GO enrichment

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Last updated: 2021-12-20

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Knit directory: Amphibolis_Posidonia_Comparison/

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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.

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

[1] “lost_in_amphi_GO.txt”

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

[1] “lost_in_posi_GO.txt”

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

[1] “lost_in_zmar_GO.txt”

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

[1] “lost_in_zmuel_GO.txt”

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

[1] “missing_amphi_vs_all_GO.txt”

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

[1] “missing_aquatics_GO.txt”

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

[1] “missing_arabidopsis_vs_all_GO.txt”

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

[1] “missing_posi_vs_all_GO.txt”

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

[1] “missing_seagrasses_GO.txt”

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

[1] “missing_zmar_vs_all_GO.txt”

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

[1] “missing_zmuel_vs_all_GO.txt”

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

[1] “only_in_posi_GO.txt”

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

[1] “only_in_zmar_GO.txt”

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

[1] “only_in_zmuel_GO.txt”

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

[1] “only_seagrasses_GO.txt”

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

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?

Session information

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