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File Version Author Date Message
Rmd 65ae03b Steve Ped 2020-03-07 Typo
Rmd 3b120d9 Steve Ped 2020-03-07 Corrected table justifications
html a5cdf5d Steve Ped 2020-03-06 Finished Revisions
Rmd 2772d42 Steve Ped 2020-03-06 Corrected UpSet names
Rmd a9781d9 Steve Ped 2020-03-06 Fixed duplicate labels
Rmd 154085b Steve Ped 2020-03-06 Reduced ranked lists to fry only
Rmd 2aa6e06 Steve Ped 2020-03-06 Removed gsea, camera & combining data. Now only using fry + goseq
Rmd 433a729 Steve Ped 2020-03-06 Prepared to remove EGSEA-type approach
Rmd 956c065 Steve Ped 2020-03-05 Revised GO exploration
html 1385ceb Steve Ped 2020-03-05 Compiled after renaming columns
Rmd 2c56cef Steve Ped 2020-03-05 Tidied column names for enrichment output
html 7fe1505 Steve Ped 2020-03-05 Updated all analyses & heatmaps after changing to cpmPostNorm instead of fit\(fitted.values for enrichment/heatmaps</td> </tr> <tr> <td>Rmd</td> <td><a href="https://github.com/UofABioinformaticsHub/20170327_Psen2S4Ter_RNASeq/blob/bad81c1731ba8bc4487d25ec2719e92ae6917e4a/analysis/3_Enrichment_MutantVsWT.Rmd" target="_blank">bad81c1</a></td> <td>Steve Ped</td> <td>2020-03-05</td> <td>Updated MutVsWt UpSet plots for KEGG/HALLMARK</td> </tr> <tr> <td>Rmd</td> <td><a href="https://github.com/UofABioinformaticsHub/20170327_Psen2S4Ter_RNASeq/blob/377410a12ca13a7e233e39fb2f77f165e846d830/analysis/3_Enrichment_MutantVsWT.Rmd" target="_blank">377410a</a></td> <td>Steve Ped</td> <td>2020-03-05</td> <td>Finished revision of Enrichment Analysis</td> </tr> <tr> <td>Rmd</td> <td><a href="https://github.com/UofABioinformaticsHub/20170327_Psen2S4Ter_RNASeq/blob/c0b89ed8f761b0c7222538c353d21cd5aa402b94/analysis/3_Enrichment_MutantVsWT.Rmd" target="_blank">c0b89ed</a></td> <td>Steve Ped</td> <td>2020-03-05</td> <td>Reran after changing to cpmPotNorm instead of the incorrect fit\)fitted.values
html 7e59d3c Steve Ped 2020-02-20 Recompiled
Rmd 4ede752 Steve Ped 2020-02-20 Added headings
html 0168824 Steve Ped 2020-02-20 Rebult after resizing
Rmd de9c4b3 Steve Ped 2020-02-20 Resized heatmaps again
html 86ffa07 Steve Ped 2020-02-20 Updated saample layout figure
Rmd 4d2af23 Steve Ped 2020-02-20 Modified heatmap sizes & initial network layout
Rmd 8fe35b0 Steve Ped 2020-02-20 Added multiple heatmaps & UpSet plots
html 679b10d Steve Ped 2020-02-19 Rendered OXPHOS Plot
Rmd 66ba4e0 Steve Ped 2020-02-19 Added OXPHOS plot
html e0288c6 Steve Ped 2020-02-19 Generated enrichment tables
Rmd 541fbf0 Steve Ped 2020-02-19 Revised Hom Vs Het Enrichment
Rmd 77f167d Steve Ped 2020-02-19 Revised enrichment
html 876e40f Steve Ped 2020-02-17 Compiled after minor corrections
Rmd 53ed0e3 Steve Ped 2020-02-17 Corrected Ensembl Release
Rmd f55be85 Steve Ped 2020-02-17 Added commas
Rmd 8f29458 Steve Ped 2020-02-17 Minor tweaks to formatting
html 9104ecd Steve Ped 2020-01-28 First draft of Hom Vs Het
Rmd 207cdc8 Steve Ped 2020-01-28 Added code for Hom Vs Het Enrichment
Rmd 468e6e3 Steve Ped 2020-01-28 Ran enrichment of Mut Vs WT
html 468e6e3 Steve Ped 2020-01-28 Ran enrichment of Mut Vs WT
Rmd 3a9933c Steve Ped 2020-01-28 Finished Enrichment analysis on MutVsWt
html 3a9933c Steve Ped 2020-01-28 Finished Enrichment analysis on MutVsWt

Setup

library(tidyverse)
library(magrittr)
library(edgeR)
library(scales)
library(pander)
library(goseq)
library(msigdbr)
library(AnnotationDbi)
library(RColorBrewer)
library(ngsReports)
library(UpSetR)
library(pheatmap)
theme_set(theme_bw())
panderOptions("table.split.table", Inf)
panderOptions("table.style", "rmarkdown")
panderOptions("big.mark", ",")
samples <- read_csv("data/samples.csv") %>%
  distinct(sampleName, .keep_all = TRUE) %>%
  dplyr::select(sample = sampleName, sampleID, genotype) %>%
  mutate(
    genotype = factor(genotype, levels = c("WT", "Het", "Hom")),
    mutant = genotype %in% c("Het", "Hom"),
    homozygous = genotype == "Hom"
  )
genoCols <- samples$genotype %>%
  levels() %>%
  length() %>%
  brewer.pal("Set1") %>%
  setNames(levels(samples$genotype))
dgeList <- here::here("data/dgeList.rds") %>% read_rds()
cpmPostNorm <- here::here("data/cpmPostNorm.rds") %>% read_rds()
entrezGenes <- dgeList$genes %>%
  dplyr::filter(!is.na(entrezid)) %>%
  unnest(entrezid) %>%
  dplyr::rename(entrez_gene = entrezid)
deTable <- here::here("output", "psen2VsWT.csv") %>% 
  read_csv() %>%
  mutate(
    entrezid = dgeList$genes$entrezid[gene_id]
  )
formatP <- function(p, m = 0.0001){
  out <- rep("", length(p))
  out[p < m] <- sprintf("%.2e", p[p<m])
  out[p >= m] <- sprintf("%.4f", p[p>=m])
  out
}

Introduction

Enrichment analysis for this dataset present some challenges. Despite normalisation to account for gene length and GC bias, some appeared to still be present in the final results. In addition, the confounding of incomplete rRNA removal with genotype may lead to other distortions in both DE genes and ranking statistics.

Two steps for enrichment analysis will be undertaken.

  1. Testing for enrichment within discrete sets of DE genes as defined in the previous steps
  2. Testing for enrichment using the complete set of results using fry.

Testing for enrichment within discrete gene sets will be performed using goseq as this allows for the incorporation of a single covariate as a predictor of differential expression. GC content, gene length and correlation with rRNA removal can all be supplied as separate covariates.

For enrichment within larger gene lists, fry can take into account inter-gene correlations. Values supplied will be logCPM for each gene/sample after being adjusted for GC and length biases.

Databases used for testing

Data was sourced using the msigdbr package. The initial database used for testing was the Hallmark Gene Sets, with mappings from gene-set to EntrezGene IDs performed by the package authors.

Hallmark Gene Sets

hm <- msigdbr("Danio rerio", category = "H")  %>% 
  left_join(entrezGenes) %>%
  dplyr::filter(!is.na(gene_id)) %>%
  distinct(gs_name, gene_id, .keep_all = TRUE)
hmByGene <- hm %>%
  split(f = .$gene_id) %>%
  lapply(extract2, "gs_name")
hmByID <- hm %>%
  split(f = .$gs_name) %>%
  lapply(extract2, "gene_id")

Mappings are required from gene to pathway, and Ensembl identifiers were used to map from gene to pathway, based on the mappings in the previously used annotations (Ensembl Release 98). A total of 3,459 Ensembl IDs were mapped to pathways from the hallmark gene sets.

KEGG Gene Sets

kg <- msigdbr("Danio rerio", category = "C2", subcategory = "CP:KEGG")  %>% 
  left_join(entrezGenes) %>%
  dplyr::filter(!is.na(gene_id)) %>%
  distinct(gs_name, gene_id, .keep_all = TRUE)
kgByGene <- kg  %>%
  split(f = .$gene_id) %>%
  lapply(extract2, "gs_name")
kgByID <- kg  %>%
  split(f = .$gs_name) %>%
  lapply(extract2, "gene_id")

The same mapping process was applied to KEGG gene sets. A total of 3,614 Ensembl IDs were mapped to pathways from the KEGG gene sets.

Gene Ontology Gene Sets

goSummaries <- url("https://uofabioinformaticshub.github.io/summaries2GO/data/goSummaries.RDS") %>%
  readRDS() %>%
  mutate(
    Term = Term(id),
    gs_name = Term %>% str_to_upper() %>% str_replace_all("[ -]", "_"),
    gs_name = paste0("GO_", gs_name)
    )
minPath <- 3
go <- msigdbr("Danio rerio", category = "C5") %>% 
  left_join(entrezGenes) %>%
  dplyr::filter(!is.na(gene_id)) %>%
  left_join(goSummaries) %>% 
  dplyr::filter(shortest_path >= minPath) %>%
  distinct(gs_name, gene_id, .keep_all = TRUE)
goByGene <- go %>%
  split(f = .$gene_id) %>%
  lapply(extract2, "gs_name")
goByID <- go %>%
  split(f = .$gs_name) %>%
  lapply(extract2, "gene_id")

For analysis of gene-sets from the GO database, gene-sets were restricted to those with 3 or more steps back to the ontology root terms. A total of 11,245 Ensembl IDs were mapped to pathways from restricted database of 8,834 GO gene sets.

gsSizes <- bind_rows(hm, kg, go) %>% 
  dplyr::select(gs_name, gene_symbol, gene_id) %>% 
  chop(c(gene_symbol, gene_id)) %>%
  mutate(
    gs_size = vapply(gene_symbol, length, integer(1)),
    de_id = lapply(
      X = gene_id, 
      FUN = intersect, 
      y = dplyr::filter(deTable, DE)$gene_id
      ),
    de_size = vapply(de_id, length, integer(1))
  )

Enrichment in the DE Gene Set

The first step of analysis using goseq, regardless of the gene-set, is estimation of the probability weight function (PWF) which quantifies the probability of a gene being considered as DE based on a single covariate. As GC content and length should have been accounted for during conditional-quantile normalisation, these were not required for any bias. However, the gene-level correlations with rRNA contamination were instead used a predictor of bias in selection of a gene as being DE.

rawFqc <- list.files(
  path = here::here("data/0_rawData/FastQC/"),
  pattern = "zip",
  full.names = TRUE
) %>%
  FastqcDataList()
gc <- getModule(rawFqc, "Per_sequence_GC") %>%
  group_by(Filename) %>% 
  mutate(Freq = Count / sum(Count)) %>%
  ungroup()
gcDev <- gc %>%
  left_join(getGC(gcTheoretical, "Drerio", "Trans")) %>%
  mutate(
    sample = str_remove(Filename, "_R[12].fastq.gz"),
    resid = Freq - Drerio
  ) %>% 
  left_join(samples) %>%
  group_by(sample) %>%
  summarise(
    ss = sum(resid^2),
    n = n(),
    sd = sqrt(ss / (n - 1))
  )
riboVec <- structure(gcDev$sd, names = gcDev$sample)
riboCors <- cpm(dgeList, log = TRUE) %>%
  apply(1, function(x){
    cor(x, riboVec[names(x)])
  })

Values were calculated as per the previous steps, using the logCPM values for each gene, with the sample-level standard deviations from the theoretical GC distribution being used as a measure of rRNA contamination. For estimation of the probability weight function, squared correlations were used to place negative and positive correlations on the same scale. This accounts for genes which are both negatively & positively biased by the presence of excessive rRNA. Clearly, the confounding of genotype with rRNA means that some genes driven by the genuine biology may be down-weighted under this approach.

riboPwf <- deTable %>%
  mutate(riboCors = riboCors[gene_id]^2) %>%
  dplyr::select(gene_id, DE, riboCors) %>%
  distinct(gene_id, .keep_all = TRUE) %>% 
  with(
    nullp(
      DEgenes = structure(
        as.integer(DE), names = gene_id
      ), 
      genome = "danRer10", 
      id = "ensGene", 
      bias.data = riboCors,
      plot.fit = FALSE
    )
  )
plotPWF(riboPwf, main = "Bias from rRNA proportions")
*Using this approach, it was clear that correlation with rRNA proportions significantly biased the probability of a gene being considered as DE.*

Using this approach, it was clear that correlation with rRNA proportions significantly biased the probability of a gene being considered as DE.

Version Author Date
468e6e3 Steve Ped 2020-01-28

All gene-sets were then tested using this PWF.

Hallmark Gene Sets

hmRiboGoseq <- goseq(riboPwf, gene2cat = hmByGene) %>%
  as_tibble %>%
  dplyr::filter(numDEInCat > 0) %>%
  mutate( 
    adjP = p.adjust(over_represented_pvalue, method = "bonf"),
    FDR = p.adjust(over_represented_pvalue, method = "fdr")
  ) %>%
  dplyr::select(-contains("under")) %>%
  dplyr::rename(
    gs_name = category,
    PValue = over_represented_pvalue
  )

No gene-sets achieved significance in the DE genes with the lowest FDR being 41%

KEGG Gene Sets

kgRiboGoseq <- goseq(riboPwf, gene2cat = kgByGene) %>%
  as_tibble %>%
  dplyr::filter(numDEInCat > 0) %>%
  mutate( 
    adjP = p.adjust(over_represented_pvalue, method = "bonf"),
    FDR = p.adjust(over_represented_pvalue, method = "fdr")
  ) %>%
  dplyr::select(-contains("under"))  %>%
  dplyr::rename(
    gs_name = category,
    PValue = over_represented_pvalue
  )
kgRiboGoseq %>%
  dplyr::slice(1:5) %>%
  mutate(
    p = formatP(PValue),
    adjP = formatP(adjP),
    FDR = formatP(FDR)
  ) %>%
  dplyr::select(
    `Gene Set` = gs_name,
    DE = numDEInCat,
    `Set Size` = numInCat,
    PValue,
    `p~bonf~` = adjP,
    `p~FDR~` = FDR
  ) %>%
  pander(
    justify = "lrrrrr",
    caption = paste(
      "The", nrow(.), "most highly-ranked KEGG pathways.",
      "Bonferroni-adjusted p-values are the most stringent and give high",
      "confidence when below 0.05."
    )
  )
The 5 most highly-ranked KEGG pathways. Bonferroni-adjusted p-values are the most stringent and give high confidence when below 0.05.
Gene Set DE Set Size PValue pbonf pFDR
KEGG_RIBOSOME 26 80 4.754e-09 5.32e-07 5.32e-07
KEGG_PRIMARY_IMMUNODEFICIENCY 2 15 0.01642 1.0000 0.7173
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 4 26 0.02959 1.0000 0.7173
KEGG_ASTHMA 1 3 0.04088 1.0000 0.7173
KEGG_RETINOL_METABOLISM 3 25 0.0512 1.0000 0.7173

Notably, the KEGG gene-set for Ribosomal genes was detected as enriched in the set of DE genes, with no other KEGG gene-sets being considered significant.

GO Gene Sets

goRiboGoseq <- goseq(riboPwf, gene2cat = goByGene) %>%
  as_tibble %>%
  dplyr::filter(numDEInCat > 0) %>%
  mutate( 
    adjP = p.adjust(over_represented_pvalue, method = "bonf"),
    FDR = p.adjust(over_represented_pvalue, method = "fdr")
  ) %>%
  dplyr::select(-contains("under")) %>%
  dplyr::rename(
    gs_name = category,
    PValue = over_represented_pvalue
  )
goRiboGoseq %>%
  dplyr::filter(adjP < 0.05) %>%
  mutate(
    p = formatP(PValue),
    adjP = formatP(adjP),
    FDR = formatP(FDR)
  ) %>%
  dplyr::select(
    `Gene Set` = gs_name,
    DE = numDEInCat,
    `Set Size` = numInCat,
    PValue,
    `p~bonf~` = adjP,
    `p~FDR~` = FDR
  ) %>%
  pander(
    justify = "lrrrrr",
    caption = paste(
      "*The", nrow(.), "most highly-ranked GO terms.",
      "Bonferroni-adjusted p-values are the most stringent and give high",
      "confidence when below 0.05, with all terms here reaching this threshold.",
      "However, most terms once again indicate the presence of rRNA.*"
    )
  )
The 14 most highly-ranked GO terms. Bonferroni-adjusted p-values are the most stringent and give high confidence when below 0.05, with all terms here reaching this threshold. However, most terms once again indicate the presence of rRNA.
Gene Set DE Set Size PValue pbonf pFDR
GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 28 93 7.36e-10 2.83e-06 2.03e-06
GO_CYTOSOLIC_RIBOSOME 27 97 1.056e-09 4.06e-06 2.03e-06
GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM 27 105 1.6e-08 6.16e-05 2.05e-05
GO_TRANSLATIONAL_INITIATION 29 177 2.178e-07 0.0008 0.0002
GO_PROTEIN_TARGETING_TO_MEMBRANE 30 171 2.533e-07 0.0010 0.0002
GO_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM 27 128 3.849e-07 0.0015 0.0002
GO_CYTOSOLIC_PART 30 206 4.424e-07 0.0017 0.0002
GO_VIRAL_GENE_EXPRESSION 29 172 6.939e-07 0.0027 0.0003
GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS 30 183 7.911e-07 0.0030 0.0003
GO_RIBOSOMAL_SUBUNIT 28 175 1.99e-06 0.0077 0.0008
GO_RIBOSOME 30 210 2.659e-06 0.0102 0.0009
GO_CYTOSOLIC_LARGE_RIBOSOMAL_SUBUNIT 15 51 2.826e-06 0.0109 0.0009
GO_SYMPORTER_ACTIVITY 10 94 7.571e-06 0.0291 0.0022
GO_ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 17 228 1.23e-05 0.0473 0.0034

Enrichment Testing on the Complete Set of Genes

Hallmark Gene Sets

hmFry <- cpmPostNorm %>%
  fry(
    index = hmByID,
    design = dgeList$design,
    contrast = "mutant",
    sort = "directional"
    ) %>%
  rownames_to_column("gs_name") %>%
  as_tibble()
hmFry %>%
  dplyr::filter(
    PValue < 0.01
  ) %>%
  left_join(gsSizes) %>%
  mutate(gs_name = str_remove(gs_name, "HALLMARK_")) %>%
  dplyr::select(
    `Hallmark Gene Set` = gs_name,
    `Expressed Genes` = NGenes,
    `DE Genes` = de_size,
    Direction,
    PValue, FDR
    ) %>%
  pander(
    justify = "lrrlrr",
    caption = "Enriched Hallmark Gene Sets, using a threshold of p < 0.01, which corresponds to an FDR of 0.02"
  )
Enriched Hallmark Gene Sets, using a threshold of p < 0.01, which corresponds to an FDR of 0.02
Hallmark Gene Set Expressed Genes DE Genes Direction PValue FDR
UV_RESPONSE_UP 141 7 Up 4.187e-06 0.0002094
XENOBIOTIC_METABOLISM 146 11 Up 8.577e-05 0.001756
REACTIVE_OXYGEN_SPECIES_PATHWAY 45 5 Up 0.0001128 0.001756
FATTY_ACID_METABOLISM 135 6 Up 0.0001574 0.001756
MTORC1_SIGNALING 194 11 Up 0.0001756 0.001756
GLYCOLYSIS 172 8 Up 0.0002864 0.002387
PEROXISOME 95 2 Up 0.0004238 0.003027
ADIPOGENESIS 186 13 Up 0.0005475 0.003236
BILE_ACID_METABOLISM 86 1 Up 0.0006345 0.003236
PROTEIN_SECRETION 92 3 Up 0.0006473 0.003236
COAGULATION 80 3 Up 0.0008365 0.003624
UNFOLDED_PROTEIN_RESPONSE 113 4 Up 0.0008697 0.003624
CHOLESTEROL_HOMEOSTASIS 69 2 Up 0.001557 0.005666
NOTCH_SIGNALING 29 0 Up 0.001623 0.005666
ESTROGEN_RESPONSE_LATE 153 3 Up 0.0017 0.005666
MYC_TARGETS_V1 192 15 Up 0.0021 0.005993
HYPOXIA 169 9 Up 0.002131 0.005993
OXIDATIVE_PHOSPHORYLATION 201 15 Up 0.002158 0.005993
EPITHELIAL_MESENCHYMAL_TRANSITION 156 7 Up 0.003453 0.009086
TNFA_SIGNALING_VIA_NFKB 149 7 Up 0.004565 0.01141
IL2_STAT5_SIGNALING 147 2 Up 0.005095 0.01213
ANDROGEN_RESPONSE 90 2 Up 0.006364 0.01446
PI3K_AKT_MTOR_SIGNALING 98 2 Up 0.00925 0.02011

Exploration of significant Hallmark Gene Sets

hmFry %>% 
  left_join(gsSizes) %>%
  dplyr::filter(de_size >= 5, FDR < 0.05) %>%
  dplyr::select(gs_name, de_id) %>%
  unnest(de_id) %>% 
  mutate(
    gs_name = str_remove(gs_name, "HALLMARK_"),
    gs_name = fct_lump(gs_name, n = 14)
    ) %>% 
  split(f = .$gs_name) %>% 
  lapply(magrittr::extract2, "de_id") %>% 
  fromList() %>% 
  upset(
    nsets = length(.), 
    nintersects = 20,
    order.by = "freq", 
    mb.ratio = c(0.6, 0.4),
    sets.x.label = "Number Of DE Genes"
    )
*UpSet plot indicating distribution of DE genes within all significant HALLMARK gene sets. Gene sets were restricted to those with an FDR < 0.05 and at least 5 DE genes. The plot is truncated at the right for simplicity. Most gene sets seem relatively independent of each other with regard to DE genes.*

UpSet plot indicating distribution of DE genes within all significant HALLMARK gene sets. Gene sets were restricted to those with an FDR < 0.05 and at least 5 DE genes. The plot is truncated at the right for simplicity. Most gene sets seem relatively independent of each other with regard to DE genes.

Version Author Date
a5cdf5d Steve Ped 2020-03-06
hmHeat <- hmFry %>% 
  left_join(gsSizes) %>%
  dplyr::filter(de_size >= 12, FDR < 0.05) %>%
  dplyr::select(gs_name, de_id) %>%
  unnest(de_id) %>%
  left_join(dgeList$genes, by = c("de_id" = "gene_id")) %>%
  dplyr::select(gs_name, de_id, gene_name) %>%
  mutate(belongs = TRUE) %>%
  pivot_wider(
    id_cols = c(de_id, gene_name),
    names_from = gs_name,
    values_from = belongs,
    values_fill = list(belongs = FALSE)
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("de_id")
  ) 
hmHeat %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    cutree_rows = 6,
    cutree_cols = 2,
    annotation_names_row = FALSE,
    annotation_row = hmHeat %>%
      dplyr::select(gene_name, starts_with("HALLMARK_")) %>%
      mutate_at(vars(starts_with("HALL")), as.character) %>%
      as.data.frame() %>%
      column_to_rownames("gene_name") %>%
      set_colnames(
        str_remove(colnames(.), "HALLMARK_")
      )
  )
*Gene expression patterns for all DE genes in HALLMARK gene sets, containing more than 12 DE genes.*

Gene expression patterns for all DE genes in HALLMARK gene sets, containing more than 12 DE genes.

Version Author Date
a5cdf5d Steve Ped 2020-03-06
7fe1505 Steve Ped 2020-03-05
86ffa07 Steve Ped 2020-02-20

KEGG Gene Sets

kgFry <- cpmPostNorm %>%
  fry(
    index = kgByID,
    design = dgeList$design,
    contrast = "mutant",
    sort = "directional"
    ) %>%
  rownames_to_column("gs_name") %>%
  as_tibble()
kgFry %>%
  dplyr::filter(
    PValue < 0.005
  ) %>%
  left_join(gsSizes) %>%
  mutate(gs_name = str_remove(gs_name, "HALLMARK_")) %>%
  dplyr::select(
    `KEGG Gene Set` = gs_name,
    `Expressed Genes` = NGenes,
    `DE Genes` = de_size,
    Direction,
    PValue, FDR
    ) %>%
  pander(
    justify = "lrrlrr",
    caption = "Enriched KEGG Gene Sets, using a threshold p < 0.005, which corresponds to an FDR of 0.02"
  )
Enriched KEGG Gene Sets, using a threshold p < 0.005, which corresponds to an FDR of 0.02
KEGG Gene Set Expressed Genes DE Genes Direction PValue FDR
KEGG_GLUTATHIONE_METABOLISM 36 4 Up 1.313e-05 0.002442
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 24 2 Up 9.541e-05 0.005307
KEGG_ARGININE_AND_PROLINE_METABOLISM 39 2 Up 9.545e-05 0.005307
KEGG_LIMONENE_AND_PINENE_DEGRADATION 8 0 Up 0.0001542 0.005307
KEGG_PRIMARY_IMMUNODEFICIENCY 15 2 Down 0.0001638 0.005307
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM 25 0 Up 0.0002012 0.005307
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 7 0 Up 0.000218 0.005307
KEGG_BETA_ALANINE_METABOLISM 18 1 Up 0.0002525 0.005307
KEGG_GLYCEROLIPID_METABOLISM 37 1 Up 0.0002568 0.005307
KEGG_PPAR_SIGNALING_PATHWAY 53 1 Up 0.0002947 0.005397
KEGG_FATTY_ACID_METABOLISM 38 1 Up 0.0003304 0.005397
KEGG_BUTANOATE_METABOLISM 26 0 Up 0.0003879 0.005397
KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY 79 3 Down 0.0004045 0.005397
KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 37 0 Up 0.0004062 0.005397
KEGG_TYROSINE_METABOLISM 29 2 Up 0.0004776 0.005698
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 26 3 Up 0.0004901 0.005698
KEGG_DRUG_METABOLISM_CYTOCHROME_P450 26 3 Up 0.0005606 0.005827
KEGG_PYRUVATE_METABOLISM 27 1 Up 0.0006084 0.005827
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 26 4 Up 0.0006305 0.005827
KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS 21 0 Up 0.0006464 0.005827
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM 13 1 Up 0.0006579 0.005827
KEGG_SELENOAMINO_ACID_METABOLISM 22 0 Up 0.0007171 0.005874
KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION 60 0 Up 0.0007358 0.005874
KEGG_VIBRIO_CHOLERAE_INFECTION 47 1 Up 0.000758 0.005874
KEGG_LYSINE_DEGRADATION 39 0 Up 0.0009213 0.006855
KEGG_PHENYLALANINE_METABOLISM 11 1 Up 0.0009648 0.006866
KEGG_RENIN_ANGIOTENSIN_SYSTEM 8 1 Up 0.001033 0.006866
KEGG_NITROGEN_METABOLISM 13 1 Up 0.001034 0.006866
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 27 1 Up 0.00112 0.007181
KEGG_RIBOSOME 80 26 Up 0.001277 0.007917
KEGG_PEROXISOME 70 0 Up 0.00135 0.008102
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 10 0 Up 0.00144 0.008369
KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION 44 3 Up 0.001755 0.009894
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 40 0 Up 0.001835 0.01004
KEGG_RETINOL_METABOLISM 25 3 Up 0.001902 0.01011
KEGG_PURINE_METABOLISM 135 4 Up 0.001958 0.01011
KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 87 1 Up 0.002044 0.01018
KEGG_ALZHEIMERS_DISEASE 141 12 Up 0.002128 0.01018
KEGG_CITRATE_CYCLE_TCA_CYCLE 26 2 Up 0.002141 0.01018
KEGG_N_GLYCAN_BIOSYNTHESIS 45 1 Up 0.00219 0.01018
KEGG_OXIDATIVE_PHOSPHORYLATION 119 14 Up 0.002373 0.01065
KEGG_PROPANOATE_METABOLISM 28 1 Up 0.002406 0.01065
KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION 15 0 Up 0.002581 0.01116
KEGG_PROTEASOME 42 2 Up 0.00284 0.01187
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 39 3 Up 0.002871 0.01187
KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY 64 3 Down 0.003085 0.01247
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM 56 1 Up 0.004306 0.01704
KEGG_ABC_TRANSPORTERS 32 0 Up 0.004993 0.01935

Exploration of Significant KEGG Gene Sets

kgFry %>% 
  left_join(gsSizes) %>%
  dplyr::filter(de_size >= 4, FDR < 0.05) %>%
  dplyr::select(gs_name, de_id) %>%
  unnest(de_id) %>% 
  mutate(
    gs_name = str_remove(gs_name, "KEGG_"),
    gs_name = fct_lump(gs_name, n = 14)
    ) %>% 
  split(f = .$gs_name) %>% 
  lapply(magrittr::extract2, "de_id") %>% 
  fromList() %>% 
  upset(
    nsets = length(.), 
    nintersects = 20,
    order.by = "freq", 
    mb.ratio = c(0.6, 0.4),
    sets.x.label = "Number Of DE Genes"
    )
*UpSet plot indicating distribution of DE genes within all significant terms from the KEGG gene sets. Gene sets were restricted to those with an FDR < 0.05 and four or more DE genes. There is considerable overlap between DE genes in Oxidative Phosphorylation and both Parkinson's and Huntington's Disease, indicating that these terms essentially capture the same expression signal within this dataset.*

UpSet plot indicating distribution of DE genes within all significant terms from the KEGG gene sets. Gene sets were restricted to those with an FDR < 0.05 and four or more DE genes. There is considerable overlap between DE genes in Oxidative Phosphorylation and both Parkinson’s and Huntington’s Disease, indicating that these terms essentially capture the same expression signal within this dataset.

Version Author Date
a5cdf5d Steve Ped 2020-03-06
riboOx <- kg %>%
  dplyr::filter(
    grepl("OXIDATIVE_PHOS", gs_name) | grepl("RIBOSOME", gs_name),
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
    ) %>%
  mutate(gs_name = str_remove(gs_name, "(KEGG|HALLMARK)_")) %>%
  distinct(gs_name, gene_id) %>%
  left_join(
    cpmPostNorm %>% 
      as.data.frame() %>% 
      rownames_to_column("gene_id") %>%
      as_tibble()
    ) %>%
  pivot_longer(cols = starts_with("Ps"), names_to = "sample", values_to = "CPM") %>%
  left_join(dgeList$samples) %>% 
  left_join(dgeList$genes) %>%
  dplyr::select(gs_name, gene_name, sampleID, genotype, CPM) %>%
  pivot_wider(
    id_cols = c(gs_name, gene_name),
    values_from = CPM,
    names_from = sampleID
  ) 
riboOx %>% 
  dplyr::select(-gs_name) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    annotation_row = data.frame(
      GeneSet = riboOx$gs_name %>% str_replace("OXI.+", "OXPHOS"), 
      row.names = riboOx$gene_name
      ),
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    annotation_names_row = FALSE,
    cutree_rows = 3,
    cutree_cols = 2
  )
*Given that the largest gene sets within the KEGG results were Oxidative Phosphorylation and Ribosomal gene sets, all DE genes associated with these KEGG terms are displayed. All genes appear to show increased expression in mutant samples.*

Given that the largest gene sets within the KEGG results were Oxidative Phosphorylation and Ribosomal gene sets, all DE genes associated with these KEGG terms are displayed. All genes appear to show increased expression in mutant samples.

Version Author Date
7fe1505 Steve Ped 2020-03-05
86ffa07 Steve Ped 2020-02-20

GO Gene Sets

goFry <- cpmPostNorm %>%
  fry(
    index = goByID,
    design = dgeList$design,
    contrast = "mutant",
    sort = "directional"
    ) %>%
  rownames_to_column("gs_name") %>%
  as_tibble()
goFry %>%
  left_join(gsSizes) %>%
  left_join(distinct(go, gs_name, shortest_path)) %>%
  dplyr::filter(
    FDR < 0.01, 
    shortest_path > 3, 
    NGenes < 1000,
    de_size >= 5
  ) %>%
  dplyr::select(
    `GO Gene Set` = gs_name,
    `Expressed Genes` = NGenes,
    `DE Genes` = de_size,
    Direction,
    PValue, FDR
    ) %>%
  pander(
    justify = "lrrlrr",
    caption = "Enriched GO Gene Sets, using the thresholds FDR < 0.01, at least 5 DE genes, a set size < 1000 and more than 3 steps back to the ontology root."
  )
Enriched GO Gene Sets, using the thresholds FDR < 0.01, at least 5 DE genes, a set size < 1000 and more than 3 steps back to the ontology root.
GO Gene Set Expressed Genes DE Genes Direction PValue FDR
GO_PEPTIDYL_LYSINE_TRIMETHYLATION 42 5 Down 6.682e-06 0.001904
GO_FATTY_ACID_BIOSYNTHETIC_PROCESS 96 6 Up 9.201e-06 0.002258
GO_ORGANIC_ACID_TRANSPORT 240 14 Up 3.617e-05 0.003991
GO_ORGANIC_ACID_BIOSYNTHETIC_PROCESS 198 12 Up 4.586e-05 0.004057
GO_PEPTIDYL_LYSINE_METHYLATION 111 5 Down 4.848e-05 0.004057
GO_RESPONSE_TO_CORTICOSTEROID 121 5 Up 4.854e-05 0.004057
GO_PEPTIDYL_LYSINE_ACETYLATION 144 5 Down 6.245e-05 0.004211
GO_MONOCARBOXYLIC_ACID_BIOSYNTHETIC_PROCESS 127 7 Up 7.071e-05 0.004534
GO_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS 138 6 Up 7.186e-05 0.004534
GO_RESPONSE_TO_ALCOHOL 177 7 Up 7.293e-05 0.004534
GO_HISTONE_METHYLATION 118 5 Down 7.92e-05 0.004536
GO_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS 315 10 Up 9.221e-05 0.004724
GO_NUCLEAR_BODY 649 21 Down 0.0001011 0.004828
GO_MONOCARBOXYLIC_ACID_TRANSPORT 110 6 Up 0.0001017 0.004829
GO_CARBOHYDRATE_BIOSYNTHETIC_PROCESS 148 6 Up 0.0001221 0.005132
GO_SYMPORTER_ACTIVITY 94 10 Up 0.0001224 0.005132
GO_LIPID_BIOSYNTHETIC_PROCESS 508 13 Up 0.0001267 0.005207
GO_DRUG_TRANSPORT 152 8 Up 0.0001461 0.005379
GO_AMINO_ACID_TRANSMEMBRANE_TRANSPORT 69 5 Up 0.0001709 0.005806
GO_ORGANIC_ACID_TRANSMEMBRANE_TRANSPORT 106 9 Up 0.0001766 0.005887
GO_ORGANIC_ANION_TRANSPORT 345 16 Up 0.0001785 0.005928
GO_SECONDARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 154 13 Up 0.0001819 0.005967
GO_COENZYME_METABOLIC_PROCESS 195 5 Up 0.000182 0.005967
GO_ANION_TRANSMEMBRANE_TRANSPORT 203 15 Up 0.0001854 0.005999
GO_ANION_TRANSPORT 434 22 Up 0.0001883 0.006049
GO_SEQUENCE_SPECIFIC_DNA_BINDING 827 29 Down 0.0001932 0.006093
GO_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II 903 31 Down 0.000212 0.006139
GO_REGULATORY_REGION_NUCLEIC_ACID_BINDING 720 24 Down 0.0002154 0.006157
GO_PROTEIN_LOCALIZATION_TO_MEMBRANE 539 35 Up 0.0002254 0.006217
GO_PROTEIN_METHYLATION 153 8 Down 0.0002353 0.006313
GO_REGULATION_OF_PHOSPHATASE_ACTIVITY 149 8 Down 0.0002413 0.006313
GO_ACTIVATING_TRANSCRIPTION_FACTOR_BINDING 70 5 Down 0.0002415 0.006313
GO_ORGANIC_ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 144 11 Up 0.000253 0.006397
GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE 287 30 Up 0.0002603 0.006429
GO_PROTEIN_ACETYLATION 168 5 Down 0.0002605 0.006429
GO_ISOPRENOID_METABOLIC_PROCESS 68 5 Up 0.0002633 0.006433
GO_PROTEIN_MATURATION 210 8 Up 0.0002641 0.006433
GO_DRUG_TRANSMEMBRANE_TRANSPORT 65 6 Up 0.0002665 0.006433
GO_REGULATION_OF_PEPTIDE_HORMONE_SECRETION 157 9 Up 0.0002996 0.00691
GO_ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 228 17 Up 0.0003288 0.007143
GO_NUCLEAR_SPECK 346 11 Down 0.0003295 0.007143
GO_PROXIMAL_PROMOTER_SEQUENCE_SPECIFIC_DNA_BINDING 413 15 Down 0.0003484 0.007241
GO_REGULATION_OF_DEPHOSPHORYLATION 180 8 Down 0.0003661 0.007384
GO_COVALENT_CHROMATIN_MODIFICATION 384 13 Down 0.0003797 0.007483
GO_REGULATION_OF_CHROMATIN_ORGANIZATION 158 7 Down 0.0003848 0.007483
GO_REGULATION_OF_INSULIN_SECRETION 140 9 Up 0.0004112 0.007729
GO_ROUGH_ENDOPLASMIC_RETICULUM 67 6 Up 0.0004221 0.00781
GO_AMINO_ACID_TRANSPORT 119 6 Up 0.0004254 0.00781
GO_SEQUENCE_SPECIFIC_DOUBLE_STRANDED_DNA_BINDING 668 23 Down 0.0004287 0.007824
GO_DOUBLE_STRANDED_DNA_BINDING 740 30 Down 0.0004372 0.007859
GO_REGULATION_OF_MRNA_PROCESSING 117 5 Down 0.0004506 0.00795
GO_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS 227 10 Up 0.0004663 0.008076
GO_NUCLEOPLASM_PART 943 31 Down 0.0004697 0.008088
GO_SECRETORY_VESICLE 713 24 Up 0.0004815 0.008218
GO_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 60 5 Up 0.000498 0.008306
GO_PURINE_CONTAINING_COMPOUND_BIOSYNTHETIC_PROCESS 170 6 Up 0.0004995 0.008306
GO_LIPID_CATABOLIC_PROCESS 221 7 Up 0.0005363 0.008614
GO_INORGANIC_ANION_TRANSPORT 117 7 Up 0.0005584 0.008701
GO_MONOVALENT_INORGANIC_CATION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 268 13 Up 0.0005832 0.00893
GO_PEPTIDE_HORMONE_SECRETION 194 9 Up 0.0005972 0.009027
GO_ALPHA_AMINO_ACID_METABOLIC_PROCESS 126 6 Up 0.0006074 0.009142
GO_ORGANIC_ACID_CATABOLIC_PROCESS 184 5 Up 0.0006398 0.009283
GO_IMPORT_INTO_CELL 532 7 Up 0.0006709 0.009508
GO_RIBOSE_PHOSPHATE_BIOSYNTHETIC_PROCESS 165 7 Up 0.0006731 0.009508
GO_TUBULIN_BINDING 258 5 Down 0.0006736 0.009508
GO_CATION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 458 18 Up 0.0006766 0.009508
GO_MRNA_METABOLIC_PROCESS 453 26 Down 0.0006959 0.009529
GO_GUANYL_NUCLEOTIDE_BINDING 317 6 Up 0.0007188 0.009678
GO_ORGANIC_HYDROXY_COMPOUND_BIOSYNTHETIC_PROCESS 183 8 Up 0.000736 0.00984

Exploration of Significant GO Gene Sets

goFry %>% 
  left_join(gsSizes) %>%
  left_join(distinct(go, gs_name, shortest_path)) %>%
  mutate(
    propDE = de_size / gs_size
  ) %>%
  dplyr::filter(
    de_size >= 15, 
    propDE > 0.05,
    FDR < 0.02,
    shortest_path > 3
  ) %>%
  dplyr::select(gs_name, de_id) %>%
  unnest(de_id) %>% 
  mutate(
    gs_name = str_remove(gs_name, "GO_"),
    gs_name = fct_lump(gs_name, n = 20)
    ) %>% 
  split(f = .$gs_name) %>% 
  lapply(magrittr::extract2, "de_id") %>% 
  fromList() %>% 
  upset(
    nsets = length(.), 
    nintersects = 20,
    order.by = "freq", 
    mb.ratio = c(0.6, 0.4),
    sets.x.label = "Number Of DE Genes"
    )
*UpSet plot indicating distribution of DE genes within significantly enriched terms from the GO gene sets. For this visualisation, GO terms were restricted to those with 15 or more DE genes, where this represented more than 5% of a gene set as being DE, along with an FDR < 0.02 and more than 3 steps back to the ontology root. The 20 largest GO terms satisfying these criteria are shown. The plot is  truncated at the right hand side for simplicity. A group of 28 genes is uniquely attributed to the Mitochondrial Envelope, with a further 18 being relatively unique to mRNA Metabolic Process. The next grouping of 15 genes are unique to Regulation Of Nucleobase-Containing Compound Metabolic Process followed by 25 genes, spread across two clusters of terms which largely represent Ribosomal activity. In between these are 13 genes uniquely associated with Anion Transport.*

UpSet plot indicating distribution of DE genes within significantly enriched terms from the GO gene sets. For this visualisation, GO terms were restricted to those with 15 or more DE genes, where this represented more than 5% of a gene set as being DE, along with an FDR < 0.02 and more than 3 steps back to the ontology root. The 20 largest GO terms satisfying these criteria are shown. The plot is truncated at the right hand side for simplicity. A group of 28 genes is uniquely attributed to the Mitochondrial Envelope, with a further 18 being relatively unique to mRNA Metabolic Process. The next grouping of 15 genes are unique to Regulation Of Nucleobase-Containing Compound Metabolic Process followed by 25 genes, spread across two clusters of terms which largely represent Ribosomal activity. In between these are 13 genes uniquely associated with Anion Transport.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Genes Associated with the Mitochondrial Envelope

go %>%
  dplyr::filter(
    gs_name == "GO_MITOCHONDRIAL_ENVELOPE",
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
  ) %>%
  dplyr::select(
    gene_id, gene_name
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("gene_id")
  ) %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    annotation_col = dgeList$samples %>%
      dplyr::select(Genotype = genotype),
    cutree_rows = 4,
    cutree_cols = 2
  )
*All DE genes associated with the GO term 'Mitochondrial Envelope'.*

All DE genes associated with the GO term ‘Mitochondrial Envelope’.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Genes Associated with RNA Metabolic Process

go %>%
  dplyr::filter(
    gs_name == "GO_MRNA_METABOLIC_PROCESS",
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
  ) %>%
  dplyr::select(
    gene_id, gene_name
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("gene_id")
  ) %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    annotation_col = dgeList$samples %>%
      dplyr::select(Genotype = genotype),
    cutree_rows = 4,
    cutree_cols = 2
  )
*All DE genes associated with the GO term 'mRNA Metabolic Process'.*

All DE genes associated with the GO term ‘mRNA Metabolic Process’.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Genes Associated with Regulation Of Nucleobase-Containing Compound Metabolic Process

go %>%
  dplyr::filter(
    gs_name == "GO_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS",
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
  ) %>%
  dplyr::select(
    gene_id, gene_name
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("gene_id")
  ) %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    annotation_col = dgeList$samples %>%
      dplyr::select(Genotype = genotype),
    cutree_rows = 4,
    cutree_cols = 2
  )
*All DE genes associated with the GO term 'mRNA Metabolic Process'.*

All DE genes associated with the GO term ‘mRNA Metabolic Process’.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Genes Associated with Anion Transport

go %>%
  dplyr::filter(
    gs_name == "GO_ANION_TRANSPORT",
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
  ) %>%
  dplyr::select(
    gene_id, gene_name
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("gene_id")
  ) %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    annotation_col = dgeList$samples %>%
      dplyr::select(Genotype = genotype),
    cutree_rows = 3,
    cutree_cols = 2
  )
*All DE genes associated with the GO term 'Anion Transport'.*

All DE genes associated with the GO term ‘Anion Transport’.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Genes Associated with Ribosomal Activity

go %>%
  dplyr::filter(
    gs_name == "GO_CYTOSOLIC_RIBOSOME",
    gene_id %in% dplyr::filter(deTable, DE)$gene_id
  ) %>%
  dplyr::select(
    gene_id, gene_name
  ) %>%
  left_join(
    cpmPostNorm %>%
      as.data.frame() %>%
      rownames_to_column("gene_id")
  ) %>%
  dplyr::select(gene_name, starts_with("Ps")) %>%
  as.data.frame() %>%
  column_to_rownames("gene_name") %>%
  as.matrix() %>%
  pheatmap(
    color = viridis_pal(option = "magma")(100),
    legend_breaks = c(seq(-2, 8, by = 2), max(.)),
    legend_labels = c(seq(-2, 8, by = 2), "logCPM\n"),
    labels_col = hmHeat %>%
      dplyr::select(starts_with("Ps")) %>% 
      colnames() %>% 
      enframe(name = NULL) %>% 
      dplyr::rename(sample = value) %>%
      left_join(dgeList$samples) %>%
      dplyr::select(sample, sampleID) %>%
      with(
        structure(sampleID, names = sample)
      ),
    annotation_col = dgeList$samples %>%
      dplyr::select(Genotype = genotype),
    cutree_rows = 3,
    cutree_cols = 2
  )
*All DE genes associated with the GO term 'Cytosolic Ribosome'.*

All DE genes associated with the GO term ‘Cytosolic Ribosome’.

Version Author Date
a5cdf5d Steve Ped 2020-03-06

Data Export

All enriched gene sets with an FDR adjusted p-value < 0.05 were exported as a single csv file.

bind_rows(
  hmFry,
  kgFry,
  goFry
) %>%
  dplyr::filter(FDR < 0.05) %>%
  left_join(gsSizes) %>%
  dplyr::select(
    gs_name, NGenes, Direction, PValue, FDR,
    gene_symbol, de_size
  ) %>%
  mutate(
    DE = lapply(
      X = gene_symbol,
      FUN =  intersect, 
      y = dplyr::filter(deTable, DE)$gene_name
    ),
    DE = vapply(DE, paste, character(1), collapse = ";")
  ) %>%
  dplyr::select(
    `Gene Set` = gs_name, 
    `Nbr Detected Genes` = NGenes, 
    `Nbr DE Genes` = de_size, 
    Direction, PValue, FDR, 
    `DE Genes` = DE
  ) %>%
  write_csv(
    here::here("output", "Enrichment_Mutant_V_WT.csv")
  )

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       Ubuntu 18.04.4 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language en_AU:en                    
 collate  en_AU.UTF-8                 
 ctype    en_AU.UTF-8                 
 tz       Australia/Melbourne         
 date     2020-03-07                  

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version  date       lib source        
 AnnotationDbi        * 1.48.0   2019-10-29 [2] Bioconductor  
 askpass                1.1      2019-01-13 [2] CRAN (R 3.6.0)
 assertthat             0.2.1    2019-03-21 [2] CRAN (R 3.6.0)
 backports              1.1.5    2019-10-02 [2] CRAN (R 3.6.1)
 BiasedUrn            * 1.07     2015-12-28 [2] CRAN (R 3.6.1)
 Biobase              * 2.46.0   2019-10-29 [2] Bioconductor  
 BiocFileCache          1.10.2   2019-11-08 [2] Bioconductor  
 BiocGenerics         * 0.32.0   2019-10-29 [2] Bioconductor  
 BiocParallel           1.20.1   2019-12-21 [2] Bioconductor  
 biomaRt                2.42.0   2019-10-29 [2] Bioconductor  
 Biostrings             2.54.0   2019-10-29 [2] Bioconductor  
 bit                    1.1-15.2 2020-02-10 [2] CRAN (R 3.6.2)
 bit64                  0.9-7    2017-05-08 [2] CRAN (R 3.6.0)
 bitops                 1.0-6    2013-08-17 [2] CRAN (R 3.6.0)
 blob                   1.2.1    2020-01-20 [2] CRAN (R 3.6.2)
 broom                  0.5.4    2020-01-27 [2] CRAN (R 3.6.2)
 callr                  3.4.2    2020-02-12 [2] CRAN (R 3.6.2)
 cellranger             1.1.0    2016-07-27 [2] CRAN (R 3.6.0)
 cli                    2.0.1    2020-01-08 [2] CRAN (R 3.6.2)
 cluster                2.1.0    2019-06-19 [2] CRAN (R 3.6.1)
 colorspace             1.4-1    2019-03-18 [2] CRAN (R 3.6.0)
 crayon                 1.3.4    2017-09-16 [2] CRAN (R 3.6.0)
 curl                   4.3      2019-12-02 [2] CRAN (R 3.6.2)
 data.table             1.12.8   2019-12-09 [2] CRAN (R 3.6.2)
 DBI                    1.1.0    2019-12-15 [2] CRAN (R 3.6.2)
 dbplyr                 1.4.2    2019-06-17 [2] CRAN (R 3.6.0)
 DelayedArray           0.12.2   2020-01-06 [2] Bioconductor  
 desc                   1.2.0    2018-05-01 [2] CRAN (R 3.6.0)
 devtools               2.2.2    2020-02-17 [2] CRAN (R 3.6.2)
 digest                 0.6.25   2020-02-23 [2] CRAN (R 3.6.2)
 dplyr                * 0.8.4    2020-01-31 [2] CRAN (R 3.6.2)
 edgeR                * 3.28.1   2020-02-26 [2] Bioconductor  
 ellipsis               0.3.0    2019-09-20 [2] CRAN (R 3.6.1)
 evaluate               0.14     2019-05-28 [2] CRAN (R 3.6.0)
 FactoMineR             2.2      2020-02-05 [2] CRAN (R 3.6.2)
 fansi                  0.4.1    2020-01-08 [2] CRAN (R 3.6.2)
 farver                 2.0.3    2020-01-16 [2] CRAN (R 3.6.2)
 flashClust             1.01-2   2012-08-21 [2] CRAN (R 3.6.1)
 forcats              * 0.4.0    2019-02-17 [2] CRAN (R 3.6.0)
 fs                     1.3.1    2019-05-06 [2] CRAN (R 3.6.0)
 geneLenDataBase      * 1.22.0   2019-11-05 [2] Bioconductor  
 generics               0.0.2    2018-11-29 [2] CRAN (R 3.6.0)
 GenomeInfoDb           1.22.0   2019-10-29 [2] Bioconductor  
 GenomeInfoDbData       1.2.2    2019-11-21 [2] Bioconductor  
 GenomicAlignments      1.22.1   2019-11-12 [2] Bioconductor  
 GenomicFeatures        1.38.2   2020-02-15 [2] Bioconductor  
 GenomicRanges          1.38.0   2019-10-29 [2] Bioconductor  
 ggdendro               0.1-20   2016-04-27 [2] CRAN (R 3.6.0)
 ggplot2              * 3.2.1    2019-08-10 [2] CRAN (R 3.6.1)
 ggrepel                0.8.1    2019-05-07 [2] CRAN (R 3.6.0)
 git2r                  0.26.1   2019-06-29 [2] CRAN (R 3.6.1)
 glue                   1.3.1    2019-03-12 [2] CRAN (R 3.6.0)
 GO.db                  3.10.0   2019-11-21 [2] Bioconductor  
 goseq                * 1.38.0   2019-10-29 [2] Bioconductor  
 gridExtra              2.3      2017-09-09 [2] CRAN (R 3.6.0)
 gtable                 0.3.0    2019-03-25 [2] CRAN (R 3.6.0)
 haven                  2.2.0    2019-11-08 [2] CRAN (R 3.6.1)
 here                   0.1      2017-05-28 [2] CRAN (R 3.6.0)
 highr                  0.8      2019-03-20 [2] CRAN (R 3.6.0)
 hms                    0.5.3    2020-01-08 [2] CRAN (R 3.6.2)
 htmltools              0.4.0    2019-10-04 [2] CRAN (R 3.6.1)
 htmlwidgets            1.5.1    2019-10-08 [2] CRAN (R 3.6.1)
 httpuv                 1.5.2    2019-09-11 [2] CRAN (R 3.6.1)
 httr                   1.4.1    2019-08-05 [2] CRAN (R 3.6.1)
 hwriter                1.3.2    2014-09-10 [2] CRAN (R 3.6.0)
 IRanges              * 2.20.2   2020-01-13 [2] Bioconductor  
 jpeg                   0.1-8.1  2019-10-24 [2] CRAN (R 3.6.1)
 jsonlite               1.6.1    2020-02-02 [2] CRAN (R 3.6.2)
 kableExtra             1.1.0    2019-03-16 [2] CRAN (R 3.6.1)
 knitr                  1.28     2020-02-06 [2] CRAN (R 3.6.2)
 labeling               0.3      2014-08-23 [2] CRAN (R 3.6.0)
 later                  1.0.0    2019-10-04 [2] CRAN (R 3.6.1)
 lattice                0.20-40  2020-02-19 [4] CRAN (R 3.6.2)
 latticeExtra           0.6-29   2019-12-19 [2] CRAN (R 3.6.2)
 lazyeval               0.2.2    2019-03-15 [2] CRAN (R 3.6.0)
 leaps                  3.1      2020-01-16 [2] CRAN (R 3.6.2)
 lifecycle              0.1.0    2019-08-01 [2] CRAN (R 3.6.1)
 limma                * 3.42.2   2020-02-03 [2] Bioconductor  
 locfit                 1.5-9.1  2013-04-20 [2] CRAN (R 3.6.0)
 lubridate              1.7.4    2018-04-11 [2] CRAN (R 3.6.0)
 magrittr             * 1.5      2014-11-22 [2] CRAN (R 3.6.0)
 MASS                   7.3-51.5 2019-12-20 [4] CRAN (R 3.6.2)
 Matrix                 1.2-18   2019-11-27 [2] CRAN (R 3.6.1)
 matrixStats            0.55.0   2019-09-07 [2] CRAN (R 3.6.1)
 memoise                1.1.0    2017-04-21 [2] CRAN (R 3.6.0)
 mgcv                   1.8-31   2019-11-09 [4] CRAN (R 3.6.1)
 modelr                 0.1.6    2020-02-22 [2] CRAN (R 3.6.2)
 msigdbr              * 7.0.1    2019-09-04 [2] CRAN (R 3.6.2)
 munsell                0.5.0    2018-06-12 [2] CRAN (R 3.6.0)
 ngsReports           * 1.1.2    2019-10-16 [1] Bioconductor  
 nlme                   3.1-144  2020-02-06 [4] CRAN (R 3.6.2)
 openssl                1.4.1    2019-07-18 [2] CRAN (R 3.6.1)
 pander               * 0.6.3    2018-11-06 [2] CRAN (R 3.6.0)
 pheatmap             * 1.0.12   2019-01-04 [2] CRAN (R 3.6.0)
 pillar                 1.4.3    2019-12-20 [2] CRAN (R 3.6.2)
 pkgbuild               1.0.6    2019-10-09 [2] CRAN (R 3.6.1)
 pkgconfig              2.0.3    2019-09-22 [2] CRAN (R 3.6.1)
 pkgload                1.0.2    2018-10-29 [2] CRAN (R 3.6.0)
 plotly                 4.9.2    2020-02-12 [2] CRAN (R 3.6.2)
 plyr                   1.8.5    2019-12-10 [2] CRAN (R 3.6.2)
 png                    0.1-7    2013-12-03 [2] CRAN (R 3.6.0)
 prettyunits            1.1.1    2020-01-24 [2] CRAN (R 3.6.2)
 processx               3.4.2    2020-02-09 [2] CRAN (R 3.6.2)
 progress               1.2.2    2019-05-16 [2] CRAN (R 3.6.0)
 promises               1.1.0    2019-10-04 [2] CRAN (R 3.6.1)
 ps                     1.3.2    2020-02-13 [2] CRAN (R 3.6.2)
 purrr                * 0.3.3    2019-10-18 [2] CRAN (R 3.6.1)
 R6                     2.4.1    2019-11-12 [2] CRAN (R 3.6.1)
 rappdirs               0.3.1    2016-03-28 [2] CRAN (R 3.6.0)
 RColorBrewer         * 1.1-2    2014-12-07 [2] CRAN (R 3.6.0)
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 readr                * 1.3.1    2018-12-21 [2] CRAN (R 3.6.0)
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 rlang                  0.4.4    2020-01-28 [2] CRAN (R 3.6.2)
 rmarkdown              2.1      2020-01-20 [2] CRAN (R 3.6.2)
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 Rsamtools              2.2.3    2020-02-23 [2] Bioconductor  
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 ShortRead              1.44.3   2020-02-03 [2] Bioconductor  
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 stringi                1.4.6    2020-02-17 [2] CRAN (R 3.6.2)
 stringr              * 1.4.0    2019-02-10 [2] CRAN (R 3.6.0)
 SummarizedExperiment   1.16.1   2019-12-19 [2] Bioconductor  
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 tibble               * 2.1.3    2019-06-06 [2] CRAN (R 3.6.0)
 tidyr                * 1.0.2    2020-01-24 [2] CRAN (R 3.6.2)
 tidyselect             1.0.0    2020-01-27 [2] CRAN (R 3.6.2)
 tidyverse            * 1.3.0    2019-11-21 [2] CRAN (R 3.6.1)
 truncnorm              1.0-8    2018-02-27 [2] CRAN (R 3.6.0)
 UpSetR               * 1.4.0    2019-05-22 [2] CRAN (R 3.6.0)
 usethis                1.5.1    2019-07-04 [2] CRAN (R 3.6.1)
 vctrs                  0.2.3    2020-02-20 [2] CRAN (R 3.6.2)
 viridisLite            0.3.0    2018-02-01 [2] CRAN (R 3.6.0)
 webshot                0.5.2    2019-11-22 [2] CRAN (R 3.6.1)
 whisker                0.4      2019-08-28 [2] CRAN (R 3.6.1)
 withr                  2.1.2    2018-03-15 [2] CRAN (R 3.6.0)
 workflowr            * 1.6.0    2019-12-19 [2] CRAN (R 3.6.2)
 xfun                   0.12     2020-01-13 [2] CRAN (R 3.6.2)
 XML                    3.99-0.3 2020-01-20 [2] CRAN (R 3.6.2)
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 XVector                0.26.0   2019-10-29 [2] Bioconductor  
 yaml                   2.2.1    2020-02-01 [2] CRAN (R 3.6.2)
 zlibbioc               1.32.0   2019-10-29 [2] Bioconductor  
 zoo                    1.8-7    2020-01-10 [2] CRAN (R 3.6.2)

[1] /home/steveped/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library