CT27 ST3D PLAC1 KD Bulk RNAseq analyses

Environment Setup

salloc -N 1 --exclusive -p amd -t 8:00:00
conda activate star
# working dir
mkdir -p /work/LAS/geetu-lab/arnstrm/hTS_CT27_ST3D_PLAC1_KD
cd /work/LAS/geetu-lab/arnstrm/hTS_CT27_ST3D_PLAC1_KD
mkdir -p 1_data
mkdir -p 2_fastqc
mkdir -p 3_STAR-mapping
mkdir -p 4_featureCounts
mkdir -p 5_multiqc
# file structure
tree -L 1
.
├── 1_data
├── 2_fastqc
├── 3_STAR-mapping
├── 4_featureCounts
└── 5_multiqc

Raw data

Raw data was downloaded from the LSS using rsync command.

cd 1_data
rsync -avP /lss/folder/path/hTS_CT27_ST3D_PLAC1_KD ./1_data
# GEO link will be included later

Genome/annotation

Additional files required for the analyses were downloaded from GenCode. The downloaded files are as follows:

cd 3_STAR-mapping
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.p13.genome.fa.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gff3.gz
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz
gunzip GRCh38.p13.genome.fa.gz
gunzip gencode.v42.primary_assembly.annotation.gtf.gz
gunzip gencode.v42.primary_assembly.annotation.gff3.gz
# ids for prot coding genes
awk '$3=="gene" && $9 ~/gene_type=protein_coding;/ {
        split($9,a,";"); print gensub(/gene_id=/, "", 1, a[2])
        }'  gencode.v42.primary_assembly.annotation.gff3 > GRCh38.protein_coding
# you should have 20,054 ids (protein-coding genes)

FastQC

Quality inspection of the reads. The multiqc report, collating all samples together are provided as html file.

cd 2_fastqc
for fq in ../1_data/*.fq.gz; do
  fastqc --threads $SLURM_JOB_CPUS_PER_NODE $fq;
done

Mapping

To index the genome, following command was run (in an interactive session).

fastaGenome="GRCh38.p13.genome.fa"
gtf="gencode.v42.primary_assembly.annotation.gtf"
STAR --runThreadN $SLURM_JOB_CPUS_PER_NODE \
     --runMode genomeGenerate \
     --genomeDir $(pwd) \
     --genomeFastaFiles $fastaGenome \
     --sjdbGTFfile $gtf \
     --sjdbOverhang 1

Each fastq file was mapped to the indexed genome as using runSTAR_map.sh script shown below:

#!/bin/bash
conda activate star
index=/work/LAS/geetu-lab/arnstrm/GRCh38_index
read1=$1
read2=$(echo ${read1} | sed 's/_R1_/_R2_/g')
cpus=${SLURM_JOB_CPUS_PER_NODE}
out=$(basename ${read1} | cut -f 1-2 -d "_")
STAR \
--runThreadN ${cpus} \
--genomeDir ${index} \
--outSAMtype BAM SortedByCoordinate \
--quantMode GeneCounts \
--outFilterScoreMinOverLread 0.3 \
--outFilterMatchNminOverLread 0.3 \
--outFileNamePrefix ${out}_ \
--readFilesCommand zcat \
--outWigType bedGraph \
--outWigStrand Unstranded \
--outWigNorm RPM \
--readFilesIn ${read1} ${read2}

Mapping was run with a simple loop:

for fq in *_R1_*fastq.gz; do
  runSTAR_map.sh $fq;
done

Counts

For generating counts from the mapped reads, we used subread package program featureCounts. All bam files were supplied together to generate a single count file for individual samples.

cd 3_STAR-mapping
realpath *.bam > ../4_featureCounts/bam.fofn
cd ../4_featureCounts
gtf="gencode.v42.primary_assembly.annotation.gtf"
while read line; do
ln -s $line;
done
featureCounts \
   -T ${SLURM_CPUS_ON_NODE} \
   -a ${gtf} \
   -t exon \
   -g gene_id \
   -p \
   -B \
   --countReadPairs \
   -o merged_counts.txt \
   --tmpDir ./tmp *.bam

The generated counts file was processed to use it direclty with DESeq2

grep -v "^#" merged_counts.txt |\
    cut -f 1,7- |\
    sed 's/_Aligned.sortedByCoord.out.bam//g' > merged_clean-counts.txt
head -n 1 merged_clean-counts.txt > header
grep -Fw -f GRCh38.protein_coding merged_clean-counts.txt > body
cat header body > counts_genes.tsv
rm body head

Create a info file:

head -n 1 counts_genes.tsv |\
   tr "\t" "\n" |\
   grep -v "^Geneid" |\
   awk '{print $1"\t"gensub(/..$/, "", 1,$1)}' > info.tsv

Differential expression analysis

Differential expression (DE) analyses using DESeq2 was performed as shown below.

Prerequisites

R packages required for this section are loaded

# set path
setwd("/work/LAS/geetu-lab/arnstrm/hTS_CT27_ST3D_PLAC1_KD")
# load the modules
library(tidyverse)
library(DESeq2)
library(pheatmap)
library(ggrepel)
library(RColorBrewer)
library(reshape2)
library(TissueEnrich)
library(plotly)
library(cowplot)
library(biomaRt)
library(scales)
library(kableExtra)
library(htmlwidgets)
library(DT)
library(enrichR)
library(clusterProfiler)
library(enrichplot)
library(org.Hs.eg.db)
#> Warning: package 'org.Hs.eg.db' was built under R version 4.2.3
library(org.Rn.eg.db)
#> Warning: package 'org.Rn.eg.db' was built under R version 4.2.3
library(data.table)
library(GOSemSim)
library(DOSE)
library(pathview)
#> Warning: package 'pathview' was built under R version 4.2.3

Import datasets

The counts data and its associated metadata (coldata) are imported for analyses.

countsFile = 'assets/counts_genes.tsv'
groupFile = 'assets/info.tsv'
coldata <-
  read.csv(
    groupFile,
    row.names = 1,
    sep = "\t",
    header = FALSE,
    stringsAsFactors = TRUE
  )
colnames(coldata) <- "condition"
cts <- as.matrix(read.delim(countsFile, row.names = 1, header = TRUE))

Reorder columns of cts according to coldata rows. Check if samples in both files match.

all(rownames(coldata) %in% colnames(cts))
#> [1] TRUE
cts <- cts[, rownames(coldata)]

DESeq2

The batch corrected read counts are then used for running DESeq2 analyses

dds <- DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design = ~ condition)
vsd <- vst(dds, blind = FALSE)
keep <- rowSums(counts(dds)) >= 10
dds <- dds[keep, ]
dds <- DESeq(dds)

PCA plot for QC

PCA plot for the dataset that includes all libraries.

rv <- rowVars(assay(vsd))
select <-
  order(rv, decreasing = TRUE)[seq_len(min(500, length(rv)))]
pca <- prcomp(t(assay(vsd)[select, ]))
percentVar <- pca$sdev ^ 2 / sum(pca$sdev ^ 2)
intgroup = "condition"
intgroup.df <- as.data.frame(colData(vsd)[, intgroup, drop = FALSE])
group <- if (length(intgroup) == 1) {
  factor(apply(intgroup.df, 1, paste, collapse = " : "))
}
d <- data.frame(
  PC1 = pca$x[, 1],
  PC2 = pca$x[, 2],
  intgroup.df,
  name = colnames(vsd)
)
ggplot(d, aes(PC1, PC2, color = condition)) +
  scale_shape_manual(values = 1:12) +
  scale_color_manual(values = c('PLAC1.4'   = '#00b462',
                                'SCR'     = '#980c80')) +
  theme_bw() +
  theme(legend.title = element_blank()) +
  geom_point(size = 2, stroke = 2) +
  geom_text_repel(aes(label = name)) +
  xlab(paste("PC1", round(percentVar[1] * 100, 2), "% variance")) +
  ylab(paste("PC2", round(percentVar[2] * 100, 2), "% variance"))
Figure 4: PCA plot for the first 2 principal components

Figure 4: PCA plot for the first 2 principal components

Sample distance for QC

sampleDists <- dist(t(assay(vsd)))
sampleDistMatrix <- as.matrix( sampleDists )
rownames(sampleDistMatrix) <- colnames(vsd)
colnames(sampleDistMatrix) <- NULL
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
pheatmap(sampleDistMatrix,
         clustering_distance_rows = sampleDists,
         clustering_distance_cols = sampleDists,
         col = colors)
Figure 5: Euclidean distance between samples

Figure 5: Euclidean distance between samples

Set contrasts and find DE genes

res.PLCvsSCR <-
  results(dds,
          contrast = c(
            "condition",
            "PLAC1.4",
            "SCR"))

Functions

Import functions for processing and plotting

source("/work/LAS/geetu-lab/arnstrm/myR_functions/plot_enrichR.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/processDE.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/rat_id_conversion.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/run_pce.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/save_pheatmap.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/theme_clean.R")
source("/work/LAS/geetu-lab/arnstrm/myR_functions/volcano_plots.R")

Gene information

ensembl = useMart("ENSEMBL_MART_ENSEMBL")
listDatasets(ensembl) %>%
  filter(str_detect(description, "Human"))
ensembl = useDataset("hsapiens_gene_ensembl", mart = ensembl)
listFilters(ensembl) %>%
  filter(str_detect(name, "ensembl"))
filterType <- "ensembl_gene_id_version"
head(rownames(counts))
counts <- read.delim("assets/counts_genes.tsv", row.names = 1, header = TRUE)
head(rownames(counts))
filterValues <- rownames(counts)
listAttributes(ensembl) %>%
  head(20)
attributeNames <- c('ensembl_gene_id_version',
                    'ensembl_gene_id',
                    'external_gene_name')
annot <- getBM(
  attributes = attributeNames,
  filters = filterType,
  values = filterValues,
  mart = ensembl
)
attributeNames <- c('ensembl_gene_id_version',
                    'gene_biotype',
                    'external_gene_name',
                    'description')
mart <- getBM(
  attributes = attributeNames,
  filters = filterType,
  values = filterValues,
  mart = ensembl
)
write_delim(
  annot,
  file = "assets/annot.tsv",
  delim = "\t"
)
write_delim(
  mart,
  file = "assets/mart.tsv",
  delim = "\t"
)

Files were saved, so we don’t query BioMart everytime we run the markdown. The files will be loaded, instead

mart <-
    read.csv(
        "assets/mart.tsv",
        sep = "\t",
        header = TRUE,
    )
annot <-
    read.csv(
        "assets/annot.tsv",
        sep = "\t",
        header = TRUE,
    )

Results

Write files

processDE.ver(res.PLCvsSCR, "PLAC1vsSCR")

Volcano plots

PLAC1 vs. SCR (fc)

g <- volcanoPlots(
  res.se = res.PLCvsSCR,
  string = "PLAC1vsSCR",
  first = "PLAC1",
  second = "SCR",
  color1 = "#00b462",
  color2 = "#4d4d4d",
  color3 = "#980c80",
  ChartTitle = "PLAC1 vs. SCR",
  labelType = "fc"
)
g
#> Warning: Removed 1992 rows containing missing values (`geom_point()`).
#> Warning: Removed 14687 rows containing missing values (`geom_label_repel()`).
Fig X: PLAC1 vs SCR (purple/negFC = overexpressed in SCR; green/posFC = overexpressed in PLAC1)

Fig X: PLAC1 vs SCR (purple/negFC = overexpressed in SCR; green/posFC = overexpressed in PLAC1)

PLAC1 vs. SCR (interactive)

ggplotly(g)
#> Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
#>   If you'd like to see this geom implemented,
#>   Please open an issue with your example code at
#>   https://github.com/ropensci/plotly/issues

#> Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
#>   If you'd like to see this geom implemented,
#>   Please open an issue with your example code at
#>   https://github.com/ropensci/plotly/issues

#> Warning in geom2trace.default(dots[[1L]][[3L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabelRepel() has yet to be implemented in plotly.
#>   If you'd like to see this geom implemented,
#>   Please open an issue with your example code at
#>   https://github.com/ropensci/plotly/issues

Fig X: PLAC1 vs SCR (purple/negFC = overexpressed in SCR; green/posFC = overexpressed in PLAC1)

PLAC1 vs. SCR (padj)

g <- volcanoPlots(
  res.se = res.PLCvsSCR,
  string = "PLAC1vsSCR",
  first = "PLAC1",
  second = "SCR",
  color1 = "#00b462",
  color2 = "#4d4d4d",
  color3 = "#980c80",
  ChartTitle = "PLAC1 vs. SCR",
  labelType = "padj"
)
g
#> Warning: Removed 1992 rows containing missing values (`geom_point()`).
#> Warning: Removed 14687 rows containing missing values (`geom_label_repel()`).
Fig X: PLAC1 vs SCR (purple/negFC = overexpressed in SCR; green/posFC = overexpressed in PLAC1)

Fig X: PLAC1 vs SCR (purple/negFC = overexpressed in SCR; green/posFC = overexpressed in PLAC1)

enrichR

setEnrichrSite("Enrichr")
websiteLive <- TRUE
myDBs <-
  c(
    "DisGeNET",
    "GO_Biological_Process_2021",
    "HDSigDB_Human_2021",
    "KEGG_2021_Human",
    "GTEx_Tissues_V8_2023",
    "MGI_Mammalian_Phenotype_Level_3",
    "MGI_Mammalian_Phenotype_Level_4_2021",
    "WikiPathways_2019_Human",
    "Panther_2015"
  )
if (websiteLive) {
  PLAC1vsSCR.up.enriched <- enrichr(PLAC1vsSCR.up.pce2, myDBs)
  PLAC1vsSCR.dw.enriched <- enrichr(PLAC1vsSCR.dw.pce2, myDBs)
}
#> Uploading data to Enrichr... Done.
#>   Querying DisGeNET... Done.
#>   Querying GO_Biological_Process_2021... Done.
#>   Querying HDSigDB_Human_2021... Done.
#>   Querying KEGG_2021_Human... Done.
#>   Querying GTEx_Tissues_V8_2023... Done.
#>   Querying MGI_Mammalian_Phenotype_Level_3... Done.
#>   Querying MGI_Mammalian_Phenotype_Level_4_2021... Done.
#>   Querying WikiPathways_2019_Human... Done.
#>   Querying Panther_2015... Done.
#> Parsing results... Done.
#> Uploading data to Enrichr... Done.
#>   Querying DisGeNET... Done.
#>   Querying GO_Biological_Process_2021... Done.
#>   Querying HDSigDB_Human_2021... Done.
#>   Querying KEGG_2021_Human... Done.
#>   Querying GTEx_Tissues_V8_2023... Done.
#>   Querying MGI_Mammalian_Phenotype_Level_3... Done.
#>   Querying MGI_Mammalian_Phenotype_Level_4_2021... Done.
#>   Querying WikiPathways_2019_Human... Done.
#>   Querying Panther_2015... Done.
#> Parsing results... Done.

PCE tests (green/posFC = overexpressed in PLAC1)

VentoTormo

plotPCE(inputGenes = PLAC1vsSCR.up.pce1, dataset = "Vt", myColor = "#00b462")
#> [1] "requires human gene names as input"

Xiang

plotPCE(inputGenes = PLAC1vsSCR.up.pce2, dataset = "Xi", myColor = "#00b462")
#> [1] "requires human ensembl gene ids"

Zhou&Petropoulos (Castel)

plotPCE(inputGenes = PLAC1vsSCR.up.pce2, dataset = "Zp", myColor = "#00b462")
#> [1] "requires human ensembl gene ids"

Rostovskaya (Hs)

plotPCE(inputGenes = PLAC1vsSCR.up.pce2, dataset = "Ro.Hs", myColor = "#00b462")
#> [1] "requires human ensembl gene ids"

Rostovskaya (Cy)

plotPCE(inputGenes = PLAC1vsSCR.up.pce2, dataset = "Ro.Cy", myColor = "#00b462")
#> [1] "requires human ensembl gene ids"

PCE tests (purple/negFC = overexpressed in SCR)

VentoTormo

plotPCE(inputGenes = PLAC1vsSCR.dw.pce1, dataset = "Vt", myColor = "#980c80")
#> [1] "requires human gene names as input"

Xiang

plotPCE(inputGenes = PLAC1vsSCR.dw.pce2, dataset = "Xi", myColor = "#980c80")
#> [1] "requires human ensembl gene ids"

Zhou&Petropoulos (Castel)

plotPCE(inputGenes = PLAC1vsSCR.dw.pce2, dataset = "Zp", myColor = "#980c80")
#> [1] "requires human ensembl gene ids"

Rostovskaya (Hs)

plotPCE(inputGenes = PLAC1vsSCR.dw.pce2, dataset = "Ro.Hs", myColor = "#980c80")
#> [1] "requires human ensembl gene ids"

Rostovskaya (Cy)

plotPCE(inputGenes = PLAC1vsSCR.dw.pce2, dataset = "Ro.Cy", myColor = "#980c80")
#> [1] "requires human ensembl gene ids"

Enrichment tests (green/posFC = overexpressed in PLAC1)

DisGeNET

plotEnrichR(PLAC1vsSCR.up.enriched, table="DisGeNET" , myColor = "#00b462")

GO_Biological_Process_2021

plotEnrichR(PLAC1vsSCR.up.enriched, table="GO_Biological_Process_2021" , "#00b462")

HDSigDB_Human_2021

plotEnrichR(PLAC1vsSCR.up.enriched, table="HDSigDB_Human_2021" , "#00b462")

KEGG_2021_Human

plotEnrichR(PLAC1vsSCR.up.enriched, table="KEGG_2021_Human" , "#00b462")

GTEx_Tissues_V8_2023

plotEnrichR(PLAC1vsSCR.up.enriched, table="GTEx_Tissues_V8_2023" , "#00b462")

MGI_Mammalian_Phenotype_Level_3

plotEnrichR(PLAC1vsSCR.up.enriched, table="MGI_Mammalian_Phenotype_Level_3" , "#00b462")

MGI_Mammalian_Phenotype_Level_4_2021

plotEnrichR(PLAC1vsSCR.up.enriched, table="MGI_Mammalian_Phenotype_Level_4_2021" , "#00b462")

WikiPathways_2019_Human

plotEnrichR(PLAC1vsSCR.up.enriched, table="WikiPathways_2019_Human" , "#00b462")

Panther_2015

plotEnrichR(PLAC1vsSCR.up.enriched, table="Panther_2015" , "#00b462")

Enrichment tests (purple/negFC = overexpressed in SCR)

DisGeNET

plotEnrichR(PLAC1vsSCR.dw.enriched, table="DisGeNET" , myColor = "#980c80")

GO_Biological_Process_2021

plotEnrichR(PLAC1vsSCR.dw.enriched, table="GO_Biological_Process_2021" , "#980c80")

HDSigDB_Human_2021

plotEnrichR(PLAC1vsSCR.dw.enriched, table="HDSigDB_Human_2021" , "#980c80")

KEGG_2021_Human

plotEnrichR(PLAC1vsSCR.dw.enriched, table="KEGG_2021_Human" , "#980c80")

GTEx_Tissues_V8_2023

plotEnrichR(PLAC1vsSCR.dw.enriched, table="GTEx_Tissues_V8_2023" , "#980c80")

MGI_Mammalian_Phenotype_Level_3

plotEnrichR(PLAC1vsSCR.dw.enriched, table="MGI_Mammalian_Phenotype_Level_3" , "#980c80")

MGI_Mammalian_Phenotype_Level_4_2021

plotEnrichR(PLAC1vsSCR.dw.enriched, table="MGI_Mammalian_Phenotype_Level_4_2021" , "#980c80")

WikiPathways_2019_Human

plotEnrichR(PLAC1vsSCR.dw.enriched, table="WikiPathways_2019_Human" , "#980c80")

Panther_2015

plotEnrichR(PLAC1vsSCR.dw.enriched, table="Panther_2015" , "#980c80")

GSEA

Prepare GeneList

filteredDE <- fread("assets/DE_PLAC1vsSCR_filtered.tsv")
original_gene_list <- filteredDE$log2FoldChange
names(original_gene_list) <- gsub("\\..*", "", filteredDE$Gene)
gene_list<-na.omit(original_gene_list)
gene_list = sort(gene_list, decreasing = TRUE)

Run GSEA

gse <- gseGO(
  geneList = gene_list,
  ont = "ALL",
  keyType = "ENSEMBL",
  minGSSize = 3,
  maxGSSize = 800,
  pvalueCutoff = 0.05,
  verbose = TRUE,
  OrgDb = org.Hs.eg.db,
  pAdjustMethod = "BH",
  eps = 0,
  exponent = 1
)
#> preparing geneSet collections...
#> GSEA analysis...
#> leading edge analysis...
#> done...
saveRDS(gse, file = "assets/gsea.rds")

Results table

gse <- readRDS(file = "assets/gsea.rds")
gseTable <- as_tibble(gse)
DT::datatable(
  gseTable,
  filter = "top",
  options = list(pageLength = 10)) %>%
  DT::formatRound(c("enrichmentScore", "NES", "pvalue", "p.adjust", "qvalue"), 2) %>%
  DT::formatStyle("core_enrichment",
              "white-space" = "nowrap")

Plots

Blobplot

dotplot(gse, showCategory=10, split=".sign") + facet_grid(.~.sign)

Enrichment Map

For the first 15 categories

mapGO <- godata('org.Hs.eg.db', ont = "BP")
emaGSE <- pairwise_termsim(gse, method="Wang", semData = mapGO)
emapplot(emaGSE, showCategory = 15)

Category Netplot

Showing 5 categories

cnetplot(gse, categorySize="pvalue", foldChange=gene_list, showCategory = 5)
#> Warning in cnetplot.enrichResult(x, ...): Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
#>  The foldChange parameter will be removed in the next version.

Ridgeplot

ridgeplot(gse) + labs(x = "enrichment distribution")

GSEA plot

For the top 20 categories

set1

gseaplot(gse, by = "all", title = gse$Description[1], geneSetID = 1)

set2

gseaplot(gse, by = "all", title = gse$Description[2], geneSetID = 2)

set3

gseaplot(gse, by = "all", title = gse$Description[3], geneSetID = 3)

set4

gseaplot(gse, by = "all", title = gse$Description[4], geneSetID = 4)

set5

gseaplot(gse, by = "all", title = gse$Description[5], geneSetID = 5)

set6

gseaplot(gse, by = "all", title = gse$Description[6], geneSetID = 6)

set7

gseaplot(gse, by = "all", title = gse$Description[7], geneSetID = 7)

set8

gseaplot(gse, by = "all", title = gse$Description[8], geneSetID = 8)

set9

gseaplot(gse, by = "all", title = gse$Description[9], geneSetID = 9)

set10

gseaplot(gse, by = "all", title = gse$Description[10], geneSetID = 10)

set11

gseaplot(gse, by = "all", title = gse$Description[11], geneSetID = 11)

set12

gseaplot(gse, by = "all", title = gse$Description[12], geneSetID = 12)

set13

gseaplot(gse, by = "all", title = gse$Description[13], geneSetID = 13)

set14

gseaplot(gse, by = "all", title = gse$Description[14], geneSetID = 14)

set15

gseaplot(gse, by = "all", title = gse$Description[15], geneSetID = 15)

KEGG

Prepare GeneList

ids <- bitr(
  names(original_gene_list),
  fromType = "ENSEMBL",
  toType = "ENTREZID",
  OrgDb = org.Hs.eg.db
)
dedup_ids = ids[!duplicated(ids[c("ENSEMBL")]),]
filteredDE$Gene <- gsub("\\..*", "", filteredDE$Gene)
filteredDE2 <- left_join(dedup_ids, 
                         filteredDE, 
                         by = c('ENSEMBL' = 'Gene'))
kegg_gene_list <- filteredDE2$log2FoldChange
names(kegg_gene_list) <- filteredDE2$ENTREZID
kegg_gene_list <- na.omit(kegg_gene_list)
kegg_gene_list = sort(kegg_gene_list, 
                      decreasing = TRUE)

run KEGG

orgCode <- "hsa"
keggPW <-gseKEGG(
  kegg_gene_list,
  organism = orgCode,
  keyType = "ncbi-geneid",
  exponent = 1,
  minGSSize = 3,
  maxGSSize = 800,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  by = "fgsea")
#> Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
#> Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
#> Reading KEGG annotation online: "https://rest.kegg.jp/conv/ncbi-geneid/hsa"...
#> preparing geneSet collections...
#> GSEA analysis...
#> leading edge analysis...
#> done...
saveRDS(keggPW, file = "assets/kegg.rds")

Results table

keggPW <- readRDS(file = "assets/kegg.rds")
keggTable <- as_tibble(keggPW)
DT::datatable(keggTable,
              filter = "top",
              options = list(pageLength = 10)) %>%
  DT::formatRound(c("enrichmentScore", "NES", "pvalue", "p.adjust", "qvalue"), 2) %>%
  DT::formatStyle("core_enrichment",
                  "white-space" = "nowrap")

Plots

Blobplot

dotplot(keggPW,
        showCategory = 10,
        title = "Enriched Pathways",
        split = ".sign") + facet_grid(. ~ .sign)

Category Netplot

Showing 5 categories

cnetplot(keggPW, categorySize="pvalue", foldChange=kegg_gene_list, showCategory = 5)
#> Warning in cnetplot.enrichResult(x, ...): Use 'color.params = list(foldChange = your_value)' instead of 'foldChange'.
#>  The foldChange parameter will be removed in the next version.

Ridgeplot

ridgeplot(keggPW) + labs(x = "enrichment distribution")

KEGG GSEA plot

For the top 20 categories

set1

gseaplot(keggPW, by = "all", title = keggPW$Description[1], geneSetID = 1)

Pathway

pathview(gene.data=kegg_gene_list, pathway.id="hsa04814", species = orgCode)
knitr::include_graphics("hsa04814.pathview.png")

Save RData

Saving the entire session as well as the DEseq2 object (as rds) for doing the overlap analyses.

save.image(file = "assets/hTS_CT27_ST3D_PLAC1_KD.RData")
save(PLAC1vsSCR.up.pce1, PLAC1vsSCR.dw.pce1, file = "assets/hTS_CT27_ST3D_PLAC1_KD_genelists.RData")

MultiQC report:

NOT YET MultiQC report is available at this link

Session Information

sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] pathview_1.38.0             DOSE_3.24.2                
#>  [3] GOSemSim_2.24.0             data.table_1.14.6          
#>  [5] org.Rn.eg.db_3.16.0         org.Hs.eg.db_3.16.0        
#>  [7] enrichplot_1.18.4           clusterProfiler_4.6.2      
#>  [9] enrichR_3.1                 DT_0.27                    
#> [11] htmlwidgets_1.5.4           kableExtra_1.3.4           
#> [13] scales_1.2.1                biomaRt_2.54.1             
#> [15] cowplot_1.1.1               plotly_4.10.1              
#> [17] TissueEnrich_1.18.0         GSEABase_1.60.0            
#> [19] graph_1.76.0                annotate_1.76.0            
#> [21] XML_3.99-0.12               AnnotationDbi_1.60.0       
#> [23] ensurer_1.1                 reshape2_1.4.4             
#> [25] RColorBrewer_1.1-3          ggrepel_0.9.3              
#> [27] pheatmap_1.0.12             DESeq2_1.38.3              
#> [29] SummarizedExperiment_1.28.0 Biobase_2.58.0             
#> [31] MatrixGenerics_1.10.0       matrixStats_0.63.0         
#> [33] GenomicRanges_1.50.1        GenomeInfoDb_1.34.3        
#> [35] IRanges_2.32.0              S4Vectors_0.36.0           
#> [37] BiocGenerics_0.44.0         forcats_0.5.2              
#> [39] stringr_1.5.0               dplyr_1.0.10               
#> [41] purrr_1.0.1                 readr_2.1.3                
#> [43] tidyr_1.3.0                 tibble_3.1.8               
#> [45] ggplot2_3.4.0               tidyverse_1.3.2            
#> 
#> loaded via a namespace (and not attached):
#>   [1] utf8_1.2.2             tidyselect_1.2.0       RSQLite_2.2.18        
#>   [4] grid_4.2.2             BiocParallel_1.32.1    scatterpie_0.1.8      
#>   [7] munsell_0.5.0          codetools_0.2-18       withr_2.5.0           
#>  [10] colorspace_2.0-3       filelock_1.0.2         highr_0.9             
#>  [13] knitr_1.41             rstudioapi_0.14        labeling_0.4.2        
#>  [16] KEGGgraph_1.58.3       GenomeInfoDbData_1.2.9 polyclip_1.10-4       
#>  [19] bit64_4.0.5            farver_2.1.1           downloader_0.4        
#>  [22] vctrs_0.6.2            treeio_1.22.0          generics_0.1.3        
#>  [25] gson_0.1.0             xfun_0.35              timechange_0.1.1      
#>  [28] BiocFileCache_2.6.1    R6_2.5.1               graphlayouts_0.8.4    
#>  [31] rmdformats_1.0.4       locfit_1.5-9.7         bitops_1.0-7          
#>  [34] cachem_1.0.6           fgsea_1.24.0           gridGraphics_0.5-1    
#>  [37] DelayedArray_0.24.0    assertthat_0.2.1       vroom_1.6.0           
#>  [40] ggraph_2.1.0           googlesheets4_1.0.1    gtable_0.3.1          
#>  [43] tidygraph_1.2.3        rlang_1.1.1            systemfonts_1.0.4     
#>  [46] splines_4.2.2          lazyeval_0.2.2         gargle_1.2.1          
#>  [49] broom_1.0.1            yaml_2.3.6             modelr_0.1.10         
#>  [52] crosstalk_1.2.0        backports_1.4.1        qvalue_2.30.0         
#>  [55] tools_4.2.2            bookdown_0.33          ggplotify_0.1.0       
#>  [58] ellipsis_0.3.2         jquerylib_0.1.4        ggridges_0.5.4        
#>  [61] Rcpp_1.0.9             plyr_1.8.8             progress_1.2.2        
#>  [64] zlibbioc_1.44.0        RCurl_1.98-1.9         prettyunits_1.1.1     
#>  [67] viridis_0.6.2          haven_2.5.1            fs_1.5.2              
#>  [70] magrittr_2.0.3         reprex_2.0.2           googledrive_2.0.0     
#>  [73] ggnewscale_0.4.8       hms_1.1.2              patchwork_1.1.2       
#>  [76] evaluate_0.18          xtable_1.8-4           HDO.db_0.99.1         
#>  [79] readxl_1.4.1           gridExtra_2.3          compiler_4.2.2        
#>  [82] shadowtext_0.1.2       crayon_1.5.2           htmltools_0.5.3       
#>  [85] ggfun_0.0.9            tzdb_0.3.0             geneplotter_1.76.0    
#>  [88] aplot_0.1.10           lubridate_1.9.0        DBI_1.1.3             
#>  [91] tweenr_2.0.2           dbplyr_2.2.1           MASS_7.3-58.1         
#>  [94] rappdirs_0.3.3         Matrix_1.5-3           cli_3.4.1             
#>  [97] parallel_4.2.2         igraph_1.3.5           pkgconfig_2.0.3       
#> [100] xml2_1.3.3             ggtree_3.6.2           svglite_2.1.0         
#> [103] bslib_0.4.1            webshot_0.5.4          XVector_0.38.0        
#> [106] rvest_1.0.3            yulab.utils_0.0.6      digest_0.6.30         
#> [109] Biostrings_2.66.0      rmarkdown_2.18         cellranger_1.1.0      
#> [112] fastmatch_1.1-3        tidytree_0.4.2         curl_4.3.3            
#> [115] rjson_0.2.21           lifecycle_1.0.3        nlme_3.1-160          
#> [118] jsonlite_1.8.3         viridisLite_0.4.1      fansi_1.0.3           
#> [121] pillar_1.8.1           lattice_0.20-45        KEGGREST_1.38.0       
#> [124] fastmap_1.1.0          httr_1.4.4            
#>  [ reached getOption("max.print") -- omitted 11 entries ]