem growth -62.316817
GO:2000280 regulation of root development -57.962462
GO:0009625 response to insect -57.851440
GO:0006952 defense response -56.366823
GO:0045926 negative regulation of growth -49.287844
GO:0010951 negative regulation of endopeptidase activity -49.045011
GO:0045168 cell-cell signaling involved in cell fate commitment -40.098376
GO:0016099 monoterpenoid biosynthetic process -37.842515
GO:1904526 regulation of microtubule binding -36.680089
GO:0000966 RNA 5’-end processing -35.554319
GO:0090615 mitochondrial mRNA processing -34.637510
GO:0009819 drought recovery -33.921860
GO:0000304 response to singlet oxygen -31.541887
GO:0016567 protein ubiquitination -31.401111
GO:0080027 response to herbivore -29.746406
GO:0097366 response to bronchodilator -29.267556
GO:0009871 jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway -27.782072
GO:0045962 positive regulation of development,heterochronic -26.146973
GO:0009969 xyloglucan biosynthetic process -25.974199
GO:0071395 cellular response to jasmonic acid stimulus -25.690645
GO:0032870 cellular response to hormone stimulus -25.204027
GO:0051554 flavonol metabolic process -25.072818
GO:0071732 cellular response to nitric oxide -24.560403
GO:0048509 regulation of meristem development -24.496572
GO:0010310 regulation of hydrogen peroxide metabolic process -24.429451
GO:0052544 defense response by callose deposition in cell wall -22.469007
GO:0010150 leaf senescence -22.322993
GO:0006334 nucleosome assembly -22.223748
GO:0045338 farnesyl diphosphate metabolic process -20.990397
GO:0071466 cellular response to xenobiotic stimulus -20.553402
GO:0048462 carpel formation -20.294388
GO:1902025 nitrate import -20.184886
GO:0010469 regulation of signaling receptor activity -19.981450
GO:0006468 protein phosphorylation -19.955290
GO:0071446 cellular response to salicylic acid stimulus -19.892445
GO:0009877 nodulation -19.544215
GO:0080003 thalianol metabolic process -18.906081
GO:0010618 aerenchyma formation -17.526209
GO:0015709 thiosulfate transport -17.014164
GO:0032350 regulation of hormone metabolic process -16.977277
GO:0010375 stomatal complex patterning -16.637979
GO:0002230 positive regulation of defense response to virus by host -16.511798
GO:0009617 response to bacterium -16.475633
GO:0010275 NAD(P)H dehydrogenase complex assembly -16.151049
GO:0006885 regulation of pH -15.718231
GO:0010233 phloem transport -15.280791
GO:0080126 ovary septum development -15.121344
GO:0009972 cytidine deamination -14.887132
GO:0002239 response to oomycetes -14.752078
GO:0061760 antifungal innate immune response -14.684490
GO:0036371 protein localization to T-tubule -13.799813
GO:1901021 positive regulation of calcium ion transmembrane transporter activity -13.799813
GO:0033292 T-tubule organization -13.799813
GO:0036309 protein localization to M-band -13.799813
GO:0009962 regulation of flavonoid biosynthetic process -13.359591
GO:0080143 regulation of amino acid export -13.226843
GO:0010942 positive regulation of cell death -12.967396
GO:0071236 cellular response to antibiotic -12.890584
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -12.868980
GO:0034626 fatty acid elongation,polyunsaturated fatty acid -12.617325
GO:0044403 biological process involved in symbiotic interaction -12.489256
GO:0061370 testosterone biosynthetic process -11.851829
GO:0006812 cation transport -11.834559
GO:0042430 indole-containing compound metabolic process -11.640271
GO:0051245 negative regulation of cellular defense response -11.104116
GO:0034090 maintenance of meiotic sister chromatid cohesion -11.006435
GO:0010970 transport along microtubule -10.948753
GO:0003341 cilium movement -10.740017
GO:0010337 regulation of salicylic acid metabolic process -10.612594
GO:0000495 box H/ACA RNA 3’-end processing -10.241991
GO:0009609 response to symbiotic bacterium -10.155539
GO:0009664 plant-type cell wall organization -9.877092
GO:0043153 entrainment of circadian clock by photoperiod -9.756528
GO:0071422 succinate transmembrane transport -9.471159
GO:1900706 positive regulation of siderophore biosynthetic process -9.429721
GO:0035725 sodium ion transmembrane transport -9.283878
GO:0006164 purine nucleotide biosynthetic process -9.283372
GO:0009311 oligosaccharide metabolic process -9.223514
GO:0071452 cellular response to singlet oxygen -9.208437
GO:0061723 glycophagy -9.144910
GO:0002238 response to molecule of fungal origin -8.989515
GO:0009644 response to high light intensity -8.889919
GO:0006813 potassium ion transport -8.845589
GO:0009961 response to 1-aminocyclopropane-1-carboxylic acid -8.733801
GO:1904962 plastid to vacuole vesicle-mediated transport -8.533431
GO:0071211 protein targeting to vacuole involved in autophagy -8.533431
GO:0015843 methylammonium transport -8.488784
GO:0044245 polysaccharide digestion -8.477229
GO:0060294 cilium movement involved in cell motility -8.400755
GO:0012502 induction of programmed cell death -8.366183
GO:0033387 putrescine biosynthetic process from ornithine -8.213157
GO:0071368 cellular response to cytokinin stimulus -8.168346
GO:0006260 DNA replication -8.131429
GO:0042742 defense response to bacterium -8.042952
GO:0080184 response to phenylpropanoid -8.019366
GO:0010500 transmitting tissue development -8.013000
GO:0033259 plastid DNA replication -7.843935
GO:0010221 negative regulation of vernalization response -7.774115
GO:0010438 cellular response to sulfur starvation -7.761069
GO:0090057 root radial pattern formation -7.618934
GO:0009684 indoleacetic acid biosynthetic process -7.549382
GO:0035998 7,8-dihydroneopterin 3’-triphosphate biosynthetic process -7.547472
GO:1904541 fungal-type cell wall disassembly involved in conjugation with cellular fusion -7.425102
GO:0015700 arsenite transport -7.398065
GO:0010258 NADH dehydrogenase complex (plastoquinone) assembly -7.397841
GO:0071229 cellular response to acid chemical -7.395724
GO:0009780 photosynthetic NADP+ reduction -7.317334
GO:0010555 response to mannitol -7.292125
GO:0009852 auxin catabolic process -7.282761
GO:0009093 cysteine catabolic process -7.249705
GO:0046330 positive regulation of JNK cascade -7.242124
GO:0080037 negative regulation of cytokinin-activated signaling pathway -7.201643
GO:0080181 lateral root branching -7.129021
GO:1902075 cellular response to salt -7.118648
GO:0048767 root hair elongation -7.087678
GO:0001680 tRNA 3’-terminal CCA addition -7.087420
GO:0032527 protein exit from endoplasmic reticulum -7.057949
GO:0001101 response to acid chemical -7.032843
GO:0016045 detection of bacterium -6.767682
GO:0030639 polyketide biosynthetic process -6.693629
GO:0048512 circadian behavior -6.692248
GO:2000630 positive regulation of miRNA metabolic process -6.661836
GO:0042773 ATP synthesis coupled electron transport -6.661836
GO:0001172 transcription,RNA-templated -6.630651
GO:0048544 recognition of pollen -6.623676
GO:0010376 stomatal complex formation -6.623515
GO:0048240 sperm capacitation -6.220075
GO:0046622 positive regulation of organ growth -6.195458
GO:1902290 positive regulation of defense response to oomycetes -6.031032
GO:0006672 ceramide metabolic process -5.977702
GO:0072756 cellular response to paraquat -5.896024
GO:0080021 response to benzoic acid -5.896024
GO:0000375 RNA splicing,via transesterification reactions -5.862753
GO:0051070 galactomannan biosynthetic process -5.647766
GO:1902265 abscisic acid homeostasis -5.647414
GO:0080155 regulation of double fertilization forming a zygote and endosperm -5.581798
GO:0010324 membrane invagination -5.425451
GO:0006778 porphyrin-containing compound metabolic process -5.415218
GO:0007267 cell-cell signaling -5.337881
GO:1905255 regulation of RNA binding transcription factor activity -5.323769
GO:0070667 negative regulation of mast cell proliferation -5.323769
GO:0033007 negative regulation of mast cell activation involved in immune response -5.323769
GO:0070562 regulation of vitamin D receptor signaling pathway -5.304743
GO:0051258 protein polymerization -5.247348
GO:0015851 nucleobase transport -5.208378
GO:0018364 peptidyl-glutamine methylation -5.201144
GO:0009089 lysine biosynthetic process via diaminopimelate -5.170693
GO:0030994 primary cell septum disassembly -5.157608
GO:0048385 regulation of retinoic acid receptor signaling pathway -5.016143
GO:0009631 cold acclimation -4.906945
GO:0071281 cellular response to iron ion -4.876646
GO:0032886 regulation of microtubule-based process -4.732038
GO:0045056 transcytosis -4.682696
GO:0048211 Golgi vesicle docking -4.682696
GO:0009608 response to symbiont -4.565462
GO:0035864 response to potassium ion -4.534107
GO:0007584 response to nutrient -4.526773
GO:0036159 inner dynein arm assembly -4.478424
GO:0071465 cellular response to desiccation -4.454452
GO:0080171 lytic vacuole organization -4.451511
GO:0006359 regulation of transcription by RNA polymerase III -4.435722
GO:2000636 positive regulation of primary miRNA processing -4.418909
GO:0006403 RNA localization -4.389670
GO:0080110 sporopollenin biosynthetic process -4.321347
GO:0010114 response to red light -4.245214
GO:0048587 regulation of short-day photoperiodism,flowering -4.157373
GO:0009268 response to pH -4.047383
GO:0072344 rescue of stalled ribosome -4.047250
GO:0006722 triterpenoid metabolic process -3.946282
GO:0045007 depurination -3.935188
GO:0015979 photosynthesis -3.877351
GO:1905034 regulation of antifungal innate immune response -3.767121
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -3.702997
GO:1900449 regulation of glutamate receptor signaling pathway -3.702997
GO:0050821 protein stabilization -3.583269
GO:0019218 regulation of steroid metabolic process -3.561907
GO:1990169 stress response to copper ion -3.561907
GO:0007263 nitric oxide mediated signal transduction -3.561389
GO:0007095 mitotic G2 DNA damage checkpoint signaling -3.532261
GO:0048584 positive regulation of response to stimulus -3.398922
GO:0098869 cellular oxidant detoxification -3.378602
GO:0090143 nucleoid organization -3.317884
GO:0035246 peptidyl-arginine N-methylation -3.309595
GO:0051090 regulation of DNA-binding transcription factor activity -3.268476
GO:0016127 sterol catabolic process -3.230535
GO:0034434 sterol esterification -3.230535
GO:0045490 pectin catabolic process -3.160321
GO:0015853 adenine transport -3.130204
GO:0031120 snRNA pseudouridine synthesis -3.083481
GO:0035024 negative regulation of Rho protein signal transduction -2.943564
GO:0080164 regulation of nitric oxide metabolic process -2.851155
GO:0090559 regulation of membrane permeability -2.849913
GO:0000914 phragmoplast assembly -2.811388
GO:0050829 defense response to Gram-negative bacterium -2.811388
GO:2000023 regulation of lateral root development -2.770101
GO:0009611 response to wounding -2.692392
GO:0001561 fatty acid alpha-oxidation -2.661712
GO:0019371 cyclooxygenase pathway -2.661712
GO:0010423 negative regulation of brassinosteroid biosynthetic process -2.632486
GO:0043457 regulation of cellular respiration -2.586543
GO:2000013 regulation of arginine biosynthetic process via ornithine -2.586543
GO:0034394 protein localization to cell surface -2.573966
GO:0010930 negative regulation of auxin mediated signaling pathway -2.569735
GO:0006264 mitochondrial DNA replication -2.425188
GO:0051607 defense response to virus -2.417605
GO:0000226 microtubule cytoskeleton organization -2.393661
GO:2000232 regulation of rRNA processing -2.371507
GO:0002011 morphogenesis of an epithelial sheet -2.355975
GO:0043100 pyrimidine nucleobase salvage -2.341970
GO:1902348 cellular response to strigolactone -2.194635
GO:0097167 circadian regulation of translation -2.194635
GO:0005995 melibiose catabolic process -2.194635
GO:0009099 valine biosynthetic process -2.075832
GO:0015886 heme transport -2.007792
GO:2000028 regulation of photoperiodism,flowering -1.891045
GO:0009786 regulation of asymmetric cell division -1.856958
GO:0000350 generation of catalytic spliceosome for second transesterification step -1.856958
GO:0006124 ferredoxin metabolic process -1.836460
GO:0051315 attachment of mitotic spindle microtubules to kinetochore -1.830805
GO:0018316 peptide cross-linking via L-cystine -1.778525
GO:0006432 phenylalanyl-tRNA aminoacylation -1.736491
GO:0046949 fatty-acyl-CoA biosynthetic process -1.706168
GO:1901599 (-)-pinoresinol biosynthetic process -1.703570
GO:0015708 silicic acid import across plasma membrane -1.703570
GO:0030150 protein import into mitochondrial matrix -1.657532
GO:0071731 response to nitric oxide -1.633238
GO:0009410 response to xenobiotic stimulus -1.585466
GO:1901684 arsenate ion transmembrane transport -1.535372
GO:0006314 intron homing -1.438530
GO:0006203 dGTP catabolic process -1.438530
GO:0007166 cell surface receptor signaling pathway -1.416541
GO:0035874 cellular response to copper ion starvation -1.331841
GO:0000028 ribosomal small subunit assembly -1.314658

[1] “missing_aquatics_GO.txt”

missing_aquatics_GO.txt
TermID Name Value
GO:0051762 sesquiterpene biosynthetic process -140.122519
GO:0006952 defense response -112.187033
GO:0010082 regulation of root meristem growth -104.101084
GO:2000280 regulation of root development -81.374590
GO:0007165 signal transduction -81.288547
GO:0046345 abscisic acid catabolic process -55.983799
GO:0000966 RNA 5’-end processing -54.651110
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -49.521214
GO:0048509 regulation of meristem development -47.797196
GO:0045338 farnesyl diphosphate metabolic process -40.331178
GO:0051554 flavonol metabolic process -36.919497
GO:2000026 regulation of multicellular organismal development -35.555401
GO:0010469 regulation of signaling receptor activity -34.419769
GO:0009819 drought recovery -34.412318
GO:0019756 cyanogenic glycoside biosynthetic process -34.342172
GO:0090615 mitochondrial mRNA processing -34.286111
GO:0080003 thalianol metabolic process -30.502960
GO:0009867 jasmonic acid mediated signaling pathway -28.343365
GO:0009617 response to bacterium -28.320920
GO:0009625 response to insect -27.178894
GO:0016567 protein ubiquitination -25.711249
GO:0006468 protein phosphorylation -25.501966
GO:0009962 regulation of flavonoid biosynthetic process -25.385631
GO:0009626 plant-type hypersensitive response -23.662726
GO:0006885 regulation of pH -21.919135
GO:0010618 aerenchyma formation -20.647083
GO:0036371 protein localization to T-tubule -20.442318
GO:0033292 T-tubule organization -20.442318
GO:1901021 positive regulation of calcium ion transmembrane transporter activity -20.442318
GO:0036309 protein localization to M-band -20.442318
GO:0045168 cell-cell signaling involved in cell fate commitment -20.327221
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -19.161283
GO:0052544 defense response by callose deposition in cell wall -18.498763
GO:0000304 response to singlet oxygen -17.925687
GO:0071236 cellular response to antibiotic -17.414451
GO:0071368 cellular response to cytokinin stimulus -16.910416
GO:0003341 cilium movement -16.666473
GO:0060294 cilium movement involved in cell motility -16.454330
GO:1902025 nitrate import -16.147194
GO:0045926 negative regulation of growth -15.727160
GO:0042742 defense response to bacterium -15.100075
GO:1902290 positive regulation of defense response to oomycetes -14.872143
GO:0097185 cellular response to azide -14.134822
GO:0010221 negative regulation of vernalization response -13.569914
GO:0080027 response to herbivore -13.062940
GO:0080184 response to phenylpropanoid -12.881606
GO:0071229 cellular response to acid chemical -12.010943
GO:0009871 jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway -11.901183
GO:0009684 indoleacetic acid biosynthetic process -11.837791
GO:0009852 auxin catabolic process -11.473243
GO:0010942 positive regulation of cell death -10.877695
GO:0036159 inner dynein arm assembly -10.806071
GO:0010114 response to red light -10.626773
GO:0071766 Actinobacterium-type cell wall biogenesis -10.192160
GO:1904526 regulation of microtubule binding -9.815879
GO:0071466 cellular response to xenobiotic stimulus -9.352212
GO:0007166 cell surface receptor signaling pathway -9.350409
GO:0009410 response to xenobiotic stimulus -9.193698
GO:1905255 regulation of RNA binding transcription factor activity -9.134702
GO:0006812 cation transport -8.598854
GO:0035024 negative regulation of Rho protein signal transduction -8.593483
GO:0009914 hormone transport -8.520136
GO:0010930 negative regulation of auxin mediated signaling pathway -8.423030
GO:0034394 protein localization to cell surface -8.422620
GO:0001101 response to acid chemical -8.247666
GO:0002213 defense response to insect -8.013172
GO:0070301 cellular response to hydrogen peroxide -7.747259
GO:0002011 morphogenesis of an epithelial sheet -7.657648
GO:0009611 response to wounding -7.598088
GO:0032870 cellular response to hormone stimulus -7.407748
GO:0016045 detection of bacterium -7.398400
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -7.135037
GO:1900449 regulation of glutamate receptor signaling pathway -7.135037
GO:1902265 abscisic acid homeostasis -7.025493
GO:0010030 positive regulation of seed germination -6.951280
GO:0003283 atrial septum development -6.840108
GO:0097237 cellular response to toxic substance -6.813398
GO:0009865 pollen tube adhesion -5.970647
GO:0090559 regulation of membrane permeability -5.932708
GO:0051607 defense response to virus -5.648221
GO:0009866 induced systemic resistance,ethylene mediated signaling pathway -5.551154
GO:0097167 circadian regulation of translation -5.541363
GO:0007584 response to nutrient -5.303508
GO:0010310 regulation of hydrogen peroxide metabolic process -5.241183
GO:0007267 cell-cell signaling -4.559472
GO:0009826 unidimensional cell growth -4.543084
GO:0071218 cellular response to misfolded protein -4.517344
GO:0009311 oligosaccharide metabolic process -4.513778
GO:0010233 phloem transport -4.279925
GO:0061157 mRNA destabilization -4.106738
GO:0010438 cellular response to sulfur starvation -3.856586
GO:0015708 silicic acid import across plasma membrane -3.788987
GO:0050821 protein stabilization -3.614097
GO:0007498 mesoderm development -3.610872
GO:0007422 peripheral nervous system development -3.610872
GO:0031542 positive regulation of anthocyanin biosynthetic process -3.567657
GO:0006335 DNA replication-dependent chromatin assembly -3.563722
GO:0009745 sucrose mediated signaling -3.552022
GO:0032504 multicellular organism reproduction -3.443456
GO:0035600 tRNA methylthiolation -3.409318
GO:0002239 response to oomycetes -3.344113
GO:1905614 negative regulation of developmental vegetative growth -3.116242
GO:0051513 regulation of monopolar cell growth -2.998690
GO:0032527 protein exit from endoplasmic reticulum -2.917539
GO:0010305 leaf vascular tissue pattern formation -2.850372
GO:0097503 sialylation -2.841938
GO:0002230 positive regulation of defense response to virus by host -2.703275
GO:0006636 unsaturated fatty acid biosynthetic process -2.644815
GO:0009751 response to salicylic acid -2.619993
GO:0006898 receptor-mediated endocytosis -2.571880
GO:0031640 killing of cells of other organism -2.509567
GO:0048312 intracellular distribution of mitochondria -2.509467
GO:1903553 positive regulation of extracellular exosome assembly -2.509467
GO:0044364 disruption of cells of other organism -2.509467
GO:0007492 endoderm development -2.509467
GO:0060465 pharynx development -2.509467
GO:0072498 embryonic skeletal joint development -2.509467
GO:0048265 response to pain -2.509467
GO:0006355 regulation of transcription,DNA-templated -2.480747
GO:0045314 regulation of compound eye photoreceptor development -2.388180
GO:0045747 positive regulation of Notch signaling pathway -2.388180
GO:0007398 ectoderm development -2.388180
GO:0035204 negative regulation of lamellocyte differentiation -2.388180
GO:0048821 erythrocyte development -2.384487
GO:0042177 negative regulation of protein catabolic process -2.367953
GO:0001666 response to hypoxia -2.354401
GO:0007369 gastrulation -2.330386
GO:2000027 regulation of animal organ morphogenesis -2.298305
GO:1905663 positive regulation of telomerase RNA reverse transcriptase activity -2.276294
GO:0019722 calcium-mediated signaling -2.188992
GO:0009960 endosperm development -2.180950
GO:0009627 systemic acquired resistance -2.073394
GO:0031347 regulation of defense response -2.037689
GO:0043086 negative regulation of catalytic activity -1.980503
GO:0010275 NAD(P)H dehydrogenase complex assembly -1.784576
GO:0009828 plant-type cell wall loosening -1.774122
GO:1900745 positive regulation of p38MAPK cascade -1.752952
GO:1904355 positive regulation of telomere capping -1.727692
GO:0010150 leaf senescence -1.519786
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process -1.513457
GO:0046482 para-aminobenzoic acid metabolic process -1.352411

[1] “missing_arabidopsis_vs_all_GO.txt”

missing_arabidopsis_vs_all_GO.txt
TermID Name Value
GO:0007165 signal transduction -119.239761
GO:0006952 defense response -96.210331
GO:0045926 negative regulation of growth -75.159828
GO:1904526 regulation of microtubule binding -61.579741
GO:0006468 protein phosphorylation -44.190986
GO:0009819 drought recovery -31.057832
GO:0010083 regulation of vegetative meristem growth -25.517715
GO:0009617 response to bacterium -23.613172
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -23.559069
GO:0000226 microtubule cytoskeleton organization -21.958043
GO:0009626 plant-type hypersensitive response -20.800214
GO:0060294 cilium movement involved in cell motility -19.092525
GO:0003341 cilium movement -17.515455
GO:0000966 RNA 5’-end processing -16.663352
GO:1901949 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate biosynthetic process -14.605293
GO:0033387 putrescine biosynthetic process from ornithine -13.401532
GO:0036159 inner dynein arm assembly -13.046176
GO:0016045 detection of bacterium -12.125293
GO:0009410 response to xenobiotic stimulus -11.386409
GO:0009877 nodulation -11.377572
GO:0071766 Actinobacterium-type cell wall biogenesis -10.738963
GO:0010233 phloem transport -10.718896
GO:0044403 biological process involved in symbiotic interaction -9.395802
GO:0010359 regulation of anion channel activity -9.197787
GO:0009690 cytokinin metabolic process -8.510983
GO:0016567 protein ubiquitination -8.233559
GO:0090615 mitochondrial mRNA processing -8.152980
GO:0009311 oligosaccharide metabolic process -7.895729
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -7.626170
GO:0071447 cellular response to hydroperoxide -7.626170
GO:1900449 regulation of glutamate receptor signaling pathway -7.626170
GO:0010305 leaf vascular tissue pattern formation -7.541784
GO:0046777 protein autophosphorylation -7.305555
GO:0009608 response to symbiont -7.017275
GO:0052544 defense response by callose deposition in cell wall -6.905833
GO:0009742 brassinosteroid mediated signaling pathway -6.885721
GO:2000023 regulation of lateral root development -6.604582
GO:0044550 secondary metabolite biosynthetic process -6.590408
GO:0015939 pantothenate metabolic process -6.369773
GO:0030240 skeletal muscle thin filament assembly -6.369436
GO:0006898 receptor-mediated endocytosis -6.047190
GO:0007369 gastrulation -5.952804
GO:0032504 multicellular organism reproduction -5.880605
GO:0042742 defense response to bacterium -5.879025
GO:0090708 specification of plant organ axis polarity -5.847839
GO:1902025 nitrate import -5.828260
GO:0007166 cell surface receptor signaling pathway -5.354689
GO:2000280 regulation of root development -5.252086
GO:0048509 regulation of meristem development -5.238104
GO:0009734 auxin-activated signaling pathway -5.072313
GO:0061157 mRNA destabilization -4.943818
GO:1903224 regulation of endodermal cell differentiation -4.810111
GO:0010470 regulation of gastrulation -4.810111
GO:0045184 establishment of protein localization -4.787121
GO:0051967 negative regulation of synaptic transmission,glutamatergic -4.712564
GO:0001701 in utero embryonic development -4.688566
GO:0048439 flower morphogenesis -4.558133
GO:0072699 protein localization to cortical microtubule cytoskeleton -4.555906
GO:0009733 response to auxin -4.547141
GO:0019878 lysine biosynthetic process via aminoadipic acid -4.260093
GO:0007275 multicellular organism development -4.193035
GO:0006335 DNA replication-dependent chromatin assembly -4.150067
GO:0009745 sucrose mediated signaling -4.100581
GO:0015708 silicic acid import across plasma membrane -4.085583
GO:0010150 leaf senescence -4.016755
GO:0035600 tRNA methylthiolation -3.993292
GO:0035024 negative regulation of Rho protein signal transduction -3.841743
GO:0006336 DNA replication-independent chromatin assembly -3.787082
GO:0098657 import into cell -3.726525
GO:0031542 positive regulation of anthocyanin biosynthetic process -3.627182
GO:0035864 response to potassium ion -3.561205
GO:0097503 sialylation -3.416393
GO:0051513 regulation of monopolar cell growth -3.381197
GO:0009826 unidimensional cell growth -3.368105
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway -3.010935
GO:0007339 binding of sperm to zona pellucida -2.995739
GO:0002011 morphogenesis of an epithelial sheet -2.995739
GO:0010114 response to red light -2.973863
GO:0006486 protein glycosylation -2.967523
GO:0031589 cell-substrate adhesion -2.835492
GO:0101030 tRNA-guanine transglycosylation -2.835031
GO:0009828 plant-type cell wall loosening -2.793297
GO:0007492 endoderm development -2.758626
GO:0031640 killing of cells of other organism -2.756107
GO:0048312 intracellular distribution of mitochondria -2.755929
GO:0044364 disruption of cells of other organism -2.755929
GO:0060465 pharynx development -2.755929
GO:0043588 skin development -2.755929
GO:0090558 plant epidermis development -2.738830
GO:0048821 erythrocyte development -2.676151
GO:0097306 cellular response to alcohol -2.674237
GO:0015969 guanosine tetraphosphate metabolic process -2.627528
GO:0009962 regulation of flavonoid biosynthetic process -2.600440
GO:0009251 glucan catabolic process -2.365504
GO:0010737 protein kinase A signaling -2.293020
GO:0009992 cellular water homeostasis -2.289354
GO:0014013 regulation of gliogenesis -2.217819
GO:0009867 jasmonic acid mediated signaling pathway -2.146426
GO:0042761 very long-chain fatty acid biosynthetic process -2.053810
GO:0007349 cellularization -1.998218
GO:0036498 IRE1-mediated unfolded protein response -1.997416
GO:1900745 positive regulation of p38MAPK cascade -1.997416
GO:0046482 para-aminobenzoic acid metabolic process -1.986689
GO:0045730 respiratory burst -1.825271
GO:0080051 cutin transport -1.773667
GO:0060548 negative regulation of cell death -1.766217
GO:0006627 protein processing involved in protein targeting to mitochondrion -1.720248
GO:0045056 transcytosis -1.617946
GO:0048211 Golgi vesicle docking -1.617946
GO:0061820 telomeric D-loop disassembly -1.596827
GO:0098530 positive regulation of strand invasion -1.596827
GO:0044806 G-quadruplex DNA unwinding -1.596827
GO:0071921 cohesin loading -1.496974
GO:0031065 positive regulation of histone deacetylation -1.496974
GO:0060325 face morphogenesis -1.496974
GO:0032526 response to retinoic acid -1.471984
GO:0008610 lipid biosynthetic process -1.447198
GO:0002182 cytoplasmic translational elongation -1.428299
GO:0009218 pyrimidine ribonucleotide metabolic process -1.426628
GO:1904851 positive regulation of establishment of protein localization to telomere -1.379635

[1] “missing_posi_vs_all_GO.txt”

missing_posi_vs_all_GO.txt
TermID Name Value
GO:0090305 nucleic acid phosphodiester bond hydrolysis -202.077576
GO:0009451 RNA modification -190.721643
GO:0051762 sesquiterpene biosynthetic process -100.297555
GO:0007165 signal transduction -63.045228
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -62.059796
GO:0045926 negative regulation of growth -56.870827
GO:0006952 defense response -56.039009
GO:0010082 regulation of root meristem growth -54.195293
GO:2000280 regulation of root development -53.716023
GO:1904526 regulation of microtubule binding -40.641336
GO:0000966 RNA 5’-end processing -40.450386
GO:0009819 drought recovery -39.762484
GO:0046345 abscisic acid catabolic process -35.511723
GO:0010469 regulation of signaling receptor activity -34.558948
GO:0010375 stomatal complex patterning -33.754478
GO:0080156 mitochondrial mRNA modification -30.657427
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion -28.972157
GO:0051554 flavonol metabolic process -27.259447
GO:0019756 cyanogenic glycoside biosynthetic process -25.518707
GO:0009969 xyloglucan biosynthetic process -24.960744
GO:0045338 farnesyl diphosphate metabolic process -24.428219
GO:0006468 protein phosphorylation -23.861870
GO:0010233 phloem transport -23.811719
GO:1902025 nitrate import -22.839119
GO:0048462 carpel formation -22.697279
GO:0045168 cell-cell signaling involved in cell fate commitment -22.581085
GO:0048509 regulation of meristem development -21.686326
GO:0080003 thalianol metabolic process -21.022129
GO:0009914 hormone transport -20.141593
GO:0016567 protein ubiquitination -19.832729
GO:0006885 regulation of pH -19.750916
GO:0010275 NAD(P)H dehydrogenase complex assembly -18.708367
GO:1905614 negative regulation of developmental vegetative growth -18.376548
GO:0031098 stress-activated protein kinase signaling cascade -17.979816
GO:0080126 ovary septum development -16.865539
GO:0009972 cytidine deamination -16.574468
GO:0009626 plant-type hypersensitive response -16.522254
GO:1902457 negative regulation of stomatal opening -16.296225
GO:0010344 seed oilbody biogenesis -16.161163
GO:0009625 response to insect -15.643489
GO:0071236 cellular response to antibiotic -15.558175
GO:0060776 simple leaf morphogenesis -15.554054
GO:0036371 protein localization to T-tubule -15.023967
GO:0033292 T-tubule organization -15.023967
GO:0036309 protein localization to M-band -15.023967
GO:0035725 sodium ion transmembrane transport -14.994073
GO:0010618 aerenchyma formation -14.702027
GO:0034614 cellular response to reactive oxygen species -14.569446
GO:0009962 regulation of flavonoid biosynthetic process -14.549538
GO:0009867 jasmonic acid mediated signaling pathway -14.238823
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -14.028558
GO:0032260 response to jasmonic acid stimulus involved in jasmonic acid and ethylene-dependent systemic resistance -13.981089
GO:0048767 root hair elongation -13.755379
GO:1900426 positive regulation of defense response to bacterium -13.256654
GO:0042176 regulation of protein catabolic process -12.811444
GO:0042273 ribosomal large subunit biogenesis -12.711372
GO:0048658 anther wall tapetum development -12.553830
GO:0034724 DNA replication-independent chromatin organization -12.343109
GO:0033206 meiotic cytokinesis -12.323855
GO:0003341 cilium movement -11.828706
GO:0071320 cellular response to cAMP -11.821209
GO:2000026 regulation of multicellular organismal development -11.646700
GO:0050434 positive regulation of viral transcription -11.444585
GO:0009653 anatomical structure morphogenesis -11.417696
GO:0000226 microtubule cytoskeleton organization -11.150007
GO:0043153 entrainment of circadian clock by photoperiod -11.106471
GO:0050728 negative regulation of inflammatory response -11.106471
GO:0006509 membrane protein ectodomain proteolysis -10.923143
GO:0035902 response to immobilization stress -10.850181
GO:0009311 oligosaccharide metabolic process -10.336692
GO:0009617 response to bacterium -10.289218
GO:0006813 potassium ion transport -10.222966
GO:0007346 regulation of mitotic cell cycle -10.155337
GO:0010500 transmitting tissue development -10.077522
GO:1900033 negative regulation of trichome patterning -9.916671
GO:0030150 protein import into mitochondrial matrix -9.888893
GO:0060291 long-term synaptic potentiation -9.880986
GO:0098703 calcium ion import across plasma membrane -9.880986
GO:0071368 cellular response to cytokinin stimulus -9.739302
GO:0010030 positive regulation of seed germination -9.733717
GO:0001667 ameboidal-type cell migration -9.728819
GO:2000117 negative regulation of cysteine-type endopeptidase activity -9.726094
GO:0046330 positive regulation of JNK cascade -9.722158
GO:2000762 regulation of phenylpropanoid metabolic process -9.682429
GO:0012502 induction of programmed cell death -9.431784
GO:0071347 cellular response to interleukin-1 -9.101635
GO:0080037 negative regulation of cytokinin-activated signaling pathway -9.070433
GO:0033387 putrescine biosynthetic process from ornithine -9.050561
GO:0032527 protein exit from endoplasmic reticulum -8.961732
GO:0080184 response to phenylpropanoid -8.913764
GO:0010221 negative regulation of vernalization response -8.832352
GO:1904837 beta-catenin-TCF complex assembly -8.582182
GO:0071229 cellular response to acid chemical -8.441768
GO:0009088 threonine biosynthetic process -8.292342
GO:0009780 photosynthetic NADP+ reduction -8.261077
GO:0033542 fatty acid beta-oxidation,unsaturated,even number -8.187130
GO:0010150 leaf senescence -8.133262
GO:0009852 auxin catabolic process -8.055166
GO:0042773 ATP synthesis coupled electron transport -7.751660
GO:0006812 cation transport -7.647909
GO:0080155 regulation of double fertilization forming a zygote and endosperm -7.626381
GO:0050826 response to freezing -7.571291
GO:1902265 abscisic acid homeostasis -7.364876
GO:0042407 cristae formation -7.288255
GO:0002213 defense response to insect -7.205055
GO:0048240 sperm capacitation -6.984336
GO:0030198 extracellular matrix organization -6.950692
GO:0000375 RNA splicing,via transesterification reactions -6.872762
GO:0018008 N-terminal peptidyl-glycine N-myristoylation -6.862429
GO:0010064 embryonic shoot morphogenesis -6.862429
GO:2000038 regulation of stomatal complex development -6.601214
GO:0051070 galactomannan biosynthetic process -6.568896
GO:0000390 spliceosomal complex disassembly -6.520794
GO:0010227 floral organ abscission -6.507642
GO:0002238 response to molecule of fungal origin -6.476875
GO:0010942 positive regulation of cell death -6.291367
GO:0010324 membrane invagination -6.184266
GO:0006778 porphyrin-containing compound metabolic process -6.174433
GO:0015851 nucleobase transport -6.123632
GO:0030994 primary cell septum disassembly -6.121054
GO:0071466 cellular response to xenobiotic stimulus -6.082287
GO:1905255 regulation of RNA binding transcription factor activity -6.024302
GO:0070667 negative regulation of mast cell proliferation -6.024302
GO:0033007 negative regulation of mast cell activation involved in immune response -6.024302
GO:0009664 plant-type cell wall organization -5.970664
GO:0048211 Golgi vesicle docking -5.955050
GO:0045056 transcytosis -5.955050
GO:0042908 xenobiotic transport -5.906055
GO:0043086 negative regulation of catalytic activity -5.846133
GO:0006005 L-fucose biosynthetic process -5.700801
GO:0002938 tRNA guanine ribose methylation -5.700801
GO:0052544 defense response by callose deposition in cell wall -5.613441
GO:0001172 transcription,RNA-templated -5.524972
GO:0048544 recognition of pollen -5.518977
GO:0010310 regulation of hydrogen peroxide metabolic process -5.432629
GO:0035864 response to potassium ion -5.334631
GO:0006359 regulation of transcription by RNA polymerase III -5.285495
GO:1900459 positive regulation of brassinosteroid mediated signaling pathway -5.248078
GO:0006470 protein dephosphorylation -5.193447
GO:1904541 fungal-type cell wall disassembly involved in conjugation with cellular fusion -5.079019
GO:0007066 female meiosis sister chromatid cohesion -5.070379
GO:0031333 negative regulation of protein-containing complex assembly -5.068979
GO:0042073 intraciliary transport -5.067553
GO:0034080 CENP-A containing chromatin assembly -5.066592
GO:0045007 depurination -5.052084
GO:1905034 regulation of antifungal innate immune response -5.043818
GO:0009268 response to pH -4.887249
GO:0000025 maltose catabolic process -4.860108
GO:0051607 defense response to virus -4.801239
GO:0015700 arsenite transport -4.650523
GO:0010120 camalexin biosynthetic process -4.492216
GO:0015853 adenine transport -4.452453
GO:0034434 sterol esterification -4.442857
GO:0051782 negative regulation of cell division -4.382314
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -4.331802
GO:1900449 regulation of glutamate receptor signaling pathway -4.331802
GO:0045861 negative regulation of proteolysis -4.202439
GO:0000028 ribosomal small subunit assembly -4.099637
GO:0019218 regulation of steroid metabolic process -4.076369
GO:0090143 nucleoid organization -4.046449
GO:0034307 regulation of ascospore formation -4.046449
GO:0007166 cell surface receptor signaling pathway -3.979747
GO:0035024 negative regulation of Rho protein signal transduction -3.940235
GO:1900865 chloroplast RNA modification -3.916060
GO:1902325 negative regulation of chlorophyll biosynthetic process -3.756088
GO:0010727 negative regulation of hydrogen peroxide metabolic process -3.745360
GO:0070846 Hsp90 deacetylation -3.744559
GO:0032418 lysosome localization -3.744559
GO:1901526 positive regulation of mitophagy -3.744559
GO:0061734 parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization -3.744559
GO:0035967 cellular response to topologically incorrect protein -3.743924
GO:2001040 positive regulation of cellular response to drug -3.743868
GO:0070848 response to growth factor -3.742023
GO:0070134 positive regulation of mitochondrial translational initiation -3.636248
GO:0034394 protein localization to cell surface -3.600617
GO:0010930 negative regulation of auxin mediated signaling pathway -3.593907
GO:1902184 negative regulation of shoot apical meristem development -3.583883
GO:0042351 ‘de novo’ GDP-L-fucose biosynthetic process -3.583883
GO:0050821 protein stabilization -3.421658
GO:0080164 regulation of nitric oxide metabolic process -3.416873
GO:0090559 regulation of membrane permeability -3.415678
GO:0071731 response to nitric oxide -3.335147
GO:0043457 regulation of cellular respiration -3.301968
GO:0006045 N-acetylglucosamine biosynthetic process -3.301968
GO:0002011 morphogenesis of an epithelial sheet -3.289730
GO:1901684 arsenate ion transmembrane transport -3.269484
GO:0018063 cytochrome c-heme linkage -3.227392
GO:0097237 cellular response to toxic substance -3.138372
GO:0080163 regulation of protein serine/threonine phosphatase activity -3.131269
GO:0010423 negative regulation of brassinosteroid biosynthetic process -3.083357
GO:0016045 detection of bacterium -3.008507
GO:2000033 regulation of seed dormancy process -2.985810
GO:0030587 sorocarp development -2.979628
GO:0007023 post-chaperonin tubulin folding pathway -2.977004
GO:0050935 iridophore differentiation -2.977004
GO:0009410 response to xenobiotic stimulus -2.970613
GO:0080027 response to herbivore -2.945089
GO:0019348 dolichol metabolic process -2.857557
GO:0097167 circadian regulation of translation -2.803332
GO:0009631 cold acclimation -2.700705
GO:0006970 response to osmotic stress -2.680020
GO:0045815 epigenetic maintenance of chromatin in transcription-competent conformation -2.677396
GO:0048439 flower morphogenesis -2.532840
GO:2000098 negative regulation of smooth muscle cell-matrix adhesion -2.526602
GO:0042308 negative regulation of protein import into nucleus -2.526602
GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway -2.526602
GO:0015886 heme transport -2.509303
GO:0046949 fatty-acyl-CoA biosynthetic process -2.400073
GO:0010365 positive regulation of ethylene biosynthetic process -2.346859
GO:0010842 retina layer formation -2.222439
GO:0040011 locomotion -2.110800
GO:0070121 Kupffer’s vesicle development -2.089786
GO:1901599 (-)-pinoresinol biosynthetic process -2.089786
GO:0006611 protein export from nucleus -2.080898
GO:0061614 pri-miRNA transcription by RNA polymerase II -2.077188
GO:0006203 dGTP catabolic process -1.983263
GO:0071289 cellular response to nickel ion -1.958210
GO:0051211 anisotropic cell growth -1.813416
GO:0009992 cellular water homeostasis -1.795237
GO:0015979 photosynthesis -1.786708
GO:0009734 auxin-activated signaling pathway -1.757187
GO:0009961 response to 1-aminocyclopropane-1-carboxylic acid -1.744255
GO:0018107 peptidyl-threonine phosphorylation -1.722416
GO:2000095 regulation of Wnt signaling pathway,planar cell polarity pathway -1.707227
GO:0043627 response to estrogen -1.596382
GO:0019915 lipid storage -1.587403
GO:0010258 NADH dehydrogenase complex (plastoquinone) assembly -1.546163
GO:0001188 RNA polymerase I preinitiation complex assembly -1.484557
GO:0090480 purine nucleotide-sugar transmembrane transport -1.440548
GO:0036290 protein trans-autophosphorylation -1.365237

[1] “missing_seagrasses_GO.txt”

missing_seagrasses_GO.txt
TermID Name Value
GO:0051762 sesquiterpene biosynthetic process -123.263200
GO:0006952 defense response -92.003340
GO:0007165 signal transduction -87.009031
GO:0010082 regulation of root meristem growth -85.813720
GO:2000280 regulation of root development -76.487902
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -71.808392
GO:0090305 nucleic acid phosphodiester bond hydrolysis -54.837630
GO:0000966 RNA 5’-end processing -49.527264
GO:0046345 abscisic acid catabolic process -46.799108
GO:0006468 protein phosphorylation -45.943129
GO:0010469 regulation of signaling receptor activity -45.181379
GO:0045338 farnesyl diphosphate metabolic process -43.241889
GO:0080156 mitochondrial mRNA modification -40.112965
GO:0009962 regulation of flavonoid biosynthetic process -35.352336
GO:0048509 regulation of meristem development -33.358186
GO:0051554 flavonol metabolic process -32.847642
GO:0009451 RNA modification -31.353508
GO:1902025 nitrate import -31.159863
GO:0019756 cyanogenic glycoside biosynthetic process -30.624232
GO:0009626 plant-type hypersensitive response -29.280582
GO:0009819 drought recovery -28.692016
GO:0080003 thalianol metabolic process -26.491320
GO:0009867 jasmonic acid mediated signaling pathway -25.814933
GO:2000026 regulation of multicellular organismal development -25.760968
GO:0016567 protein ubiquitination -24.814192
GO:0045168 cell-cell signaling involved in cell fate commitment -23.213581
GO:0071229 cellular response to acid chemical -21.633441
GO:0009617 response to bacterium -21.588290
GO:0010375 stomatal complex patterning -20.044409
GO:0006885 regulation of pH -19.446794
GO:0071236 cellular response to antibiotic -19.250722
GO:0010942 positive regulation of cell death -18.391164
GO:0009625 response to insect -18.198404
GO:0036371 protein localization to T-tubule -18.160410
GO:1901021 positive regulation of calcium ion transmembrane transporter activity -18.160410
GO:0033292 T-tubule organization -18.160410
GO:0036309 protein localization to M-band -18.160410
GO:0010618 aerenchyma formation -18.139990
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -16.999532
GO:0009734 auxin-activated signaling pathway -16.624630
GO:0009914 hormone transport -16.231674
GO:0010030 positive regulation of seed germination -15.745440
GO:0032527 protein exit from endoplasmic reticulum -15.058593
GO:0003341 cilium movement -14.626165
GO:0000304 response to singlet oxygen -14.098692
GO:2000117 negative regulation of cysteine-type endopeptidase activity -13.861990
GO:0071368 cellular response to cytokinin stimulus -13.837441
GO:1905034 regulation of antifungal innate immune response -13.646261
GO:0045926 negative regulation of growth -13.458879
GO:0060294 cilium movement involved in cell motility -13.305352
GO:0010221 negative regulation of vernalization response -13.253502
GO:0052544 defense response by callose deposition in cell wall -12.781323
GO:0097185 cellular response to azide -12.341169
GO:0015700 arsenite transport -12.058546
GO:0098660 inorganic ion transmembrane transport -11.268271
GO:0080184 response to phenylpropanoid -11.208254
GO:0033387 putrescine biosynthetic process from ornithine -11.194175
GO:0048211 Golgi vesicle docking -10.411023
GO:0045056 transcytosis -10.411023
GO:0006654 phosphatidic acid biosynthetic process -10.365896
GO:1901684 arsenate ion transmembrane transport -10.319721
GO:1902290 positive regulation of defense response to oomycetes -10.069439
GO:0009852 auxin catabolic process -10.033313
GO:0042742 defense response to bacterium -9.971460
GO:0035024 negative regulation of Rho protein signal transduction -9.928858
GO:0007166 cell surface receptor signaling pathway -9.718756
GO:0009961 response to 1-aminocyclopropane-1-carboxylic acid -9.695553
GO:0007267 cell-cell signaling -9.465565
GO:0009871 jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway -9.345083
GO:0009820 alkaloid metabolic process -9.047597
GO:0002011 morphogenesis of an epithelial sheet -9.046140
GO:0009664 plant-type cell wall organization -8.936784
GO:0071466 cellular response to xenobiotic stimulus -8.870023
GO:0080027 response to herbivore -8.477227
GO:0009684 indoleacetic acid biosynthetic process -8.410423
GO:0036159 inner dynein arm assembly -8.286640
GO:0001101 response to acid chemical -7.876771
GO:1905255 regulation of RNA binding transcription factor activity -7.822215
GO:0012502 induction of programmed cell death -7.493662
GO:0035864 response to potassium ion -7.406889
GO:1904526 regulation of microtubule binding -7.008658
GO:0016045 detection of bacterium -6.852833
GO:0060776 simple leaf morphogenesis -6.747710
GO:0009865 pollen tube adhesion -6.744444
GO:0042177 negative regulation of protein catabolic process -6.581183
GO:0010930 negative regulation of auxin mediated signaling pathway -6.338787
GO:0034394 protein localization to cell surface -6.337011
GO:0009410 response to xenobiotic stimulus -6.200545
GO:0010376 stomatal complex formation -6.020245
GO:0071447 cellular response to hydroperoxide -5.949636
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -5.949636
GO:1900449 regulation of glutamate receptor signaling pathway -5.949636
GO:0009311 oligosaccharide metabolic process -5.851302
GO:0010114 response to red light -5.748793
GO:0010233 phloem transport -5.714913
GO:0009960 endosperm development -5.605621
GO:0002084 protein depalmitoylation -5.504809
GO:0080141 regulation of jasmonic acid biosynthetic process -5.405514
GO:0009733 response to auxin -4.959063
GO:0009609 response to symbiotic bacterium -4.928401
GO:0009740 gibberellic acid mediated signaling pathway -4.867794
GO:0090559 regulation of membrane permeability -4.867058
GO:0003283 atrial septum development -4.737842
GO:0009611 response to wounding -4.682342
GO:0002213 defense response to insect -4.652790
GO:1902265 abscisic acid homeostasis -4.605998
GO:0097167 circadian regulation of translation -4.377239
GO:0031930 mitochondria-nucleus signaling pathway -4.333619
GO:0009737 response to abscisic acid -4.235759
GO:0009826 unidimensional cell growth -4.149882
GO:0017148 negative regulation of translation -4.095920
GO:0035725 sodium ion transmembrane transport -3.931946
GO:0009742 brassinosteroid mediated signaling pathway -3.724605
GO:0051607 defense response to virus -3.609544
GO:0010150 leaf senescence -3.522762
GO:0018342 protein prenylation -3.422514
GO:0010025 wax biosynthetic process -3.394830
GO:0060305 regulation of cell diameter -3.355775
GO:0061025 membrane fusion -3.333018
GO:0010310 regulation of hydrogen peroxide metabolic process -3.310012
GO:0009866 induced systemic resistance,ethylene mediated signaling pathway -3.234087
GO:0010555 response to mannitol -3.074696
GO:1901599 (-)-pinoresinol biosynthetic process -3.071305
GO:0015708 silicic acid import across plasma membrane -3.071305
GO:0006649 phospholipid transfer to membrane -3.066668
GO:0043086 negative regulation of catalytic activity -2.990442
GO:0097237 cellular response to toxic substance -2.921033
GO:0071218 cellular response to misfolded protein -2.846974
GO:0009644 response to high light intensity -2.721079
GO:0046394 carboxylic acid biosynthetic process -2.668466
GO:0019722 calcium-mediated signaling -2.599013
GO:0010208 pollen wall assembly -2.259532
GO:0009745 sucrose mediated signaling -2.254390
GO:0071805 potassium ion transmembrane transport -2.235091
GO:0010438 cellular response to sulfur starvation -2.224533
GO:0006335 DNA replication-dependent chromatin assembly -2.182306
GO:0048438 floral whorl development -2.152846
GO:0051513 regulation of monopolar cell growth -2.081591
GO:0035600 tRNA methylthiolation -2.034953
GO:0007584 response to nutrient -1.943252
GO:1900865 chloroplast RNA modification -1.937036
GO:0008053 mitochondrial fusion -1.911618
GO:1903553 positive regulation of extracellular exosome assembly -1.911602
GO:0044364 disruption of cells of other organism -1.911602
GO:0007492 endoderm development -1.911602
GO:0060465 pharynx development -1.911602
GO:0048312 intracellular distribution of mitochondria -1.911602
GO:0072498 embryonic skeletal joint development -1.911602
GO:0031640 killing of cells of other organism -1.911602
GO:0048265 response to pain -1.911602
GO:0048512 circadian behavior -1.869036
GO:0048658 anther wall tapetum development -1.852856
GO:1905614 negative regulation of developmental vegetative growth -1.756960
GO:0048821 erythrocyte development -1.679676
GO:0031542 positive regulation of anthocyanin biosynthetic process -1.676296
GO:0007498 mesoderm development -1.651274
GO:0007422 peripheral nervous system development -1.651274
GO:0048235 pollen sperm cell differentiation -1.640496
GO:0032504 multicellular organism reproduction -1.631797
GO:0050821 protein stabilization -1.499445
GO:0097503 sialylation -1.496617
GO:1905663 positive regulation of telomerase RNA reverse transcriptase activity -1.471697
GO:0032197 transposition,RNA-mediated -1.308417

[1] “missing_zmar_vs_all_GO.txt”

missing_zmar_vs_all_GO.txt
TermID Name Value
GO:0051762 sesquiterpene biosynthetic process -178.473129
GO:0007165 signal transduction -140.613488
GO:0006952 defense response -112.399149
GO:0009626 plant-type hypersensitive response -90.965700
GO:0010082 regulation of root meristem growth -65.058597
GO:0002239 response to oomycetes -58.651888
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -58.398957
GO:1900000 regulation of anthocyanin catabolic process -58.235448
GO:2000280 regulation of root development -50.621305
GO:0009819 drought recovery -49.271654
GO:0009625 response to insect -46.560252
GO:0052544 defense response by callose deposition in cell wall -45.430189
GO:1904526 regulation of microtubule binding -44.692162
GO:0016099 monoterpenoid biosynthetic process -44.057848
GO:0000966 RNA 5’-end processing -43.193677
GO:0006468 protein phosphorylation -40.763992
GO:0046345 abscisic acid catabolic process -40.398158
GO:0016567 protein ubiquitination -37.811969
GO:0080027 response to herbivore -35.422927
GO:0009871 jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway -33.260491
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion -31.134784
GO:0045926 negative regulation of growth -30.727605
GO:0010469 regulation of signaling receptor activity -29.831756
GO:0051554 flavonol metabolic process -29.467082
GO:0009690 cytokinin metabolic process -29.269152
GO:0071236 cellular response to antibiotic -28.340526
GO:0045338 farnesyl diphosphate metabolic process -27.993512
GO:0090615 mitochondrial mRNA processing -27.921063
GO:1901527 abscisic acid-activated signaling pathway involved in stomatal movement -27.719958
GO:0019756 cyanogenic glycoside biosynthetic process -27.544023
GO:0009962 regulation of flavonoid biosynthetic process -26.956820
GO:1902025 nitrate import -25.565208
GO:0071475 cellular hyperosmotic salinity response -25.518451
GO:0045168 cell-cell signaling involved in cell fate commitment -25.077146
GO:0071466 cellular response to xenobiotic stimulus -24.704446
GO:0018874 benzoate metabolic process -24.132287
GO:0071398 cellular response to fatty acid -23.248938
GO:0080003 thalianol metabolic process -23.185147
GO:0046900 tetrahydrofolylpolyglutamate metabolic process -23.148594
GO:0002230 positive regulation of defense response to virus by host -23.040381
GO:0070301 cellular response to hydrogen peroxide -22.946515
GO:0071669 plant-type cell wall organization or biogenesis -22.659946
GO:0010150 leaf senescence -22.361394
GO:0006885 regulation of pH -21.758538
GO:0042631 cellular response to water deprivation -21.407502
GO:0090305 nucleic acid phosphodiester bond hydrolysis -20.943718
GO:0009083 branched-chain amino acid catabolic process -20.784983
GO:0010618 aerenchyma formation -20.516176
GO:0000720 pyrimidine dimer repair by nucleotide-excision repair -18.648794
GO:0048509 regulation of meristem development -18.319363
GO:0009727 detection of ethylene stimulus -17.881501
GO:0046482 para-aminobenzoic acid metabolic process -17.318271
GO:0071446 cellular response to salicylic acid stimulus -16.698116
GO:2000026 regulation of multicellular organismal development -16.454846
GO:0036371 protein localization to T-tubule -16.269247
GO:0033292 T-tubule organization -16.269247
GO:0036309 protein localization to M-band -16.269247
GO:0097366 response to bronchodilator -15.805890
GO:0097237 cellular response to toxic substance -15.715204
GO:0071229 cellular response to acid chemical -15.446531
GO:0090136 epithelial cell-cell adhesion -15.423612
GO:0045218 zonula adherens maintenance -15.423612
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -15.208309
GO:0009451 RNA modification -15.068086
GO:0009611 response to wounding -13.994126
GO:0007613 memory -13.659670
GO:0010030 positive regulation of seed germination -13.607739
GO:0003341 cilium movement -12.938618
GO:0000304 response to singlet oxygen -12.794415
GO:0009801 cinnamic acid ester metabolic process -12.547408
GO:0016045 detection of bacterium -12.507868
GO:0080184 response to phenylpropanoid -12.023888
GO:0035902 response to immobilization stress -11.892224
GO:0010439 regulation of glucosinolate biosynthetic process -11.890992
GO:0080024 indolebutyric acid metabolic process -11.831338
GO:0032870 cellular response to hormone stimulus -11.812818
GO:0007267 cell-cell signaling -11.712089
GO:1902290 positive regulation of defense response to oomycetes -11.533178
GO:0018106 peptidyl-histidine phosphorylation -11.443885
GO:0071368 cellular response to cytokinin stimulus -11.332566
GO:0043617 cellular response to sucrose starvation -11.048683
GO:0097502 mannosylation -10.991734
GO:0009617 response to bacterium -10.985497
GO:0032527 protein exit from endoplasmic reticulum -10.973980
GO:0036376 sodium ion export across plasma membrane -10.962936
GO:0060291 long-term synaptic potentiation -10.857594
GO:0098703 calcium ion import across plasma membrane -10.857594
GO:0060294 cilium movement involved in cell motility -10.751648
GO:0071732 cellular response to nitric oxide -10.024297
GO:0010221 negative regulation of vernalization response -9.913795
GO:0033387 putrescine biosynthetic process from ornithine -9.901953
GO:0009646 response to absence of light -9.882841
GO:0010942 positive regulation of cell death -9.756210
GO:0010104 regulation of ethylene-activated signaling pathway -9.485067
GO:0000023 maltose metabolic process -9.397924
GO:0001680 tRNA 3’-terminal CCA addition -9.315195
GO:0010016 shoot system morphogenesis -9.300459
GO:0010375 stomatal complex patterning -9.239498
GO:0009780 photosynthetic NADP+ reduction -9.224979
GO:0030639 polyketide biosynthetic process -9.213466
GO:0044403 biological process involved in symbiotic interaction -8.969484
GO:0009852 auxin catabolic process -8.841270
GO:1902075 cellular response to salt -8.793402
GO:0009649 entrainment of circadian clock -8.786995
GO:0032508 DNA duplex unwinding -8.740588
GO:0080110 sporopollenin biosynthetic process -8.596184
GO:0098660 inorganic ion transmembrane transport -8.590303
GO:0048512 circadian behavior -8.585635
GO:1901726 negative regulation of histone deacetylase activity -8.437473
GO:0015768 maltose transport -8.225758
GO:0002237 response to molecule of bacterial origin -8.204322
GO:0000226 microtubule cytoskeleton organization -7.960852
GO:0010731 protein glutathionylation -7.897618
GO:0007166 cell surface receptor signaling pathway -7.866601
GO:0006097 glyoxylate cycle -7.795499
GO:0019450 L-cysteine catabolic process to pyruvate -7.764462
GO:0019752 carboxylic acid metabolic process -7.747054
GO:0010891 negative regulation of sequestering of triglyceride -7.518312
GO:0010898 positive regulation of triglyceride catabolic process -7.518312
GO:0071266 ‘de novo’ L-methionine biosynthetic process -7.513695
GO:0048211 Golgi vesicle docking -7.280960
GO:0045056 transcytosis -7.280960
GO:0048316 seed development -7.268778
GO:0015700 arsenite transport -7.248628
GO:0006368 transcription elongation from RNA polymerase II promoter -7.027962
GO:0007263 nitric oxide mediated signal transduction -6.950778
GO:1905255 regulation of RNA binding transcription factor activity -6.738528
GO:0010412 mannan metabolic process -6.629378
GO:1905034 regulation of antifungal innate immune response -6.383180
GO:0070365 hepatocyte differentiation -6.381409
GO:0060213 positive regulation of nuclear-transcribed mRNA poly(A) tail shortening -6.381409
GO:0036159 inner dynein arm assembly -6.262662
GO:0006293 nucleotide-excision repair,preincision complex stabilization -6.189060
GO:0032194 ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate -6.158100
GO:0012502 induction of programmed cell death -6.158100
GO:0035864 response to potassium ion -6.154876
GO:0000025 maltose catabolic process -6.061973
GO:0050829 defense response to Gram-negative bacterium -5.789530
GO:1901684 arsenate ion transmembrane transport -5.722287
GO:2001294 malonyl-CoA catabolic process -5.384890
GO:0005983 starch catabolic process -5.349583
GO:0043966 histone H3 acetylation -5.253700
GO:0009311 oligosaccharide metabolic process -5.250044
GO:0010730 negative regulation of hydrogen peroxide biosynthetic process -5.234106
GO:0006629 lipid metabolic process -5.178395
GO:0002238 response to molecule of fungal origin -5.145763
GO:0031347 regulation of defense response -5.011113
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -4.973551
GO:1900449 regulation of glutamate receptor signaling pathway -4.973551
GO:0060359 response to ammonium ion -4.895017
GO:0006432 phenylalanyl-tRNA aminoacylation -4.788760
GO:0010930 negative regulation of auxin mediated signaling pathway -4.664218
GO:0034394 protein localization to cell surface -4.662473
GO:1990169 stress response to copper ion -4.599134
GO:0106004 tRNA (guanine-N7)-methylation -4.538367
GO:0009877 nodulation -4.476728
GO:0009410 response to xenobiotic stimulus -4.474451
GO:0009608 response to symbiont -4.377533
GO:0006898 receptor-mediated endocytosis -4.215610
GO:0090559 regulation of membrane permeability -3.990589
GO:0006183 GTP biosynthetic process -3.957863
GO:1902198 3-methylbut-2-enoyl-CoA(4-) metabolic process -3.911273
GO:0009773 photosynthetic electron transport in photosystem I -3.872559
GO:0008298 intracellular mRNA localization -3.700549
GO:0010114 response to red light -3.646740
GO:0071731 response to nitric oxide -3.642485
GO:0002215 defense response to nematode -3.631838
GO:0010119 regulation of stomatal movement -3.608488
GO:0019348 dolichol metabolic process -3.425914
GO:0097167 circadian regulation of translation -3.424748
GO:0006696 ergosterol biosynthetic process -3.317833
GO:0045199 maintenance of epithelial cell apical/basal polarity -3.134638
GO:0003283 atrial septum development -3.074783
GO:2000122 negative regulation of stomatal complex development -3.053135
GO:0015886 heme transport -3.017938
GO:0044255 cellular lipid metabolic process -2.977720
GO:0009992 cellular water homeostasis -2.939957
GO:0009961 response to 1-aminocyclopropane-1-carboxylic acid -2.849513
GO:0006165 nucleoside diphosphate phosphorylation -2.837631
GO:0052324 plant-type cell wall cellulose biosynthetic process -2.751928
GO:1902265 abscisic acid homeostasis -2.721576
GO:0005977 glycogen metabolic process -2.640777
GO:0048767 root hair elongation -2.636992
GO:0060776 simple leaf morphogenesis -2.621028
GO:1901599 (-)-pinoresinol biosynthetic process -2.479543
GO:0046477 glycosylceramide catabolic process -2.369658
GO:0070914 UV-damage excision repair -2.353867
GO:0072089 stem cell proliferation -2.235250
GO:0001101 response to acid chemical -2.228327
GO:0034721 histone H3-K4 demethylation,trimethyl-H3-K4-specific -2.012384
GO:1903507 negative regulation of nucleic acid-templated transcription -1.958349
GO:0048599 oocyte development -1.946502
GO:0051729 germline cell cycle switching,mitotic to meiotic cell cycle -1.944420
GO:0006739 NADP metabolic process -1.889197
GO:0000454 snoRNA guided rRNA pseudouridine synthesis -1.851063
GO:0016074 sno(s)RNA metabolic process -1.846556
GO:0071805 potassium ion transmembrane transport -1.841910
GO:0006260 DNA replication -1.831471
GO:0010310 regulation of hydrogen peroxide metabolic process -1.816874
GO:0051607 defense response to virus -1.773648
GO:1901255 nucleotide-excision repair involved in interstrand cross-link repair -1.694668
GO:0008277 regulation of G protein-coupled receptor signaling pathway -1.694668
GO:0035518 histone H2A monoubiquitination -1.668789
GO:0042550 photosystem I stabilization -1.664732
GO:0008356 asymmetric cell division -1.634371
GO:0032775 DNA methylation on adenine -1.562079
GO:0050821 protein stabilization -1.545126
GO:0071218 cellular response to misfolded protein -1.530161
GO:0044364 disruption of cells of other organism -1.420387
GO:0007492 endoderm development -1.420387
GO:0048312 intracellular distribution of mitochondria -1.420387
GO:0060465 pharynx development -1.420387
GO:0072498 embryonic skeletal joint development -1.420387
GO:0031640 killing of cells of other organism -1.420387
GO:0048265 response to pain -1.420387
GO:0002213 defense response to insect -1.414236
GO:0006654 phosphatidic acid biosynthetic process -1.388060
GO:0070911 global genome nucleotide-excision repair -1.368073
GO:0051513 regulation of monopolar cell growth -1.337060
GO:0032504 multicellular organism reproduction -1.308625

[1] “missing_zmuel_vs_all_GO.txt”

missing_zmuel_vs_all_GO.txt
TermID Name Value
GO:0051762 sesquiterpene biosynthetic process -181.717133
GO:0007165 signal transduction -130.964462
GO:0009626 plant-type hypersensitive response -93.136155
GO:0006952 defense response -77.842261
GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process -70.924487
GO:0010082 regulation of root meristem growth -68.162621
GO:0006468 protein phosphorylation -60.750918
GO:0052544 defense response by callose deposition in cell wall -56.608053
GO:0016567 protein ubiquitination -54.100002
GO:2000280 regulation of root development -50.486827
GO:0009625 response to insect -48.167708
GO:0045168 cell-cell signaling involved in cell fate commitment -45.831663
GO:0016099 monoterpenoid biosynthetic process -44.932002
GO:0090615 mitochondrial mRNA processing -43.900684
GO:0000966 RNA 5’-end processing -42.278057
GO:0046345 abscisic acid catabolic process -40.691415
GO:0090305 nucleic acid phosphodiester bond hydrolysis -39.740579
GO:0080027 response to herbivore -36.907775
GO:0009871 jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway -34.033423
GO:0006597 spermine biosynthetic process -33.656807
GO:0071236 cellular response to antibiotic -32.390998
GO:0044550 secondary metabolite biosynthetic process -31.883123
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion -31.738087
GO:0010469 regulation of signaling receptor activity -31.275882
GO:0051554 flavonol metabolic process -30.086084
GO:0045338 farnesyl diphosphate metabolic process -28.998426
GO:0048509 regulation of meristem development -27.802412
GO:0071466 cellular response to xenobiotic stimulus -26.952461
GO:1902025 nitrate import -26.329774
GO:0071475 cellular hyperosmotic salinity response -26.267986
GO:0018874 benzoate metabolic process -24.723612
GO:0009451 RNA modification -24.705821
GO:0070301 cellular response to hydrogen peroxide -24.083938
GO:0002230 positive regulation of defense response to virus by host -23.982792
GO:0071398 cellular response to fatty acid -23.828574
GO:0080003 thalianol metabolic process -23.789992
GO:0046900 tetrahydrofolylpolyglutamate metabolic process -23.721833
GO:0009962 regulation of flavonoid biosynthetic process -22.227242
GO:0010618 aerenchyma formation -20.935965
GO:0071446 cellular response to salicylic acid stimulus -20.847283
GO:0060294 cilium movement involved in cell motility -20.759764
GO:0009819 drought recovery -20.745503
GO:0097366 response to bronchodilator -19.329640
GO:0000720 pyrimidine dimer repair by nucleotide-excision repair -19.147167
GO:0071229 cellular response to acid chemical -18.646332
GO:0009727 detection of ethylene stimulus -18.408248
GO:0046482 para-aminobenzoic acid metabolic process -17.998248
GO:0009611 response to wounding -17.276112
GO:0009617 response to bacterium -17.072972
GO:0097237 cellular response to toxic substance -16.933808
GO:0036371 protein localization to T-tubule -16.616139
GO:0033292 T-tubule organization -16.616139
GO:0036309 protein localization to M-band -16.616139
GO:0002239 response to oomycetes -15.875443
GO:0006885 regulation of pH -15.787702
GO:2000083 negative regulation of L-ascorbic acid biosynthetic process -15.536707
GO:0010105 negative regulation of ethylene-activated signaling pathway -15.525570
GO:0015700 arsenite transport -15.521384
GO:0008202 steroid metabolic process -15.171247
GO:0032870 cellular response to hormone stimulus -14.968531
GO:0042742 defense response to bacterium -14.961942
GO:2000026 regulation of multicellular organismal development -13.816111
GO:0010030 positive regulation of seed germination -13.622275
GO:0000304 response to singlet oxygen -13.389297
GO:0034090 maintenance of meiotic sister chromatid cohesion -13.377534
GO:0003341 cilium movement -13.254910
GO:1901684 arsenate ion transmembrane transport -13.199874
GO:0016045 detection of bacterium -13.150286
GO:0009801 cinnamic acid ester metabolic process -13.089991
GO:0071732 cellular response to nitric oxide -13.088987
GO:0007166 cell surface receptor signaling pathway -13.075849
GO:0009914 hormone transport -12.890690
GO:0031347 regulation of defense response -12.817341
GO:0007267 cell-cell signaling -12.693990
GO:0006509 membrane protein ectodomain proteolysis -12.551149
GO:0080024 indolebutyric acid metabolic process -12.490669
GO:1902290 positive regulation of defense response to oomycetes -12.360237
GO:0080184 response to phenylpropanoid -12.298286
GO:0035902 response to immobilization stress -12.183306
GO:1900706 positive regulation of siderophore biosynthetic process -12.168786
GO:0071368 cellular response to cytokinin stimulus -11.780061
GO:0018106 peptidyl-histidine phosphorylation -11.606010
GO:0071281 cellular response to iron ion -11.562767
GO:0009143 nucleoside triphosphate catabolic process -11.547948
GO:0032527 protein exit from endoplasmic reticulum -11.527071
GO:0010438 cellular response to sulfur starvation -11.472929
GO:0070462 plus-end specific microtubule depolymerization -11.321631
GO:0036376 sodium ion export across plasma membrane -11.218898
GO:0009664 plant-type cell wall organization -11.167694
GO:0060291 long-term synaptic potentiation -11.130410
GO:0098703 calcium ion import across plasma membrane -11.130410
GO:0098660 inorganic ion transmembrane transport -10.737609
GO:0010942 positive regulation of cell death -10.466450
GO:0010221 negative regulation of vernalization response -10.216725
GO:0010305 leaf vascular tissue pattern formation -10.168418
GO:0010114 response to red light -10.030785
GO:0010016 shoot system morphogenesis -9.930844
GO:0000023 maltose metabolic process -9.773194
GO:0009088 threonine biosynthetic process -9.669230
GO:0044403 biological process involved in symbiotic interaction -9.564115
GO:0009649 entrainment of circadian clock -9.376970
GO:0009852 auxin catabolic process -9.060693
GO:1902075 cellular response to salt -9.029474
GO:0048512 circadian behavior -8.853277
GO:0071347 cellular response to interleukin-1 -8.739769
GO:1901726 negative regulation of histone deacetylase activity -8.720248
GO:0015768 maltose transport -8.593896
GO:0010731 protein glutathionylation -8.376087
GO:0042631 cellular response to water deprivation -8.324906
GO:0019752 carboxylic acid metabolic process -8.261766
GO:0007613 memory -7.987966
GO:0019450 L-cysteine catabolic process to pyruvate -7.982055
GO:0010898 positive regulation of triglyceride catabolic process -7.797760
GO:0010891 negative regulation of sequestering of triglyceride -7.797760
GO:0071266 ‘de novo’ L-methionine biosynthetic process -7.778089
GO:0048211 Golgi vesicle docking -7.655842
GO:0045056 transcytosis -7.655842
GO:0045926 negative regulation of growth -7.549587
GO:0099402 plant organ development -7.443147
GO:0071219 cellular response to molecule of bacterial origin -7.355856
GO:0030150 protein import into mitochondrial matrix -7.293749
GO:0006778 porphyrin-containing compound metabolic process -7.149977
GO:0070667 negative regulation of mast cell proliferation -6.937809
GO:1905255 regulation of RNA binding transcription factor activity -6.937809
GO:0033007 negative regulation of mast cell activation involved in immune response -6.937809
GO:0001841 neural tube formation -6.892856
GO:0010412 mannan metabolic process -6.890912
GO:1905034 regulation of antifungal innate immune response -6.763737
GO:0033473 indoleacetic acid conjugate metabolic process -6.508933
GO:1903711 spermidine transmembrane transport -6.503290
GO:0048658 anther wall tapetum development -6.492437
GO:0007263 nitric oxide mediated signal transduction -6.441332
GO:0000025 maltose catabolic process -6.402236
GO:0035864 response to potassium ion -6.384732
GO:0032232 negative regulation of actin filament bundle assembly -5.942017
GO:0090559 regulation of membrane permeability -5.895177
GO:1903507 negative regulation of nucleic acid-templated transcription -5.889535
GO:0005983 starch catabolic process -5.865772
GO:0031508 pericentric heterochromatin assembly -5.799869
GO:0002238 response to molecule of fungal origin -5.783769
GO:0019079 viral genome replication -5.731469
GO:0001101 response to acid chemical -5.560432
GO:0010730 negative regulation of hydrogen peroxide biosynthetic process -5.445886
GO:0046938 phytochelatin biosynthetic process -5.445886
GO:0050829 defense response to Gram-negative bacterium -5.405397
GO:1904526 regulation of microtubule binding -5.193765
GO:0018107 peptidyl-threonine phosphorylation -5.188056
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors -5.153496
GO:1900449 regulation of glutamate receptor signaling pathway -5.153496
GO:0012502 induction of programmed cell death -5.115042
GO:0010930 negative regulation of auxin mediated signaling pathway -4.968536
GO:0034394 protein localization to cell surface -4.966521
GO:0009877 nodulation -4.911798
GO:0009644 response to high light intensity -4.900573
GO:0006898 receptor-mediated endocytosis -4.752375
GO:0009854 oxidative photosynthetic carbon pathway -4.677642
GO:0009608 response to symbiont -4.556275
GO:1902616 acyl carnitine transmembrane transport -4.435575
GO:0038018 Wnt receptor catabolic process -4.390571
GO:0006629 lipid metabolic process -4.332034
GO:0009410 response to xenobiotic stimulus -4.287566
GO:0009052 pentose-phosphate shunt,non-oxidative branch -4.247369
GO:0009638 phototropism -4.027267
GO:0071731 response to nitric oxide -3.940569
GO:0000914 phragmoplast assembly -3.761422
GO:0009820 alkaloid metabolic process -3.710300
GO:0097167 circadian regulation of translation -3.599961
GO:0006696 ergosterol biosynthetic process -3.585889
GO:0002215 defense response to nematode -3.584755
GO:0010119 regulation of stomatal movement -3.570823
GO:2000142 regulation of DNA-templated transcription,initiation -3.491777
GO:0003283 atrial septum development -3.375052
GO:0010150 leaf senescence -3.287542
GO:0044255 cellular lipid metabolic process -3.248190
GO:0030435 sporulation resulting in formation of a cellular spore -3.232252
GO:0009311 oligosaccharide metabolic process -3.206762
GO:0006165 nucleoside diphosphate phosphorylation -3.191198
GO:0009961 response to 1-aminocyclopropane-1-carboxylic acid -3.168515
GO:1902265 abscisic acid homeostasis -3.059058
GO:0060776 simple leaf morphogenesis -2.956538
GO:0019323 pentose catabolic process -2.936443
GO:0044262 cellular carbohydrate metabolic process -2.920548
GO:0032508 DNA duplex unwinding -2.916109
GO:0009865 pollen tube adhesion -2.838595
GO:0042177 negative regulation of protein catabolic process -2.832164
GO:0015840 urea transport -2.786399
GO:0010106 cellular response to iron ion starvation -2.715632
GO:0006314 intron homing -2.696105
GO:0070914 UV-damage excision repair -2.695172
GO:0048587 regulation of short-day photoperiodism,flowering -2.668406
GO:0005977 glycogen metabolic process -2.633283
GO:1901599 (-)-pinoresinol biosynthetic process -2.589659
GO:0016024 CDP-diacylglycerol biosynthetic process -2.501440
GO:0034721 histone H3-K4 demethylation,trimethyl-H3-K4-specific -2.288318
GO:0051607 defense response to virus -2.216937
GO:0009314 response to radiation -2.104823
GO:1901255 nucleotide-excision repair involved in interstrand cross-link repair -1.955409
GO:0002213 defense response to insect -1.890326
GO:0035518 histone H2A monoubiquitination -1.807329
GO:0006739 NADP metabolic process -1.769930
GO:0071218 cellular response to misfolded protein -1.767598
GO:0032212 positive regulation of telomere maintenance via telomerase -1.707599
GO:0043603 cellular amide metabolic process -1.610456
GO:0006654 phosphatidic acid biosynthetic process -1.576801
GO:0044364 disruption of cells of other organism -1.511515
GO:0048312 intracellular distribution of mitochondria -1.511515
GO:1903553 positive regulation of extracellular exosome assembly -1.511515
GO:0031640 killing of cells of other organism -1.511515
GO:0060465 pharynx development -1.511515
GO:0072498 embryonic skeletal joint development -1.511515
GO:0007492 endoderm development -1.511509
GO:0051513 regulation of monopolar cell growth -1.473899
GO:0051090 regulation of DNA-binding transcription factor activity -1.439312
GO:0010310 regulation of hydrogen peroxide metabolic process -1.409169
GO:0009745 sucrose mediated signaling -1.408307
GO:0051258 protein polymerization -1.407216
GO:0009992 cellular water homeostasis -1.388395
GO:0007584 response to nutrient -1.321440
GO:0010376 stomatal complex formation -1.310240

[1] “only_in_posi_GO.txt”

only_in_posi_GO.txt
TermID Name Value
GO:0005983 starch catabolic process -2.055820
GO:0034721 histone H3-K4 demethylation,trimethyl-H3-K4-specific -1.884385
GO:0046686 response to cadmium ion -1.754551
GO:0071333 cellular response to glucose stimulus -1.582738
GO:0030174 regulation of DNA-dependent DNA replication initiation -1.307768

[1] “only_in_zmar_GO.txt”

only_in_zmar_GO.txt
TermID Name Value
GO:0051603 proteolysis involved in cellular protein catabolic process -23.445501
GO:0046785 microtubule polymerization -13.774183
GO:0006624 vacuolar protein processing -9.895786
GO:1990019 protein storage vacuole organization -8.591400
GO:0080156 mitochondrial mRNA modification -7.414447
GO:0010157 response to chlorate -5.513515
GO:0048281 inflorescence morphogenesis -4.588824
GO:0032989 cellular component morphogenesis -4.508650
GO:0090156 cellular sphingolipid homeostasis -4.494330
GO:0010090 trichome morphogenesis -4.097280
GO:1901332 negative regulation of lateral root development -2.847257
GO:0006278 RNA-dependent DNA biosynthetic process -2.761258
GO:0032197 transposition,RNA-mediated -2.708915
GO:0010286 heat acclimation -2.016484
GO:0090709 regulation of timing of plant organ formation -1.857388
GO:0006537 glutamate biosynthetic process -1.818101
GO:0090305 nucleic acid phosphodiester bond hydrolysis -1.818070
GO:0048194 Golgi vesicle budding -1.775108
GO:0009408 response to heat -1.548177
GO:0045332 phospholipid translocation -1.546385
GO:0015770 sucrose transport -1.318982

[1] “only_in_zmuel_GO.txt”

only_in_zmuel_GO.txt
TermID Name Value
GO:0090284 positive regulation of protein glycosylation in Golgi -5.506616
GO:0010222 stem vascular tissue pattern formation -5.047945
GO:0008347 glial cell migration -4.650340
GO:0090303 positive regulation of wound healing -4.387055
GO:0040007 growth -4.373448
GO:1900049 regulation of histone exchange -4.140205
GO:2000114 regulation of establishment of cell polarity -3.856587
GO:0043007 maintenance of rDNA -3.318770
GO:2001240 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand -2.928272
GO:0046328 regulation of JNK cascade -2.672143
GO:0080119 ER body organization -2.146026
GO:0007030 Golgi organization -1.799156
GO:0034260 negative regulation of GTPase activity -1.793183
GO:0046459 short-chain fatty acid metabolic process -1.740640
GO:0006336 DNA replication-independent chromatin assembly -1.395115

[1] “only_seagrasses_GO.txt”

only_seagrasses_GO.txt
TermID Name Value
GO:0051603 proteolysis involved in cellular protein catabolic process -11.456833
GO:0006278 RNA-dependent DNA biosynthetic process -9.577934
GO:0032197 transposition,RNA-mediated -9.168511
GO:0033275 actin-myosin filament sliding -6.682353
GO:0090501 RNA phosphodiester bond hydrolysis -6.648430
GO:0043007 maintenance of rDNA -6.455202
GO:0033298 contractile vacuole organization -5.583611
GO:0032060 bleb assembly -5.583611
GO:0050982 detection of mechanical stimulus -5.431629
GO:1900049 regulation of histone exchange -5.042366
GO:0016131 brassinosteroid metabolic process -4.909247
GO:1902466 positive regulation of histone H3-K27 trimethylation -4.579819
GO:0051591 response to cAMP -4.509703
GO:0001932 regulation of protein phosphorylation -3.934885
GO:0032989 cellular component morphogenesis -3.724531
GO:0048578 positive regulation of long-day photoperiodism,flowering -3.385409
GO:0006468 protein phosphorylation -3.226314
GO:0080156 mitochondrial mRNA modification -3.221374
GO:0097193 intrinsic apoptotic signaling pathway -3.003236
GO:0009048 dosage compensation by inactivation of X chromosome -2.792735
GO:0090701 specification of plant organ identity -2.713400
GO:0010022 meristem determinacy -2.675579
GO:0006971 hypotonic response -2.372108
GO:0010090 trichome morphogenesis -2.336224
GO:0051707 response to other organism -2.284036
GO:0051555 flavonol biosynthetic process -2.102840
GO:1904872 regulation of telomerase RNA localization to Cajal body -1.978326
GO:0051127 positive regulation of actin nucleation -1.905381
GO:0097242 amyloid-beta clearance -1.718349
GO:0010992 ubiquitin recycling -1.718349
GO:0010815 bradykinin catabolic process -1.718349
GO:2001240 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand -1.641177
GO:0016926 protein desumoylation -1.543029
GO:0071048 nuclear retention of unspliced pre-mRNA at the site of transcription -1.532452
GO:0010222 stem vascular tissue pattern formation -1.487551
GO:0010492 maintenance of shoot apical meristem identity -1.433920
GO:0048576 positive regulation of short-day photoperiodism,flowering -1.364131
GO:0043086 negative regulation of catalytic activity -1.351735
GO:0031154 culmination involved in sorocarp development -1.309504

Venn diagram GO overlaps

Let’s also check which GO terms overlap between the 4 seagrasses!

Let’s have a look at all of these plots. Manually zooming in leads to ggrepel reloading labels, so on the small scale a lot of these plots don’t have labels.

for(i in names(plot_list)) {
  file_name = paste('output/',  i, '.png', sep='')
  
  cowplot::save_plot(file_name, plot_list[[i]], base_height=8)
  
}

How many shared lost GO-terms are there? Hopefully, all four species will have lost the most GO-terms.

a <- list(`P. australis` = results_list$missing_posi_vs_all_GO.txt$Name,
          `A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$Name,
          `Z. marina` = results_list$missing_zmar_vs_all_GO.txt$Name,
          `Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$Name,
          `A. thaliana` = results_list$missing_arabidopsis_vs_all_GO.txt$Name)

a_go_ids <- list(`P. australis` = results_list$missing_posi_vs_all_GO.txt$TermID,
          `A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$TermID,
          `Z. marina` = results_list$missing_zmar_vs_all_GO.txt$TermID,
          `Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$TermID,
          `A. thaliana` = results_list$missing_arabidopsis_vs_all_GO.txt$TermID)
plot(euler(a), 
     quantities = TRUE,
     fill = rev(wes_palette("Zissou1", 15, type = 'continuous')),
    alpha = 0.5,
     labels = list(font = 4))

upset(fromList(a), order.by='freq', )

a_no_ara <- list(`P. australis` = results_list$missing_posi_vs_all_GO.txt$Name,
          `A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$Name,
          `Z. marina` = results_list$missing_zmar_vs_all_GO.txt$Name,
          `Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$Name)

What are the shared GO-terms in seagrasses, WITHOUT the Ara loss??

setdiff(Reduce(intersect, a_no_ara), Reduce(intersect, a)) %>% enframe() %>% writexl::write_xlsx('./data/shared_lost_genes.xlsx')

What if we remove Posidonia?

b <- list(`A. antarctica` = results_list$missing_amphi_vs_all_GO.txt$Name,
          `Z. marina` = results_list$missing_zmar_vs_all_GO.txt$Name,
          `Z. muelleri` = results_list$missing_zmuel_vs_all_GO.txt$Name)
intersections <- Reduce(intersect, b)
intersections[grepl('ethylene', intersections)]
[1] "jasmonic acid and ethylene-dependent systemic resistance,ethylene mediated signaling pathway"
[2] "regulation of ethylene-activated signaling pathway"                                          

OK we need a big list of all GO-terms here - which GO-term is lost in which species. That will be a supplementary table.

all_species <- c("P. australis","A. antarctica","Z. marina","Z. muelleri", 'A. thaliana')  
all_go_terms <- Reduce(union, a)
all_go_ids <- Reduce(union, a_go_ids)
results_d <- data.frame('GOID' = character(),
                        'GO' = character(),
                        'P. australis' = character(),
                        'A. antarctica' = character(),
                        'Z. marina' = character(),
                        'Z. muelleri' = character(),
                        'A. thaliana' = character())


for (index in seq_along(all_go_terms)){
  go <- all_go_terms[index]
  go_id <- all_go_ids[index]
  specs <- c()
  for (species in names(a)) {
    if ( length(a[[species]][grep(paste('^', go, '$', sep=''), a[[species]])]) > 0 ) {
      specs <- c(specs, species)
    }
  }
  
  results_d[index,] <- c(go_id, go, gsub('FALSE', 'Present', gsub('TRUE', 'Lost', all_species %in% specs)))
}
writexl::write_xlsx(results_d, 'data/Lost_GO_terms_in_five_species.xlsx')

after filtering for plant-specific GO-terms

We will use the GO-terms that are plant-specific as identified by the GOMAP paper. See https://github.com/wkpalan/GOMAP-maize-analysis/blob/main/6.plantSpecific/1.getSppSpecific.R or https://plantmethods.biomedcentral.com/articles/10.1186/s13007-021-00754-1

go_plant <- read_tsv('https://raw.githubusercontent.com/wkpalan/GOMAP-maize-analysis/main/data/go/speciesSpecificGOTerms.txt')
Rows: 45031 Columns: 5
-- Column specification --------------------------------------------------------
Delimiter: "\t"
chr (1): GOterm
dbl (4): NCBITaxon:10090, NCBITaxon:33090, NCBITaxon:3702, NCBITaxon:40674

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
# taxon 33090 is Viridiplantae
plantSpecificGO <- go_plant %>% dplyr::filter(`NCBITaxon:33090`==1) %>% pull(GOterm)
plantSpecificGO <- c(plantSpecificGO,c("GO:0005575","GO:0008150","GO:0003674"))
results_d %>% filter(GOID %in% plantSpecificGO) %>% writexl::write_xlsx('data/Lost_GO_terms_in_five_species.PlantSpecific.xlsx')

Now let’s redo the Venn diagram with those filtered GO-terms

filters <- lapply(a_go_ids, function(ch) ch %in% plantSpecificGO)

newa <- list()
for (species in names(filters)) {
  before <- a[[species]]
  after <- before[filters[[species]]]
  newa[[species]] <- after
}
plot(euler(newa), 
     quantities = TRUE,
     fill = rev(wes_palette("Zissou1", 15, type = 'continuous')),
    alpha = 0.5,
     labels = list(font = 4))

Not much difference?


sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] rrvgo_1.4.4          UpSetR_1.4.0         eulerr_6.1.1        
 [4] ggrepel_0.9.1        stringi_1.7.5        httr_1.4.2          
 [7] wesanderson_0.3.6    rvest_1.0.2          forcats_0.5.1       
[10] stringr_1.4.0        dplyr_1.0.7          purrr_0.3.4         
[13] readr_2.0.2          tidyr_1.1.4          tibble_3.1.5        
[16] ggplot2_3.3.5        tidyverse_1.3.1      topGO_2.44.0        
[19] SparseM_1.81         GO.db_3.13.0         AnnotationDbi_1.54.1
[22] IRanges_2.26.0       S4Vectors_0.30.2     Biobase_2.52.0      
[25] graph_1.70.0         BiocGenerics_0.38.0  workflowr_1.6.2     

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2       ellipsis_0.3.2         rprojroot_2.0.2       
  [4] XVector_0.32.0         fs_1.5.0               rstudioapi_0.13       
  [7] farver_2.1.0           bit64_4.0.5            fansi_0.5.0           
 [10] lubridate_1.8.0        xml2_1.3.2             cachem_1.0.6          
 [13] GOSemSim_2.18.1        knitr_1.36             polyclip_1.10-0       
 [16] jsonlite_1.7.2         broom_0.7.9            gridBase_0.4-7        
 [19] dbplyr_2.1.1           png_0.1-7              pheatmap_1.0.12       
 [22] shiny_1.7.1            compiler_4.1.0         backports_1.2.1       
 [25] assertthat_0.2.1       fastmap_1.1.0          cli_3.0.1             
 [28] later_1.3.0            htmltools_0.5.2        tools_4.1.0           
 [31] igraph_1.2.7           NLP_0.2-1              gtable_0.3.0          
 [34] glue_1.4.2             GenomeInfoDbData_1.2.6 Rcpp_1.0.7            
 [37] slam_0.1-48            cellranger_1.1.0       jquerylib_0.1.4       
 [40] vctrs_0.3.8            Biostrings_2.60.2      writexl_1.4.0         
 [43] polylabelr_0.2.0       xfun_0.27              mime_0.12             
 [46] lifecycle_1.0.1        zlibbioc_1.38.0        scales_1.1.1          
 [49] treemap_2.4-3          vroom_1.5.5            hms_1.1.1             
 [52] promises_1.2.0.1       RColorBrewer_1.1-2     yaml_2.2.1            
 [55] curl_4.3.2             memoise_2.0.0          gridExtra_2.3         
 [58] sass_0.4.0             RSQLite_2.2.8          highr_0.9             
 [61] GenomeInfoDb_1.28.4    rlang_0.4.12           pkgconfig_2.0.3       
 [64] matrixStats_0.61.0     bitops_1.0-7           evaluate_0.14         
 [67] lattice_0.20-44        labeling_0.4.2         cowplot_1.1.1         
 [70] bit_4.0.4              tidyselect_1.1.1       plyr_1.8.6            
 [73] magrittr_2.0.1         R6_2.5.1               generics_0.1.1        
 [76] DBI_1.1.1              pillar_1.6.4           haven_2.4.3           
 [79] whisker_0.4            withr_2.4.2            KEGGREST_1.32.0       
 [82] RCurl_1.98-1.5         modelr_0.1.8           crayon_1.4.1          
 [85] wordcloud_2.6          utf8_1.2.2             tzdb_0.1.2            
 [88] rmarkdown_2.11         grid_4.1.0             readxl_1.3.1          
 [91] data.table_1.14.2      blob_1.2.2             git2r_0.28.0          
 [94] reprex_2.0.1           digest_0.6.28          xtable_1.8-4          
 [97] tm_0.7-8               httpuv_1.6.3           munsell_0.5.0         
[100] bslib_0.3.1