This is an analysis of differential expression at the gene level between supershedder groupings based on shedding rates measured on the day of sacrifice for infected mallard ileum samples.
## Load packages and data
library(limma)
library(edgeR)
library(Glimma)
library(gplots)
library(ggrepel)
library(RColorBrewer)
library(gridExtra)
library(kableExtra)
library(tidyverse)
## Load data
cnt1 <- read_delim("G:/Shared drives/RNA Seq Supershedder Project/MALL DE manuscript/mallardLPAIV/extData/ileumCounts.txt", delim = "\t") %>% distinct(gene, .keep_all = TRUE)
covars <- read_delim("G:/Shared drives/RNA Seq Supershedder Project/MALL DE manuscript/mallardLPAIV/extData/MALL70_SSgroup_RAW_11.5.20.csv", delim = ",")
annot <- read_delim("G:/Shared drives/RNA Seq Supershedder Project/MALL DE manuscript/mallardLPAIV/extData/annotationGenesIleum110120.txt", delim = "\t")
cnt <- cnt1 %>%
as_tibble() %>%
select(-gene)
newNames.ileum <- names(cnt) %>%
as_tibble() %>%
mutate(value = gsub("Iluem_", "", .$value)) %>%
separate(value, into = c(NA, "pt1", "pt2")) %>%
mutate(pt1 = na_if(pt1, "MALL"),
pt2 = na_if(pt2, "ileum")) %>%
mutate(bird = ifelse(is.na(pt1), pt2, pt1)) %>%
mutate(bird = as.numeric(bird),
bird = formatC(bird, width = 2, format = "d", flag = "0")) %>%
mutate(newName = paste0("ileum_", bird))
colnames(cnt) <- newNames.ileum$newName
cnt <- cnt[,order(colnames(cnt))] %>%
mutate(gene = cnt1$gene) %>%
column_to_rownames("gene") %>%
as_tibble(rownames = NA)
### Covars
covars <- covars %>%
mutate(bird = as.numeric(bird)) %>%
mutate(bird = formatC(bird, width = 2, format = "d", flag = "0")) %>%
arrange(bird) %>%
mutate(bird = as.factor(bird)) %>%
mutate(group = str_remove(group, "-"))
covars.ileum <- covars %>%
filter(bird %in% newNames.ileum$bird)
cnt <- cnt %>% select(-ileum_01, -ileum_72)
covars.ileum <- covars.ileum %>% filter(bird != "01",
bird != "72")
Here we standardize expression levels across samples of varying depth by using the counts per million (CPM) and trimmed mean of M-values (TMM) methods. We also remove any genes that are expressed at few than 0.5 CPM in at least 25% of individuals.
#Convert to DGEList object
dge <- DGEList(counts=cnt)
dge$genes <- annot[match(rownames(dge$counts), annot$ensembl_gene_id),]
#CPM and log-CPM
cpm <- cpm(dge)
lcpm <- cpm(dge, log = TRUE)
#### Retain only genes expressed at >0.5 CPM in at least 25% of individuals
table(rowSums(dge$counts==0) == length(cnt[1,]))
##
## FALSE TRUE
## 17388 728
keep.exprs <- rowSums(cpm>0.5) >= length(cnt[1,])/4
sum(keep.exprs)
## [1] 14563
dge <- dge[keep.exprs,, keep.lib.sizes=FALSE]
table(rowSums(dge$counts==0) == length(cnt[1,]))
##
## FALSE
## 14563
dim(dge)
## [1] 14563 40
Following normalization, we subset the data based on infection groups.
#Assign groups in DGElist
group <- recode(covars.ileum$group, C1 = "Ctl", C29 = "Ctl") %>%
as.factor()
dge$samples$group <- group
### Divide out I1 and I2
dge.I1 <- dge[,grep('\\bI1\\b', dge$samples$group)]
dge.I1 <- calcNormFactors(dge.I1, method = "TMM")
dge.I2 <- dge[,grep('\\bI2\\b', dge$samples$group)]
dge.I2 <- calcNormFactors(dge.I2, method = "TMM")
covars.I1 <- covars %>% filter(group == "I1", bird != "14", bird != "32", bird != "47")
covars.I2 <- covars %>% filter(group == "I2")
## Establish design matrix: I1
design.I1 = model.matrix(~ 0 +
factor(covars.I1$SSgroup.virus.sac) +
covars.I1$age +
covars.I1$sex +
covars.I1$Bursa_pool)
colnames(design.I1) <- c("HIGH", "LOW", "MODERATE",
"age", "sexM", "poolMSU2",
"poolMSU3", "poolMSU4", "poolMSU5")
contr.matrix.I1 = makeContrasts(
LvM = LOW - MODERATE,
MvH = MODERATE - HIGH,
LvH = LOW - HIGH,
levels = colnames(design.I1))
## Mean-variance trend plots
v.I1 <- voomWithQualityWeights(dge.I1, design.I1, plot = FALSE)
#Fitting models
vfit.I1 <- lmFit(v.I1, design.I1)
vfit.I1 <- contrasts.fit(vfit.I1, contrasts = contr.matrix.I1)
tfit.I1 <- treat(vfit.I1, lfc = 0.5)
## Identify DE genes
dt.I1 <- decideTests(tfit.I1, p.value = 0.1, adjust.method = "fdr")
dt.tib.I1 <- as_tibble(dt.I1, rownames = NA) %>%
rownames_to_column("gene") %>%
mutate_at(vars(starts_with("L")), as.numeric) %>%
mutate_at(vars(starts_with("M")), as.numeric) %>%
rename(LvM.I1 = LvM,
MvH.I1 = MvH,
LvH.I1 = LvH) %>%
filter_at(vars(LvM.I1:LvH.I1), any_vars(. != 0))
## Establish design matrix: I2
design.I2 = model.matrix(
~ 0 +
factor(covars.I2$SSgroup.virus.sac) +
covars.I2$age +
covars.I2$sex +
covars.I2$Bursa_pool
)
colnames(design.I2) <- c(
"HIGH",
"LOW",
"MODERATE",
"age",
"sexM",
"poolMSU2",
"poolMSU3",
"poolMSU4",
"poolMSU5"
)
contr.matrix.I2 = makeContrasts(
LvM = LOW - MODERATE,
MvH = MODERATE - HIGH,
LvH = LOW - HIGH,
levels = colnames(design.I2))
## Mean-variance trend plots
v.I2 <- voomWithQualityWeights(dge.I2, design.I2, plot = FALSE)
#Fitting models
vfit.I2 <- lmFit(v.I2, design.I2)
vfit.I2 <- contrasts.fit(vfit.I2, contrasts = contr.matrix.I2)
tfit.I2 <- treat(vfit.I2, lfc = 0.5)
## Identify DE genes
dt.I2 <- decideTests(tfit.I2, p.value = 0.1, adjust.method = "fdr")
dt.tib.I2 <- as_tibble(dt.I2, rownames = NA) %>%
rownames_to_column("gene") %>%
mutate_at(vars(starts_with("L")), as.numeric) %>%
mutate_at(vars(starts_with("M")), as.numeric) %>%
rename(LvM.I2 = LvM,
MvH.I2 = MvH,
LvH.I2 = LvH) %>%
filter_at(vars(LvM.I2:LvH.I2), any_vars(. != 0))
## Bring it all together
dt.tib <- full_join(dt.tib.I1, dt.tib.I2) %>%
mutate_at(vars(starts_with("L")), as.numeric) %>%
mutate_at(vars(starts_with("M")), as.numeric) %>%
replace(is.na(.), 0)
## Joining, by = "gene"
For a gene to be considered differentially expressed, we require a p-value of 0.1 with a false discovery rate correction and a log fold count difference of 1.
allResults <- rbind(
as.data.frame(summary(dt.I1)),
as.data.frame(summary(dt.I2))) %>%
filter(Var1 != "NotSig")
kable(allResults) %>%
kable_styling("striped", full_width = F) %>%
pack_rows("1 Day Post Infection", 1, 6) %>%
pack_rows("2 Days Post Infection", 7, 12)
Var1 | Var2 | Freq |
---|---|---|
1 Day Post Infection | ||
Down | LvM | 1 |
Up | LvM | 0 |
Down | MvH | 0 |
Up | MvH | 0 |
Down | LvH | 0 |
Up | LvH | 0 |
2 Days Post Infection | ||
Down | LvM | 4 |
Up | LvM | 2 |
Down | MvH | 8 |
Up | MvH | 25 |
Down | LvH | 27 |
Up | LvH | 106 |
tmp1 <- topTreat(tfit.I1, coef = 1, n = Inf)
results1 <- mutate(tmp1, sig=ifelse(tmp1$adj.P.Val<0.1, "Sig", "Not Sig"))
p1 <- ggplot(results1, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Low vs. Moderate shedding, Day 1") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp2 <- topTreat(tfit.I1, coef = 2, n = Inf)
results2 <- mutate(tmp2, sig=ifelse(tmp2$adj.P.Val<0.1, "Sig", "Not Sig"))
p2 <- ggplot(results2, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Moderate vs. High shedding, Day 1") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp3 <- topTreat(tfit.I1, coef = 3, n = Inf)
results3 <- mutate(tmp3, sig=ifelse(tmp3$adj.P.Val<0.1, "Sig", "Not Sig"))
p3 <- ggplot(results3, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Low vs. High shedding, Day 1") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp4 <- topTreat(tfit.I2, coef = 1, n = Inf)
results4 <- mutate(tmp4, sig=ifelse(tmp4$adj.P.Val<0.1, "Sig", "Not Sig"))
p4 <- ggplot(results4, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Low vs. Moderate shedding, Day 2") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp5 <- topTreat(tfit.I2, coef = 2, n = Inf)
results5 <- mutate(tmp5, sig=ifelse(tmp5$adj.P.Val<0.1, "Sig", "Not Sig"))
p5 <- ggplot(results5, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Moderate vs. High shedding, Day 2") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
tmp6 <- topTreat(tfit.I2, coef = 3, n = Inf)
results6 <- mutate(tmp6, sig=ifelse(tmp6$adj.P.Val<0.1, "Sig", "Not Sig"))
p6 <- ggplot(results6, aes(logFC, -log10(P.Value))) +
geom_point(aes(col = sig)) +
scale_color_manual(values=c("black", "red")) +
ggtitle("Low vs. High shedding, Day 2") +
ylab("-Log10(p-value)") +
xlab("Log(Fold count)") +
theme_bw() +
theme(legend.position = "none")
grid.arrange(p1, p2, p3, p4, p5, p6, nrow = 2)
# Get the gene names for DE genes
lcpm2 <- as_tibble(dge.I2$counts, rownames = NA) %>%
cpm(., log = TRUE)
newNames <- colnames(lcpm2) %>%
as_tibble() %>%
separate(value, into = c(NA, "bird")) %>%
bind_cols(covars.I2) %>%
unite("newNames", SSgroup.virus.sac, group, bird)
colOrder <- bind_cols(covars.I2) %>%
mutate(SSgroup.virus.sac = fct_relevel(SSgroup.virus.sac, "LOW", "MODERATE", "HIGH")) %>%
arrange(SSgroup.virus.sac, group, bird) %>%
unite("newNames", SSgroup.virus.sac, group, bird)
colnames(lcpm2) <- newNames$newNames
lcpm2 <- lcpm2[, colOrder$newNames]
heatmap.annot <- annot %>%
filter(ensembl_gene_id %in% dt.tib$gene) %>%
mutate(hgnc_symbol = replace_na(hgnc_symbol, ".")) %>%
unite(annot.hm, c(ensembl_gene_id, hgnc_symbol), sep = "-", remove = FALSE) %>%
select(annot.hm, ensembl_gene_id) %>%
distinct(ensembl_gene_id, .keep_all = TRUE)
deGeneCounts <- lcpm2 %>%
as_tibble() %>%
mutate(ensembl_gene_id = rownames(dge.I2$counts)) %>%
filter(ensembl_gene_id %in% dt.tib$gene) %>%
left_join(heatmap.annot) %>%
column_to_rownames("annot.hm") %>%
select(-ensembl_gene_id) %>%
as.matrix()
## Set up palette
mypalette <- brewer.pal(11,"RdYlBu")
morecols <- colorRampPalette(mypalette)
hc <- hclust(as.dist(1-cor(t(deGeneCounts))))
# Plot the heatmap
heatmap.2(deGeneCounts,
Colv = FALSE,
Rowv = as.dendrogram(hc),
col = rev(morecols(50)),
trace = "none",
colsep = c(4, 8),
dendrogram = "row",
density.info = "none",
key = TRUE,
margins = c(12, 12),
scale ="row")
lcpm.DE <- lcpm %>%
as_tibble(rownames = NA) %>%
rownames_to_column("identifier") %>%
filter(identifier %in% dt.tib.I1$gene) %>%
pivot_longer(cols = contains("_"),
names_to = "sample",
values_to = "lcpm") %>%
separate(sample, into = c("tissue", "bird")) %>%
mutate(bird = as.factor(bird)) %>%
left_join(covars, by = "bird") %>%
filter(group == "C1" | group == "C14" | group == "I1") %>%
select(identifier, bird, lcpm, SSgroup.virus.sac, group) %>%
mutate(group = recode(group, C29 = "Control"),
group = recode(group, C1 = "Control"),
tmpID = ifelse(group == "Control", 'Control', 'Infected'))
aprioriPlotting <- function(target, ...) {
annot.target <- annot %>%
select(
ensembl_gene_id,
hgnc_symbol) %>%
filter(ensembl_gene_id == target) %>%
mutate(hgnc_symbol = replace_na(hgnc_symbol, "."))
plot <- lcpm.DE %>%
filter(identifier == target) %>%
mutate(SSgroup.virus.sac = fct_relevel(SSgroup.virus.sac, "LOW", "MODERATE", "HIGH")) %>%
ggplot(aes(x = SSgroup.virus.sac, y = lcpm)) +
facet_grid(. ~ tmpID, scales = "free", space = "free") +
ylab("Log2(Counts per million)") +
xlab("Shedding Group") +
scale_fill_grey(start = 0.35, end = 1) +
geom_point(position = position_dodge(width=0.75), aes(group = group), show.legend = FALSE) +
geom_boxplot(alpha = 0.5) +
geom_label_repel(aes(label = bird, group = group, fill = NULL), position = position_dodge(width=0.75), show.legend=FALSE) +
theme_classic() +
labs(title = paste0("I1: ", target, " - ", annot.target[1,2])) +
theme(legend.title = element_blank())
print(plot)
}
for(target in sort(unique(dt.tib.I1$gene))) {
aprioriPlotting(target)
}
lcpm.DE <- lcpm %>%
as_tibble(rownames = NA) %>%
rownames_to_column("identifier") %>%
filter(identifier %in% dt.tib.I2$gene) %>%
pivot_longer(cols = contains("_"),
names_to = "sample",
values_to = "lcpm") %>%
separate(sample, into = c("tissue", "bird")) %>%
mutate(bird = as.factor(bird)) %>%
left_join(covars, by = "bird") %>%
filter(group == "C1" | group == "C14" | group == "I2") %>%
select(identifier, bird, lcpm, SSgroup.virus.sac, group) %>%
mutate(group = recode(group, C29 = "Control"),
group = recode(group, C1 = "Control"),
tmpID = ifelse(group == "Control", 'Control', 'Infected'))
aprioriPlotting <- function(target, ...) {
annot.target <- annot %>%
select(
ensembl_gene_id,
hgnc_symbol) %>%
filter(ensembl_gene_id == target) %>%
mutate(hgnc_symbol = replace_na(hgnc_symbol, "."))
plot <- lcpm.DE %>%
filter(identifier == target) %>%
mutate(SSgroup.virus.sac = fct_relevel(SSgroup.virus.sac, "LOW", "MODERATE", "HIGH")) %>%
ggplot(aes(x = SSgroup.virus.sac, y = lcpm)) +
facet_grid(. ~ tmpID, scales = "free", space = "free") +
ylab("Log2(Counts per million)") +
xlab("Shedding Group") +
scale_fill_grey(start = 0.35, end = 1) +
geom_point(position = position_dodge(width=0.75), aes(group = group), show.legend = FALSE) +
geom_boxplot(alpha = 0.5) +
geom_label_repel(aes(label = bird, group = group, fill = NULL), position = position_dodge(width=0.75), show.legend=FALSE) +
theme_classic() +
labs(title = paste0("I2: ", target, " - ", annot.target[1,2])) +
theme(legend.title = element_blank())
print(plot)
}
for(target in sort(unique(dt.tib.I2$gene))) {
aprioriPlotting(target)
}
ns denotes non-significant genes for each comparison and numerical values are the log(fold count) difference
tmp1a <- tmp1 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "LvM.I1")
tmp2a <- tmp2 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "MvH.I1")
tmp3a <- tmp3 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "LvH.I1")
tmp4a <- tmp4 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "LvM.I2")
tmp5a <- tmp5 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "MvH.I2")
tmp6a <- tmp6 %>% select(ensembl_gene_id, adj.P.Val, gene_biotype, logFC, hgnc_symbol, description) %>% mutate(comp = "LvH.I2")
bind_rows(tmp1a, tmp2a, tmp3a, tmp4a, tmp5a, tmp6a) %>%
select(-description) %>%
filter(ensembl_gene_id %in% dt.tib$gene) %>%
mutate(logFoldCount = ifelse(adj.P.Val < 0.10, round(logFC, 2), "ns")) %>%
select(-adj.P.Val, -logFC, -gene_biotype) %>%
pivot_wider(names_from = comp, values_from = logFoldCount) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
ensembl_gene_id | hgnc_symbol | LvM.I1 | MvH.I1 | LvH.I1 | LvM.I2 | MvH.I2 | LvH.I2 |
---|---|---|---|---|---|---|---|
ENSAPLG00020007325 | NA | -3.72 | ns | ns | ns | ns | ns |
ENSAPLG00020005151 | NA | ns | ns | ns | -7.67 | 29.06 | 21.4 |
ENSAPLG00020002099 | SUSD2 | ns | ns | ns | ns | ns | 12.11 |
ENSAPLG00020012418 | LAMB3 | ns | ns | ns | ns | ns | 10.97 |
ENSAPLG00020001571 | NA | ns | ns | ns | ns | 16.95 | 13.54 |
ENSAPLG00020001757 | NA | ns | ns | ns | ns | 15.36 | 13.19 |
ENSAPLG00020001436 | CPO | ns | ns | ns | ns | 13.76 | 11.89 |
ENSAPLG00020016143 | PCK1 | ns | ns | ns | ns | ns | 11.08 |
ENSAPLG00020013723 | NA | ns | ns | ns | ns | ns | 11.33 |
ENSAPLG00020016534 | NA | ns | ns | ns | ns | ns | 9.26 |
ENSAPLG00020015167 | MME | ns | ns | ns | ns | ns | 8.45 |
ENSAPLG00020009971 | NA | ns | ns | ns | ns | 16.15 | 12.97 |
ENSAPLG00020005323 | PLB1 | ns | ns | ns | ns | ns | 11.28 |
ENSAPLG00020009050 | NA | ns | ns | ns | ns | ns | 10.98 |
ENSAPLG00020003693 | NA | ns | ns | ns | ns | ns | 8.58 |
ENSAPLG00020000462 | SULT1C3 | ns | ns | ns | ns | 16.51 | 12.52 |
ENSAPLG00020001772 | NA | ns | ns | ns | ns | 23.22 | 16.33 |
ENSAPLG00020006634 | SLC10A2 | ns | ns | ns | ns | 22.35 | 19.58 |
ENSAPLG00020016544 | ACE2 | ns | ns | ns | ns | ns | 10.76 |
ENSAPLG00020005311 | SLC3A1 | ns | ns | ns | ns | ns | 8.97 |
ENSAPLG00020005022 | ADGRG7 | ns | ns | ns | ns | ns | 9.42 |
ENSAPLG00020008901 | PEPD | ns | ns | ns | ns | ns | 9.27 |
ENSAPLG00020009556 | CDKN2A | ns | ns | ns | ns | ns | 8.93 |
ENSAPLG00020008627 | NQO1 | ns | ns | ns | ns | 19.74 | 15.84 |
ENSAPLG00020004729 | HKDC1 | ns | ns | ns | ns | ns | 8.68 |
ENSAPLG00020004842 | NA | ns | ns | ns | 9.84 | ns | ns |
ENSAPLG00020010989 | NA | ns | ns | ns | ns | ns | 10.23 |
ENSAPLG00020001209 | APOB | ns | ns | ns | ns | 14.58 | 13.03 |
ENSAPLG00020003190 | SLC5A1 | ns | ns | ns | ns | ns | 11.4 |
ENSAPLG00020013029 | NA | ns | ns | ns | ns | ns | 9.18 |
ENSAPLG00020007419 | DPEP1 | ns | ns | ns | ns | ns | 10.13 |
ENSAPLG00020017883 | XPNPEP2 | ns | ns | ns | ns | ns | 8.47 |
ENSAPLG00020013655 | ENTPD5 | ns | ns | ns | ns | ns | 9.2 |
ENSAPLG00020000801 | NA | ns | ns | ns | ns | ns | 8.32 |
ENSAPLG00020007676 | NA | ns | ns | ns | ns | ns | 8.67 |
ENSAPLG00020007551 | NA | ns | ns | ns | ns | ns | 10.43 |
ENSAPLG00020011928 | NA | ns | ns | ns | ns | ns | 12.34 |
ENSAPLG00020006270 | NA | ns | ns | ns | ns | ns | 8.75 |
ENSAPLG00020017864 | NA | ns | ns | ns | ns | ns | 8.77 |
ENSAPLG00020009266 | GDA | ns | ns | ns | ns | ns | 11.15 |
ENSAPLG00020003980 | NA | ns | ns | ns | ns | ns | 16.09 |
ENSAPLG00020014973 | AQP4 | ns | ns | ns | ns | ns | 12.72 |
ENSAPLG00020008932 | SLC5A12 | ns | ns | ns | ns | 17.05 | 14.69 |
ENSAPLG00020008682 | ALDOB | ns | ns | ns | ns | 14.9 | 11.94 |
ENSAPLG00020000944 | TMEM37 | ns | ns | ns | ns | ns | 8.19 |
ENSAPLG00020004413 | AQP8 | ns | ns | ns | ns | ns | 33.87 |
ENSAPLG00020015106 | CYP4F8 | ns | ns | ns | ns | ns | 9.46 |
ENSAPLG00020004241 | NA | ns | ns | ns | ns | 16.32 | 14.36 |
ENSAPLG00020000579 | NA | ns | ns | ns | ns | ns | 8.72 |
ENSAPLG00020017868 | NA | ns | ns | ns | ns | ns | 13.81 |
ENSAPLG00020003684 | NA | ns | ns | ns | ns | 21 | 15.78 |
ENSAPLG00020013926 | OLFM4 | ns | ns | ns | ns | ns | -10.08 |
ENSAPLG00020018096 | SLC2A5 | ns | ns | ns | ns | ns | 8.96 |
ENSAPLG00020000128 | SERPINB1 | ns | ns | ns | ns | ns | 9.37 |
ENSAPLG00020005067 | NA | ns | ns | ns | ns | ns | 13.41 |
ENSAPLG00020005597 | KCNJ15 | ns | ns | ns | ns | ns | 8.99 |
ENSAPLG00020017448 | LGALS3 | ns | ns | ns | ns | ns | 10.15 |
ENSAPLG00020008527 | F2RL1 | ns | ns | ns | ns | ns | 9.86 |
ENSAPLG00020015547 | NA | ns | ns | ns | ns | 20.22 | 17.16 |
ENSAPLG00020005500 | NR0B2 | ns | ns | ns | ns | ns | 8.56 |
ENSAPLG00020000836 | NA | ns | ns | ns | ns | 19.54 | 16 |
ENSAPLG00020011820 | NA | ns | ns | ns | ns | ns | 9.1 |
ENSAPLG00020007487 | NA | ns | ns | ns | ns | ns | 10.49 |
ENSAPLG00020013900 | NA | ns | ns | ns | ns | 25.22 | 22.86 |
ENSAPLG00020017865 | NA | ns | ns | ns | ns | ns | 8.83 |
ENSAPLG00020007413 | NA | ns | ns | ns | ns | ns | 12 |
ENSAPLG00020008194 | NA | ns | ns | ns | ns | ns | 9.66 |
ENSAPLG00020011484 | NA | ns | ns | ns | ns | ns | 8.6 |
ENSAPLG00020016671 | NA | ns | ns | ns | ns | -17.69 | -12.91 |
ENSAPLG00020006372 | CALB1 | ns | ns | ns | ns | 22.87 | 18.72 |
ENSAPLG00020000985 | KY | ns | ns | ns | ns | ns | 10.98 |
ENSAPLG00020007294 | NA | ns | ns | ns | ns | 22.15 | 18.51 |
ENSAPLG00020001254 | NA | ns | ns | ns | ns | ns | 14.54 |
ENSAPLG00020013906 | NA | ns | ns | ns | ns | 26.56 | 24.64 |
ENSAPLG00020007723 | NA | ns | ns | ns | ns | ns | 8.67 |
ENSAPLG00020010330 | NA | ns | ns | ns | ns | ns | -8.52 |
ENSAPLG00020009562 | ACOT12 | ns | ns | ns | ns | ns | 15.92 |
ENSAPLG00020005630 | NA | ns | ns | ns | ns | ns | 8.19 |
ENSAPLG00020003187 | SLC44A2 | ns | ns | ns | ns | ns | 9.99 |
ENSAPLG00020016235 | SLC13A1 | ns | ns | ns | ns | ns | 12.61 |
ENSAPLG00020008862 | NR4A3 | ns | ns | ns | ns | -20.64 | -16.85 |
ENSAPLG00020013917 | NA | ns | ns | ns | ns | ns | 21.96 |
ENSAPLG00020016406 | PCSK9 | ns | ns | ns | ns | ns | 10.85 |
ENSAPLG00020008172 | NA | ns | ns | ns | ns | ns | 9.45 |
ENSAPLG00020003114 | TKFC | ns | ns | ns | ns | 13.71 | 10.34 |
ENSAPLG00020003094 | NA | ns | ns | ns | ns | -15.89 | -10.9 |
ENSAPLG00020004137 | NA | ns | ns | ns | ns | ns | -15.59 |
ENSAPLG00020004389 | DDX47 | ns | ns | ns | ns | ns | 8.59 |
ENSAPLG00020003497 | KLF4 | ns | ns | ns | ns | ns | 10.02 |
ENSAPLG00020017346 | PIPOX | ns | ns | ns | ns | ns | 23.87 |
ENSAPLG00020008534 | SLCO4A1 | ns | ns | ns | ns | ns | 9.67 |
ENSAPLG00020000599 | NA | ns | ns | ns | ns | ns | 9.15 |
ENSAPLG00020003474 | DNAJC22 | ns | ns | ns | ns | ns | 14.7 |
ENSAPLG00020008855 | NA | ns | ns | ns | ns | ns | -33.28 |
ENSAPLG00020011196 | NA | ns | ns | ns | ns | ns | 35.03 |
ENSAPLG00020002652 | NA | ns | ns | ns | ns | ns | 10.95 |
ENSAPLG00020017229 | SLC6A4 | ns | ns | ns | ns | ns | 9.74 |
ENSAPLG00020004558 | NA | ns | ns | ns | ns | ns | 9.41 |
ENSAPLG00020007890 | NA | ns | ns | ns | -7.54 | 25.01 | 17.47 |
ENSAPLG00020015505 | NA | ns | ns | ns | ns | ns | -9.35 |
ENSAPLG00020013563 | SQLE | ns | ns | ns | ns | ns | 11.17 |
ENSAPLG00020012578 | CREB3L3 | ns | ns | ns | ns | ns | 11.02 |
ENSAPLG00020002747 | NA | ns | ns | ns | ns | ns | -24.64 |
ENSAPLG00020007878 | B3GALT5 | ns | ns | ns | -6.66 | 20.19 | 13.53 |
ENSAPLG00020004812 | NPC1L1 | ns | ns | ns | ns | ns | 8.98 |
ENSAPLG00020004008 | NA | ns | ns | ns | ns | ns | 18.56 |
ENSAPLG00020004098 | NA | ns | ns | ns | ns | ns | 18.75 |
ENSAPLG00020008569 | MFSD4B | ns | ns | ns | ns | ns | 8.8 |
ENSAPLG00020017400 | LTF | ns | ns | ns | 8.36 | -15.22 | ns |
ENSAPLG00020010722 | DUOX2 | ns | ns | ns | -6.19 | 27.45 | 21.26 |
ENSAPLG00020007929 | PCP4 | ns | ns | ns | ns | ns | -8.45 |
ENSAPLG00020006588 | S100A13 | ns | ns | ns | ns | ns | -12.82 |
ENSAPLG00020000169 | INSIG1 | ns | ns | ns | ns | ns | 8.91 |
ENSAPLG00020017133 | NA | ns | ns | ns | ns | ns | -8.36 |
ENSAPLG00020012336 | NA | ns | ns | ns | ns | ns | -9.98 |
ENSAPLG00020006537 | S100A12 | ns | ns | ns | ns | -30.3 | -23 |
ENSAPLG00020015804 | APOA4 | ns | ns | ns | ns | ns | 17.14 |
ENSAPLG00020000876 | MSMO1 | ns | ns | ns | ns | ns | 9.87 |
ENSAPLG00020005335 | NA | ns | ns | ns | ns | ns | -16.89 |
ENSAPLG00020003263 | NA | ns | ns | ns | ns | ns | 13.02 |
ENSAPLG00020000190 | NA | ns | ns | ns | ns | ns | -36.82 |
ENSAPLG00020014632 | SERPING1 | ns | ns | ns | ns | ns | -19.93 |
ENSAPLG00020014118 | MRPS23 | ns | ns | ns | ns | ns | -8.86 |
ENSAPLG00020004059 | NA | ns | ns | ns | ns | ns | 13.17 |
ENSAPLG00020008356 | SLC2A2 | ns | ns | ns | ns | 41.41 | 31.4 |
ENSAPLG00020017609 | NA | ns | ns | ns | ns | ns | 12.31 |
ENSAPLG00020007966 | NA | ns | ns | ns | ns | -41.95 | -33.71 |
ENSAPLG00020014477 | NA | ns | ns | ns | ns | ns | -9.93 |
ENSAPLG00020015261 | NA | ns | ns | ns | ns | -14.74 | -12.14 |
ENSAPLG00020014557 | SCARNA1 | ns | ns | ns | ns | ns | -15.68 |
ENSAPLG00020016540 | NA | ns | ns | ns | ns | -36.34 | -29.96 |
ENSAPLG00020003062 | NA | ns | ns | ns | ns | ns | -13.1 |
ENSAPLG00020007013 | NA | ns | ns | ns | ns | ns | 14.69 |
ENSAPLG00020010278 | RPL29 | ns | ns | ns | ns | ns | -10.61 |
ENSAPLG00020017598 | LECT2 | ns | ns | ns | ns | ns | -9.95 |
ENSAPLG00020007861 | NA | ns | ns | ns | ns | ns | -22.2 |
bind_rows(tmp1a, tmp2a, tmp3a, tmp4a, tmp5a, tmp6a) %>%
select(-comp, -adj.P.Val, -logFC) %>%
filter(ensembl_gene_id %in% dt.tib$gene) %>%
distinct(.) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
ensembl_gene_id | gene_biotype | hgnc_symbol | description |
---|---|---|---|
ENSAPLG00020007325 | protein_coding | NA | NA |
ENSAPLG00020005151 | protein_coding | NA | NA |
ENSAPLG00020002099 | protein_coding | SUSD2 | sushi domain containing 2 [Source:HGNC Symbol;Acc:HGNC:30667] |
ENSAPLG00020012418 | protein_coding | LAMB3 | laminin subunit beta 3 [Source:HGNC Symbol;Acc:HGNC:6490] |
ENSAPLG00020001571 | protein_coding | NA | acyl-coenzyme A amino acid N-acyltransferase 2 [Source:NCBI gene;Acc:101797844] |
ENSAPLG00020001757 | protein_coding | NA | NA |
ENSAPLG00020001436 | protein_coding | CPO | carboxypeptidase O [Source:HGNC Symbol;Acc:HGNC:21011] |
ENSAPLG00020016143 | protein_coding | PCK1 | phosphoenolpyruvate carboxykinase 1 [Source:NCBI gene;Acc:101793637] |
ENSAPLG00020013723 | protein_coding | NA | NA |
ENSAPLG00020016534 | protein_coding | NA | guanylin-like [Source:NCBI gene;Acc:101803958] |
ENSAPLG00020015167 | protein_coding | MME | membrane metalloendopeptidase [Source:HGNC Symbol;Acc:HGNC:7154] |
ENSAPLG00020009971 | protein_coding | NA | NA |
ENSAPLG00020005323 | protein_coding | PLB1 | phospholipase B1 [Source:HGNC Symbol;Acc:HGNC:30041] |
ENSAPLG00020009050 | protein_coding | NA | receptor accessory protein 6 [Source:HGNC Symbol;Acc:HGNC:30078] |
ENSAPLG00020003693 | protein_coding | NA | NA |
ENSAPLG00020000462 | protein_coding | SULT1C3 | sulfotransferase 1C1 [Source:NCBI gene;Acc:101797216] |
ENSAPLG00020001772 | protein_coding | NA | NA |
ENSAPLG00020006634 | protein_coding | SLC10A2 | solute carrier family 10 member 2 [Source:HGNC Symbol;Acc:HGNC:10906] |
ENSAPLG00020016544 | protein_coding | ACE2 | angiotensin I converting enzyme 2 [Source:HGNC Symbol;Acc:HGNC:13557] |
ENSAPLG00020005311 | protein_coding | SLC3A1 | solute carrier family 3 member 1 [Source:HGNC Symbol;Acc:HGNC:11025] |
ENSAPLG00020005022 | protein_coding | ADGRG7 | adhesion G protein-coupled receptor G7 [Source:HGNC Symbol;Acc:HGNC:19241] |
ENSAPLG00020008901 | protein_coding | PEPD | peptidase D [Source:HGNC Symbol;Acc:HGNC:8840] |
ENSAPLG00020009556 | protein_coding | CDKN2A | cyclin-dependent kinase 4 inhibitor B-like [Source:NCBI gene;Acc:113840168] |
ENSAPLG00020008627 | protein_coding | NQO1 | NAD(P)H quinone dehydrogenase 1 [Source:HGNC Symbol;Acc:HGNC:2874] |
ENSAPLG00020004729 | protein_coding | HKDC1 | hexokinase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23302] |
ENSAPLG00020004842 | protein_coding | NA | NA |
ENSAPLG00020010989 | protein_coding | NA | NA |
ENSAPLG00020001209 | protein_coding | APOB | apolipoprotein B [Source:HGNC Symbol;Acc:HGNC:603] |
ENSAPLG00020003190 | protein_coding | SLC5A1 | solute carrier family 5 member 1 [Source:HGNC Symbol;Acc:HGNC:11036] |
ENSAPLG00020013029 | protein_coding | NA | p53 apoptosis effector related to PMP22 [Source:NCBI gene;Acc:101797297] |
ENSAPLG00020007419 | protein_coding | DPEP1 | dipeptidase 1 [Source:NCBI gene;Acc:101797901] |
ENSAPLG00020017883 | protein_coding | XPNPEP2 | X-prolyl aminopeptidase 2 [Source:HGNC Symbol;Acc:HGNC:12823] |
ENSAPLG00020013655 | protein_coding | ENTPD5 | ectonucleoside triphosphate diphosphohydrolase 5 (inactive) [Source:HGNC Symbol;Acc:HGNC:3367] |
ENSAPLG00020000801 | protein_coding | NA | NA |
ENSAPLG00020007676 | protein_coding | NA | NA |
ENSAPLG00020007551 | protein_coding | NA | NA |
ENSAPLG00020011928 | protein_coding | NA | NA |
ENSAPLG00020006270 | protein_coding | NA | NA |
ENSAPLG00020017864 | protein_coding | NA | NA |
ENSAPLG00020009266 | protein_coding | GDA | guanine deaminase [Source:HGNC Symbol;Acc:HGNC:4212] |
ENSAPLG00020003980 | protein_coding | NA | histone H4 [Source:NCBI gene;Acc:110351447] |
ENSAPLG00020014973 | protein_coding | AQP4 | aquaporin 4 [Source:HGNC Symbol;Acc:HGNC:637] |
ENSAPLG00020008932 | protein_coding | SLC5A12 | solute carrier family 5 member 12 [Source:HGNC Symbol;Acc:HGNC:28750] |
ENSAPLG00020008682 | protein_coding | ALDOB | aldolase, fructose-bisphosphate B [Source:NCBI gene;Acc:101796090] |
ENSAPLG00020000944 | protein_coding | TMEM37 | transmembrane protein 37 [Source:NCBI gene;Acc:101805462] |
ENSAPLG00020004413 | protein_coding | AQP8 | aquaporin 8 [Source:HGNC Symbol;Acc:HGNC:642] |
ENSAPLG00020015106 | protein_coding | CYP4F8 | cytochrome P450 family 4 subfamily F member 8 [Source:HGNC Symbol;Acc:HGNC:2648] |
ENSAPLG00020004241 | protein_coding | NA | NA |
ENSAPLG00020000579 | protein_coding | NA | NA |
ENSAPLG00020017868 | protein_coding | NA | NA |
ENSAPLG00020003684 | protein_coding | NA | NA |
ENSAPLG00020013926 | protein_coding | OLFM4 | olfactomedin 4 [Source:HGNC Symbol;Acc:HGNC:17190] |
ENSAPLG00020018096 | protein_coding | SLC2A5 | solute carrier family 2, facilitated glucose transporter member 5 [Source:NCBI gene;Acc:101804741] |
ENSAPLG00020000128 | protein_coding | SERPINB1 | serpin family B member 1 [Source:NCBI gene;Acc:101799613] |
ENSAPLG00020005067 | pseudogene | NA | NA |
ENSAPLG00020005597 | protein_coding | KCNJ15 | potassium inwardly rectifying channel subfamily J member 15 [Source:NCBI gene;Acc:101795505] |
ENSAPLG00020017448 | protein_coding | LGALS3 | galectin 3 [Source:HGNC Symbol;Acc:HGNC:6563] |
ENSAPLG00020008527 | protein_coding | F2RL1 | F2R like trypsin receptor 1 [Source:HGNC Symbol;Acc:HGNC:3538] |
ENSAPLG00020015547 | rRNA | NA | NA |
ENSAPLG00020005500 | protein_coding | NR0B2 | nuclear receptor subfamily 0 group B member 2 [Source:NCBI gene;Acc:101799243] |
ENSAPLG00020000836 | protein_coding | NA | NA |
ENSAPLG00020011820 | lncRNA | NA | NA |
ENSAPLG00020007487 | protein_coding | NA | C-factor [Source:NCBI gene;Acc:101802025] |
ENSAPLG00020013900 | protein_coding | NA | NA |
ENSAPLG00020017865 | protein_coding | NA | NA |
ENSAPLG00020007413 | protein_coding | NA | NA |
ENSAPLG00020008194 | protein_coding | NA | NA |
ENSAPLG00020011484 | protein_coding | NA | NA |
ENSAPLG00020016671 | protein_coding | NA | Metallothionein [Source:UniProtKB/Swiss-Prot;Acc:P68494] |
ENSAPLG00020006372 | protein_coding | CALB1 | calbindin 1 [Source:NCBI gene;Acc:101802006] |
ENSAPLG00020000985 | protein_coding | KY | kyphoscoliosis peptidase [Source:HGNC Symbol;Acc:HGNC:26576] |
ENSAPLG00020007294 | protein_coding | NA | NA |
ENSAPLG00020001254 | protein_coding | NA | NA |
ENSAPLG00020013906 | protein_coding | NA | NA |
ENSAPLG00020007723 | protein_coding | NA | NA |
ENSAPLG00020010330 | protein_coding | NA | NA |
ENSAPLG00020009562 | protein_coding | ACOT12 | acyl-CoA thioesterase 12 [Source:HGNC Symbol;Acc:HGNC:24436] |
ENSAPLG00020005630 | pseudogene | NA | NA |
ENSAPLG00020003187 | protein_coding | SLC44A2 | solute carrier family 44 member 2 [Source:HGNC Symbol;Acc:HGNC:17292] |
ENSAPLG00020016235 | protein_coding | SLC13A1 | solute carrier family 13 member 1 [Source:HGNC Symbol;Acc:HGNC:10916] |
ENSAPLG00020008862 | protein_coding | NR4A3 | nuclear receptor subfamily 4 group A member 3 [Source:HGNC Symbol;Acc:HGNC:7982] |
ENSAPLG00020013917 | protein_coding | NA | NA |
ENSAPLG00020016406 | protein_coding | PCSK9 | proprotein convertase subtilisin/kexin type 9 [Source:HGNC Symbol;Acc:HGNC:20001] |
ENSAPLG00020008172 | protein_coding | NA | NA |
ENSAPLG00020003114 | protein_coding | TKFC | triokinase and FMN cyclase [Source:HGNC Symbol;Acc:HGNC:24552] |
ENSAPLG00020003094 | lncRNA | NA | NA |
ENSAPLG00020004137 | protein_coding | NA | NA |
ENSAPLG00020004389 | protein_coding | DDX47 | DEAD-box helicase 47 [Source:HGNC Symbol;Acc:HGNC:18682] |
ENSAPLG00020003497 | protein_coding | KLF4 | Kruppel like factor 4 [Source:HGNC Symbol;Acc:HGNC:6348] |
ENSAPLG00020017346 | protein_coding | PIPOX | pipecolic acid and sarcosine oxidase [Source:HGNC Symbol;Acc:HGNC:17804] |
ENSAPLG00020008534 | protein_coding | SLCO4A1 | solute carrier organic anion transporter family member 4A1 [Source:HGNC Symbol;Acc:HGNC:10953] |
ENSAPLG00020000599 | protein_coding | NA | NA |
ENSAPLG00020003474 | protein_coding | DNAJC22 | DnaJ heat shock protein family (Hsp40) member C22 [Source:HGNC Symbol;Acc:HGNC:25802] |
ENSAPLG00020008855 | protein_coding | NA | NA |
ENSAPLG00020011196 | protein_coding | NA | NA |
ENSAPLG00020002652 | protein_coding | NA | gamma-glutamyltransferase 1 [Source:NCBI gene;Acc:101799199] |
ENSAPLG00020017229 | protein_coding | SLC6A4 | solute carrier family 6 member 4 [Source:HGNC Symbol;Acc:HGNC:11050] |
ENSAPLG00020004558 | protein_coding | NA | NA |
ENSAPLG00020007890 | lncRNA | NA | NA |
ENSAPLG00020015505 | protein_coding | NA | NA |
ENSAPLG00020013563 | protein_coding | SQLE | squalene epoxidase [Source:HGNC Symbol;Acc:HGNC:11279] |
ENSAPLG00020012578 | protein_coding | CREB3L3 | cAMP responsive element binding protein 3 like 3 [Source:HGNC Symbol;Acc:HGNC:18855] |
ENSAPLG00020002747 | snoRNA | NA | NA |
ENSAPLG00020007878 | protein_coding | B3GALT5 | beta-1,3-galactosyltransferase 5 [Source:HGNC Symbol;Acc:HGNC:920] |
ENSAPLG00020004812 | protein_coding | NPC1L1 | NPC1 like intracellular cholesterol transporter 1 [Source:HGNC Symbol;Acc:HGNC:7898] |
ENSAPLG00020004008 | protein_coding | NA | histone H4 [Source:NCBI gene;Acc:110351447] |
ENSAPLG00020004098 | protein_coding | NA | NA |
ENSAPLG00020008569 | protein_coding | MFSD4B | major facilitator superfamily domain containing 4B [Source:HGNC Symbol;Acc:HGNC:21053] |
ENSAPLG00020017400 | protein_coding | LTF | transferrin [Source:NCBI gene;Acc:101795303] |
ENSAPLG00020010722 | protein_coding | DUOX2 | dual oxidase 2 [Source:HGNC Symbol;Acc:HGNC:13273] |
ENSAPLG00020007929 | protein_coding | PCP4 | Purkinje cell protein 4 [Source:HGNC Symbol;Acc:HGNC:8742] |
ENSAPLG00020006588 | protein_coding | S100A13 | S100 calcium binding protein A13 [Source:HGNC Symbol;Acc:HGNC:10490] |
ENSAPLG00020000169 | protein_coding | INSIG1 | insulin induced gene 1 [Source:HGNC Symbol;Acc:HGNC:6083] |
ENSAPLG00020017133 | protein_coding | NA | 60S ribosomal protein L36a [Source:NCBI gene;Acc:101801033] |
ENSAPLG00020012336 | snoRNA | NA | small nucleolar RNA, C/D box 94 [Source:HGNC Symbol;Acc:HGNC:32756] |
ENSAPLG00020006537 | protein_coding | S100A12 | S100 calcium binding protein A12 [Source:HGNC Symbol;Acc:HGNC:10489] |
ENSAPLG00020015804 | protein_coding | APOA4 | apolipoprotein A4 [Source:HGNC Symbol;Acc:HGNC:602] |
ENSAPLG00020000876 | protein_coding | MSMO1 | methylsterol monooxygenase 1 [Source:NCBI gene;Acc:101804996] |
ENSAPLG00020005335 | protein_coding | NA | NA |
ENSAPLG00020003263 | protein_coding | NA | NA |
ENSAPLG00020000190 | protein_coding | NA | NA |
ENSAPLG00020014632 | protein_coding | SERPING1 | serpin family G member 1 [Source:HGNC Symbol;Acc:HGNC:1228] |
ENSAPLG00020014118 | protein_coding | MRPS23 | mitochondrial ribosomal protein S23 [Source:HGNC Symbol;Acc:HGNC:14509] |
ENSAPLG00020004059 | protein_coding | NA | NA |
ENSAPLG00020008356 | protein_coding | SLC2A2 | solute carrier family 2 member 2 [Source:HGNC Symbol;Acc:HGNC:11006] |
ENSAPLG00020017609 | protein_coding | NA | solute carrier family 6 member 14 [Source:NCBI gene;Acc:101802830] |
ENSAPLG00020007966 | lncRNA | NA | NA |
ENSAPLG00020014477 | protein_coding | NA | NA |
ENSAPLG00020015261 | protein_coding | NA | podocalyxin like [Source:HGNC Symbol;Acc:HGNC:9171] |
ENSAPLG00020014557 | scaRNA | SCARNA1 | small Cajal body-specific RNA 1 [Source:HGNC Symbol;Acc:HGNC:32555] |
ENSAPLG00020016540 | lncRNA | NA | NA |
ENSAPLG00020003062 | lncRNA | NA | NA |
ENSAPLG00020007013 | protein_coding | NA | NA |
ENSAPLG00020010278 | protein_coding | RPL29 | ribosomal protein L29 [Source:HGNC Symbol;Acc:HGNC:10331] |
ENSAPLG00020017598 | protein_coding | LECT2 | leukocyte cell derived chemotaxin 2 [Source:HGNC Symbol;Acc:HGNC:6550] |
ENSAPLG00020007861 | protein_coding | NA | ribosomal protein L23 [Source:NCBI gene;Acc:101793494] |
de.entrez <- annot %>% filter(ensembl_gene_id %in% dt.tib$gene) %>% na.omit(entrezgene_id)
entrez.universe <- annot %>% na.omit(entrezgene_id)
K <- kegga(de.entrez$entrezgene_id, universe = entrez.universe$entrezgene_id, species.KEGG = "apla") %>%
as_tibble(rownames = NA) %>%
rownames_to_column("PathwayID") %>%
filter(P.DE < 0.05) %>%
arrange(P.DE)
keggList <- getGeneKEGGLinks(species.KEGG = "apla") %>%
as_tibble() %>%
rename("entrezgene_id" = GeneID)
keggGenes = data.frame()
for (path in nrow(K)){
procPath <- filter(keggList, entrezgene_id %in% de.entrez$entrezgene_id)
df <- data.frame(procPath)
keggGenes <- rbind(keggGenes, df)
}
inner_join(keggGenes, K) %>%
as_tibble() %>%
mutate(entrezgene_id = as.numeric(entrezgene_id)) %>%
left_join(annot) %>%
select(Pathway, PathwayID, N, DE, P.DE, ensembl_gene_id, hgnc_symbol, entrezgene_id) %>%
kable() %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
Pathway | PathwayID | N | DE | P.DE | ensembl_gene_id | hgnc_symbol | entrezgene_id |
---|---|---|---|---|---|---|---|
Glycolysis / Gluconeogenesis | path:apla00010 | 14 | 2 | 0.0011323 | ENSAPLG00020016143 | PCK1 | 101793637 |
Glycolysis / Gluconeogenesis | path:apla00010 | 14 | 2 | 0.0011323 | ENSAPLG00020008682 | ALDOB | 101796090 |
Citrate cycle (TCA cycle) | path:apla00020 | 9 | 1 | 0.0330012 | ENSAPLG00020016143 | PCK1 | 101793637 |
Pentose phosphate pathway | path:apla00030 | 9 | 1 | 0.0330012 | ENSAPLG00020008682 | ALDOB | 101796090 |
Fructose and mannose metabolism | path:apla00051 | 10 | 1 | 0.0366053 | ENSAPLG00020008682 | ALDOB | 101796090 |
Steroid biosynthesis | path:apla00100 | 5 | 1 | 0.0184602 | ENSAPLG00020000876 | MSMO1 | 101804996 |
Pyruvate metabolism | path:apla00620 | 8 | 1 | 0.0293847 | ENSAPLG00020016143 | PCK1 | 101793637 |
FoxO signaling pathway | path:apla04068 | 31 | 2 | 0.0055831 | ENSAPLG00020016143 | PCK1 | 101793637 |
FoxO signaling pathway | path:apla04068 | 31 | 2 | 0.0055831 | ENSAPLG00020009556 | CDKN2A | 113840168 |
Ferroptosis | path:apla04216 | 11 | 1 | 0.0401970 | ENSAPLG00020017400 | LTF | 101795303 |