suppressPackageStartupMessages(library(tidyverse))
## Warning: package 'ggplot2' was built under R version 4.2.3
## Warning: package 'tidyr' was built under R version 4.2.3
## Warning: package 'readr' was built under R version 4.2.3
## Warning: package 'dplyr' was built under R version 4.2.3
## Warning: package 'stringr' was built under R version 4.2.3
library(patchwork)
## Warning: package 'patchwork' was built under R version 4.2.3
devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')
## ℹ Loading myUtilities
Settings
data_dir <- '/Volumes/Mitsu_NGS_3/METTL2A/'
wd <- "~/Google Drive/My Drive/Analysis/METTL2A/"
setwd(wd)
figdir <- paste0(wd, 'Figures/Shortread/Stringtie_tximport_DESeq2_Gprofiler/')
dir.create(figdir, recursive = TRUE)
## Warning in dir.create(figdir, recursive = TRUE): '/Users/s-mitsutomi/Google
## Drive/My
## Drive/Analysis/METTL2A/Figures/Shortread/Stringtie_tximport_DESeq2_Gprofiler'
## already exists
tabledir <- paste0(wd, 'Tables/Shortread/Stringtie_tximport_DESeq2_Gprofiler/')
theme_set(
theme_classic(base_size = 7) +
theme(legend.position = 'bottom')
)
Functions
gprofiler_gost <- function(ordered = TRUE, highlight = FALSE) {
gostres <-
gprofiler2::gost(
query = list(
'up' = str_remove(shortread_stringtie_txi_DESeq2_commonup$gene_id,
'[.][0-9]+$'),
'down' = str_remove(shortread_stringtie_txi_DESeq2_commondown$gene_id,
'[.][0-9]+$')
),
organism = 'hsapiens',
ordered_query = ordered,
significant = TRUE,
highlight = highlight,
#multi_query = TRUE
)
gostres$result |>
as_tibble()
}
calc_signed_log10p <- function(df) {
df |>
mutate(
signed_log10p =
ifelse(query == 'up', -log10(p_value), log10(p_value))
) |>
arrange(p_value)
}
quickview_gprofiler_result <- function(df) {
for (gp_source in unique(df$source)) {
df |>
filter(source == gp_source) |>
select(query, p_value, term_name, source) |>
head(20) |>
print()
}
}
# If parent has smaller pvalue, drop the term
simplify_terms <- function(df) {
term_ranks <-
df |>
arrange(p_value) |>
select(rank, query, term_id) |>
dplyr::rename(
parent_term_rank = rank, parent_term_id = term_id
)
df |>
arrange(p_value) |>
select(rank, query, signed_log10p, source, term_name,
term_id, source_order, parents) |>
unnest_longer(col = parents) |>
dplyr::rename(parent_term_id = parents) |>
left_join(term_ranks) |>
group_by(rank) |>
filter(is.na(parent_term_rank) | rank == min(parent_term_rank)) |>
ungroup() |>
select(-starts_with('parent_')) |>
distinct()
}
dual_barplot_theme <- function() {
theme_classic(base_size = 7) +
theme(
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.line.y = element_blank(),
axis.ticks.y = element_blank()
)
}
plot_dual_barplot_each_source <- function(.source, df) {
barplot_basename <- paste0(
df |> substitute() |> deparse(), '_', .source, '_dualbarplot'
)
df_source_simplified <-
df |>
filter(source == .source) |>
rownames_to_column(var = 'rank')
# |>
# simplify_terms()
#
yrange_max <- df_source_simplified$signed_log10p |> abs() |> max(na.rm = TRUE)
p1 <-
df_source_simplified |>
select(query, signed_log10p, term_name, source) |>
#filter(source == 'GO:BP') |>
filter(query == 'down') |>
head(10) |>
ggplot(aes(x = reorder(term_name, -signed_log10p),
y = signed_log10p, label = term_name)) +
geom_bar(stat = 'identity', fill = 'blue', alpha = .2) +
geom_text(hjust = 1, colour = 'black', y = -0.2, size = 7 * 0.36) +
scale_y_continuous(limits = c(-yrange_max, 0)) +
labs(title = .source) +
coord_flip() +
dual_barplot_theme()
p2 <-
df_source_simplified |>
select(query, signed_log10p, term_name, source) |>
#filter(source == 'GO:BP') |>
filter(query == 'up') |>
head(10) |>
ggplot(aes(x = reorder(term_name, signed_log10p),
y = signed_log10p, label = term_name)) +
geom_bar(stat = 'identity', fill = 'red', alpha = 0.2) +
geom_text(hjust = 0, colour = 'black', y = 0.2, size = 7 * 0.36) +
scale_y_continuous(limits = c(0, yrange_max)) +
coord_flip() +
dual_barplot_theme()
dual_barplot <- p1 | p2
print(dual_barplot)
ggsave(
plot = dual_barplot,
filename = paste0(figdir, barplot_basename, '.pdf'),
width = 12, height = 6, units = 'cm',
)
}
Read data
shortread_stringtie_txi_DESeq2 <- read_tsv(
paste0(
wd,
#'Tables/Shortread/shortread_DESeq2_results_DRSm3C_DETinfo_2024-04-06.tsv'
'Tables/Shortread/shortread_stringtie_txi_DESeq2_DEG_methylation_2024-04-17.tsv.gz'
)
) |>
arrange(siMETTL2A_pvalue)
## Rows: 12974 Columns: 27
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (9): gene_name, gene_id, methylation, isUp, isDown, common_DEGs, gene_t...
## dbl (18): siMETTL2A_baseMean, siMETTL2A_log2FoldChange, siMETTL2A_lfcSE, siM...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
shortread_stringtie_txi_DESeq2
## # A tibble: 12,974 × 27
## gene_name siMETTL2A_baseMean siMETTL2A_log2FoldChange siMETTL2A_lfcSE
## <chr> <dbl> <dbl> <dbl>
## 1 LIPH 45984. 1.84 0.0597
## 2 ANGPTL2 4420. 1.92 0.0652
## 3 TMED4 36154. 1.28 0.0455
## 4 CPVL 34696. 1.71 0.0622
## 5 ANTXR2 31176. 1.83 0.0743
## 6 RNF26 8173. -1.28 0.0543
## 7 TOMM22 15243. 0.949 0.0418
## 8 PLAUR 20487. 2.32 0.107
## 9 ERBB3 14174. -1.05 0.0500
## 10 TSC22D1 24238. 0.876 0.0417
## # ℹ 12,964 more rows
## # ℹ 23 more variables: siMETTL2A_stat <dbl>, siMETTL2A_pvalue <dbl>,
## # siMETTL2A_padj <dbl>, siMETTL2A_G_baseMean <dbl>,
## # siMETTL2A_G_log2FoldChange <dbl>, siMETTL2A_G_lfcSE <dbl>,
## # siMETTL2A_G_stat <dbl>, siMETTL2A_G_pvalue <dbl>, siMETTL2A_G_padj <dbl>,
## # siMETTL2A_I_baseMean <dbl>, siMETTL2A_I_log2FoldChange <dbl>,
## # siMETTL2A_I_lfcSE <dbl>, siMETTL2A_I_stat <dbl>, …
Filter common DEGs
shortread_stringtie_txi_DESeq2_commonup <-
shortread_stringtie_txi_DESeq2 |>
filter(common_DEGs == 'up')
# filter(common_DETs == 'up')
shortread_stringtie_txi_DESeq2_commonup
## # A tibble: 1,685 × 27
## gene_name siMETTL2A_baseMean siMETTL2A_log2FoldChange siMETTL2A_lfcSE
## <chr> <dbl> <dbl> <dbl>
## 1 LIPH 45984. 1.84 0.0597
## 2 ANGPTL2 4420. 1.92 0.0652
## 3 TMED4 36154. 1.28 0.0455
## 4 CPVL 34696. 1.71 0.0622
## 5 ANTXR2 31176. 1.83 0.0743
## 6 TOMM22 15243. 0.949 0.0418
## 7 PLAUR 20487. 2.32 0.107
## 8 TSC22D1 24238. 0.876 0.0417
## 9 RNF149 16660. 1.67 0.0951
## 10 TRMT61A-DT 2523. 2.75 0.161
## # ℹ 1,675 more rows
## # ℹ 23 more variables: siMETTL2A_stat <dbl>, siMETTL2A_pvalue <dbl>,
## # siMETTL2A_padj <dbl>, siMETTL2A_G_baseMean <dbl>,
## # siMETTL2A_G_log2FoldChange <dbl>, siMETTL2A_G_lfcSE <dbl>,
## # siMETTL2A_G_stat <dbl>, siMETTL2A_G_pvalue <dbl>, siMETTL2A_G_padj <dbl>,
## # siMETTL2A_I_baseMean <dbl>, siMETTL2A_I_log2FoldChange <dbl>,
## # siMETTL2A_I_lfcSE <dbl>, siMETTL2A_I_stat <dbl>, …
shortread_stringtie_txi_DESeq2_commondown <-
shortread_stringtie_txi_DESeq2 |>
filter(common_DEGs == 'down')
shortread_stringtie_txi_DESeq2_commondown
## # A tibble: 1,805 × 27
## gene_name siMETTL2A_baseMean siMETTL2A_log2FoldChange siMETTL2A_lfcSE
## <chr> <dbl> <dbl> <dbl>
## 1 RNF26 8173. -1.28 0.0543
## 2 ERBB3 14174. -1.05 0.0500
## 3 PCNA 12488. -1.65 0.0789
## 4 HAUS1 2470. -1.49 0.0717
## 5 HMGB2 9558. -1.39 0.0746
## 6 SHCBP1 9012. -1.24 0.0715
## 7 BLMH 9459. -0.995 0.0574
## 8 CCNB2 3962. -1.90 0.110
## 9 ACADSB 984. -1.38 0.0813
## 10 TADA3 5293. -0.932 0.0584
## # ℹ 1,795 more rows
## # ℹ 23 more variables: siMETTL2A_stat <dbl>, siMETTL2A_pvalue <dbl>,
## # siMETTL2A_padj <dbl>, siMETTL2A_G_baseMean <dbl>,
## # siMETTL2A_G_log2FoldChange <dbl>, siMETTL2A_G_lfcSE <dbl>,
## # siMETTL2A_G_stat <dbl>, siMETTL2A_G_pvalue <dbl>, siMETTL2A_G_padj <dbl>,
## # siMETTL2A_I_baseMean <dbl>, siMETTL2A_I_log2FoldChange <dbl>,
## # siMETTL2A_I_lfcSE <dbl>, siMETTL2A_I_stat <dbl>, …
Enrichment analysis using gprofiler
gprofiler_result_ordered <-
gprofiler_gost(ordered = TRUE) |>
calc_signed_log10p()
gprofiler_result_ordered |>
export_tsv(outdir = tabledir, compression = 'gz')
##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/Shortread/Stringtie_tximport_DESeq2_Gprofiler/gprofiler_result_ordered_2024-07-30.tsv.gz
## # A tibble: 1,183 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 7.68e-60 4220 1805 631 0.350
## 2 down TRUE 3.08e-44 1276 1429 235 0.164
## 3 down TRUE 9.49e-44 1040 1760 234 0.133
## 4 down TRUE 1.80e-43 1819 1018 235 0.231
## 5 down TRUE 1.97e-40 635 1540 157 0.102
## 6 down TRUE 4.31e-39 281 1167 88 0.0754
## 7 down TRUE 6.50e-39 402 1302 107 0.0822
## 8 down TRUE 4.14e-38 5487 1805 693 0.384
## 9 down TRUE 6.82e-38 162 826 59 0.0714
## 10 down TRUE 2.27e-37 425 1711 128 0.0748
## # ℹ 1,173 more rows
## # ℹ 8 more variables: recall <dbl>, term_id <chr>, source <chr>,
## # term_name <chr>, effective_domain_size <int>, source_order <int>,
## # parents <list>, signed_log10p <dbl>
gprofiler_result_notordered <-
gprofiler_gost(ordered = FALSE) |>
calc_signed_log10p()
gprofiler_result_notordered |>
export_tsv(outdir = tabledir, compression = 'gz')
##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/Shortread/Stringtie_tximport_DESeq2_Gprofiler/gprofiler_result_notordered_2024-07-30.tsv.gz
## # A tibble: 3,083 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 3.14e-79 4220 1636 631 0.386
## 2 up TRUE 5.16e-68 12345 1404 1093 0.778
## 3 down TRUE 2.89e-67 12345 1636 1245 0.761
## 4 down TRUE 2.33e-56 5487 1636 693 0.424
## 5 down TRUE 3.91e-56 1819 1587 338 0.213
## 6 down TRUE 7.13e-56 7899 1141 1030 0.903
## 7 down TRUE 1.97e-54 1276 1587 269 0.170
## 8 down TRUE 1.24e-53 677 1094 211 0.193
## 9 down TRUE 4.13e-53 1040 1587 236 0.149
## 10 down TRUE 3.06e-52 16076 1687 1574 0.933
## # ℹ 3,073 more rows
## # ℹ 8 more variables: recall <dbl>, term_id <chr>, source <chr>,
## # term_name <chr>, effective_domain_size <int>, source_order <int>,
## # parents <list>, signed_log10p <dbl>
gprofiler_result_highlighted <-
gprofiler_gost(ordered = FALSE, highlight = TRUE) |>
calc_signed_log10p() |>
filter(highlighted == TRUE)
gprofiler_result_highlighted |>
export_tsv(outdir = tabledir, compression = 'gz')
##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/Shortread/Stringtie_tximport_DESeq2_Gprofiler/gprofiler_result_highlighted_2024-07-30.tsv.gz
## # A tibble: 61 × 16
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 3.14e-79 4220 1636 631 0.386
## 2 up TRUE 5.16e-68 12345 1404 1093 0.778
## 3 down TRUE 3.91e-56 1819 1587 338 0.213
## 4 down TRUE 4.13e-53 1040 1587 236 0.149
## 5 down TRUE 6.91e-44 14838 1631 1426 0.874
## 6 up TRUE 5.08e-36 14838 1391 1214 0.873
## 7 down TRUE 7.13e-31 656 1587 147 0.0926
## 8 down TRUE 4.97e-25 5758 1631 661 0.405
## 9 up TRUE 2.43e-23 4912 1328 477 0.359
## 10 down TRUE 1.29e-20 436 1636 97 0.0593
## # ℹ 51 more rows
## # ℹ 9 more variables: recall <dbl>, term_id <chr>, source <chr>,
## # term_name <chr>, effective_domain_size <int>, source_order <int>,
## # parents <list>, highlighted <lgl>, signed_log10p <dbl>
gprofiler_result_ordered
## # A tibble: 1,183 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 7.68e-60 4220 1805 631 0.350
## 2 down TRUE 3.08e-44 1276 1429 235 0.164
## 3 down TRUE 9.49e-44 1040 1760 234 0.133
## 4 down TRUE 1.80e-43 1819 1018 235 0.231
## 5 down TRUE 1.97e-40 635 1540 157 0.102
## 6 down TRUE 4.31e-39 281 1167 88 0.0754
## 7 down TRUE 6.50e-39 402 1302 107 0.0822
## 8 down TRUE 4.14e-38 5487 1805 693 0.384
## 9 down TRUE 6.82e-38 162 826 59 0.0714
## 10 down TRUE 2.27e-37 425 1711 128 0.0748
## # ℹ 1,173 more rows
## # ℹ 8 more variables: recall <dbl>, term_id <chr>, source <chr>,
## # term_name <chr>, effective_domain_size <int>, source_order <int>,
## # parents <list>, signed_log10p <dbl>
Briefly check gprofiler results grouped by source
quickview_gprofiler_result(gprofiler_result_ordered)
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 7.68e-60 nucleoplasm GO:CC
## 2 down 6.50e-39 chromosomal region GO:CC
## 3 down 4.14e-38 cytosol GO:CC
## 4 down 7.18e-34 chromosome GO:CC
## 5 down 3.30e-30 cytoplasm GO:CC
## 6 down 3.83e-30 membrane-enclosed lumen GO:CC
## 7 down 3.83e-30 organelle lumen GO:CC
## 8 down 3.83e-30 intracellular organelle lumen GO:CC
## 9 down 4.61e-30 nuclear lumen GO:CC
## 10 down 6.02e-27 chromosome, centromeric region GO:CC
## 11 down 4.24e-26 condensed chromosome GO:CC
## 12 down 4.36e-23 condensed chromosome, centromeric region GO:CC
## 13 down 7.84e-23 kinetochore GO:CC
## 14 up 1.43e-20 endomembrane system GO:CC
## 15 down 8.22e-20 microtubule cytoskeleton GO:CC
## 16 down 7.61e-19 nuclear chromosome GO:CC
## 17 down 1.42e-18 replication fork GO:CC
## 18 down 3.96e-18 spindle GO:CC
## 19 up 8.10e-18 vesicle GO:CC
## 20 down 5.05e-16 centrosome GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.08e-44 cell cycle process GO:BP
## 2 down 9.49e-44 DNA metabolic process GO:BP
## 3 down 1.80e-43 cell cycle GO:BP
## 4 down 1.97e-40 chromosome organization GO:BP
## 5 down 4.31e-39 DNA replication GO:BP
## 6 down 6.82e-38 DNA-templated DNA replication GO:BP
## 7 down 2.27e-37 chromosome segregation GO:BP
## 8 down 1.93e-35 DNA repair GO:BP
## 9 down 8.85e-35 mitotic cell cycle GO:BP
## 10 down 7.65e-33 mitotic cell cycle process GO:BP
## 11 down 3.39e-30 DNA damage response GO:BP
## 12 down 4.78e-29 sister chromatid segregation GO:BP
## 13 down 6.22e-29 mitotic sister chromatid segregation GO:BP
## 14 down 4.56e-26 nuclear chromosome segregation GO:BP
## 15 down 1.82e-25 cell division GO:BP
## 16 down 5.04e-25 regulation of cell cycle process GO:BP
## 17 down 9.09e-25 regulation of cell cycle GO:BP
## 18 down 2.67e-23 double-strand break repair GO:BP
## 19 down 4.93e-23 DNA recombination GO:BP
## 20 down 7.60e-23 recombinational repair GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 2.90e-23 Cell Cycle REAC
## 2 down 5.12e-22 Cell Cycle, Mitotic REAC
## 3 down 2.51e-17 DNA strand elongation REAC
## 4 down 2.18e-15 Activation of the pre-replicative complex REAC
## 5 down 5.78e-14 Cell Cycle Checkpoints REAC
## 6 down 3.62e-13 Mitotic G1 phase and G1/S transition REAC
## 7 down 4.71e-13 G1/S Transition REAC
## 8 down 6.44e-13 S Phase REAC
## 9 down 2.00e-12 Mitotic Prometaphase REAC
## 10 down 2.45e-11 Activation of ATR in response to replication stress REAC
## 11 down 2.91e-11 Synthesis of DNA REAC
## 12 down 1.36e-10 Resolution of Sister Chromatid Cohesion REAC
## 13 down 3.16e-10 Unwinding of DNA REAC
## 14 down 3.64e-10 Amplification of signal from unattached kinetochores… REAC
## 15 down 3.64e-10 Amplification of signal from the kinetochores REAC
## 16 down 1.58e- 9 Mitotic Spindle Checkpoint REAC
## 17 down 4.76e- 9 Mitotic Metaphase and Anaphase REAC
## 18 down 1.03e- 8 Mitotic Anaphase REAC
## 19 down 1.06e- 8 Telomere C-strand (Lagging Strand) Synthesis REAC
## 20 down 1.32e- 8 EML4 and NUDC in mitotic spindle formation REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 5.85e-19 Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 TF
## 2 down 2.54e-18 Factor: E2F-4; motif: NTTTCSCGCC TF
## 3 down 7.90e-18 Factor: ER81; motif: RCCGGAARYN; match class: 1 TF
## 4 down 1.18e-16 Factor: E2F-1; motif: NNNSSCGCSAANN TF
## 5 down 6.77e-16 Factor: ZF5; motif: GSGCGCGR; match class: 1 TF
## 6 down 3.16e-15 Factor: E2F-1; motif: TTTSGCGS TF
## 7 down 6.98e-15 Factor: E2F-1:DP-1; motif: TTTCSCGC TF
## 8 down 9.64e-15 Factor: E2F-4:DP-1; motif: TTTSGCGC TF
## 9 down 1.03e-14 Factor: SAP-1; motif: NNCCGGAAGTGN TF
## 10 down 1.30e-14 Factor: E2F-2; motif: GCGCGCGCGYW TF
## 11 down 2.45e-14 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 12 down 2.81e-14 Factor: E2F; motif: GGCGSG TF
## 13 down 2.89e-14 Factor: E2F-4; motif: SNGGGCGGGAANN; match class: 1 TF
## 14 down 3.75e-14 Factor: E2F-1; motif: TTTSGCGS; match class: 1 TF
## 15 down 3.97e-14 Factor: Elk-1; motif: NNNNCCGGAARTNN TF
## 16 down 4.23e-14 Factor: E2F; motif: TTTCGCGC; match class: 1 TF
## 17 down 1.05e-13 Factor: E2F-4; motif: NNTTCCCGCCNN TF
## 18 down 1.07e-13 Factor: FLI-1; motif: NAYTTCCGGT TF
## 19 down 1.43e-13 Factor: E2F-1; motif: NTTTCGCGCS TF
## 20 down 2.46e-13 Factor: E2F; motif: NNTTTCGCGCN TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 4.56e-18 catalytic activity, acting on a nucleic acid GO:MF
## 2 down 2.65e-17 single-stranded DNA binding GO:MF
## 3 down 1.07e-12 catalytic activity GO:MF
## 4 down 1.41e-11 catalytic activity, acting on DNA GO:MF
## 5 down 3.29e-11 DNA secondary structure binding GO:MF
## 6 down 4.09e-11 ATP-dependent activity, acting on DNA GO:MF
## 7 down 7.77e-11 single-stranded DNA helicase activity GO:MF
## 8 down 2.72e-10 nucleotide binding GO:MF
## 9 down 2.87e-10 nucleoside phosphate binding GO:MF
## 10 down 3.14e-10 heterocyclic compound binding GO:MF
## 11 down 6.78e- 9 DNA helicase activity GO:MF
## 12 down 1.47e- 8 adenyl nucleotide binding GO:MF
## 13 down 3.15e- 8 catalytic activity, acting on RNA GO:MF
## 14 down 3.15e- 8 four-way junction DNA binding GO:MF
## 15 down 5.05e- 8 transferase activity GO:MF
## 16 down 6.47e- 8 ATP binding GO:MF
## 17 down 9.17e- 8 purine nucleotide binding GO:MF
## 18 down 1.22e- 7 damaged DNA binding GO:MF
## 19 down 2.92e- 7 purine ribonucleoside triphosphate binding GO:MF
## 20 down 3.96e- 7 DNA binding GO:MF
## # A tibble: 9 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 2.96e-16 Retinoblastoma gene in cancer WP
## 2 down 6.29e-16 DNA replication WP
## 3 down 1.37e- 7 G1 to S cell cycle control WP
## 4 down 8.54e- 7 DNA mismatch repair WP
## 5 down 5.95e- 6 DNA repair pathways full network WP
## 6 down 3.33e- 4 Cell cycle WP
## 7 down 5.78e- 4 Base excision repair WP
## 8 down 3.62e- 3 Nucleotide excision repair WP
## 9 down 3.13e- 2 Gastric cancer network 1 WP
## # A tibble: 7 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 8.50e-14 hsa-miR-193b-3p MIRNA
## 2 down 2.10e-12 hsa-miR-215-5p MIRNA
## 3 down 2.09e- 8 hsa-miR-192-5p MIRNA
## 4 up 5.73e- 3 hsa-miR-1296-3p MIRNA
## 5 up 1.46e- 2 hsa-miR-668-3p MIRNA
## 6 up 2.31e- 2 hsa-miR-29b-3p MIRNA
## 7 up 4.43e- 2 hsa-miR-29c-3p MIRNA
## # A tibble: 7 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.42e-12 DNA replication KEGG
## 2 down 8.08e- 7 Cell cycle KEGG
## 3 down 2.01e- 5 Base excision repair KEGG
## 4 down 1.69e- 4 Mismatch repair KEGG
## 5 down 8.14e- 4 Homologous recombination KEGG
## 6 down 4.54e- 3 Fanconi anemia pathway KEGG
## 7 down 2.22e- 2 Nucleotide excision repair KEGG
## # A tibble: 8 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.0104 duodenum; endocrine cells[High] HPA
## 2 down 0.0123 duodenum; enterocytes[≥Medium] HPA
## 3 down 0.0163 skin 1; eccrine glands[≥Medium] HPA
## 4 down 0.0321 rectum; enterocytes[≥Medium] HPA
## 5 down 0.0369 skin 1; eccrine glands[≥Low] HPA
## 6 down 0.0394 duodenum; endocrine cells[≥Low] HPA
## 7 down 0.0448 duodenum; enterocytes[≥Low] HPA
## 8 down 0.0473 skin 1; lymphocytes[High] HPA
## # A tibble: 3 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.0243 DNA synthesome complex (15 subunits) CORUM
## 2 down 0.0333 DNA synthesome complex (17 subunits) CORUM
## 3 down 0.0333 DNA synthesome complex (17 subunits) CORUM
quickview_gprofiler_result(gprofiler_result_notordered)
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.14e-79 nucleoplasm GO:CC
## 2 up 5.16e-68 cytoplasm GO:CC
## 3 down 2.89e-67 cytoplasm GO:CC
## 4 down 2.33e-56 cytosol GO:CC
## 5 down 5.74e-49 intracellular organelle lumen GO:CC
## 6 down 5.74e-49 membrane-enclosed lumen GO:CC
## 7 down 5.74e-49 organelle lumen GO:CC
## 8 down 3.56e-46 nuclear lumen GO:CC
## 9 down 1.11e-45 intracellular anatomical structure GO:CC
## 10 up 6.81e-43 endomembrane system GO:CC
## 11 down 8.52e-41 membrane-bounded organelle GO:CC
## 12 down 2.55e-39 intracellular membrane-bounded organelle GO:CC
## 13 down 2.61e-39 chromosomal region GO:CC
## 14 down 1.54e-38 intracellular organelle GO:CC
## 15 down 1.23e-37 organelle GO:CC
## 16 up 1.78e-36 vesicle GO:CC
## 17 down 4.97e-35 chromosome GO:CC
## 18 up 2.06e-31 organelle membrane GO:CC
## 19 down 3.25e-29 condensed chromosome GO:CC
## 20 down 1.47e-27 chromosome, centromeric region GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.91e-56 cell cycle GO:BP
## 2 down 1.97e-54 cell cycle process GO:BP
## 3 down 4.13e-53 DNA metabolic process GO:BP
## 4 down 4.58e-46 chromosome organization GO:BP
## 5 down 3.47e-43 chromosome segregation GO:BP
## 6 down 5.81e-42 mitotic cell cycle GO:BP
## 7 down 9.72e-42 DNA repair GO:BP
## 8 down 2.37e-39 DNA replication GO:BP
## 9 down 1.60e-38 mitotic cell cycle process GO:BP
## 10 down 9.48e-37 DNA damage response GO:BP
## 11 down 1.22e-36 DNA-templated DNA replication GO:BP
## 12 down 4.74e-32 sister chromatid segregation GO:BP
## 13 down 5.18e-32 mitotic sister chromatid segregation GO:BP
## 14 down 7.13e-31 cell division GO:BP
## 15 down 2.38e-29 nuclear chromosome segregation GO:BP
## 16 down 1.27e-28 regulation of cell cycle process GO:BP
## 17 down 1.68e-28 organelle organization GO:BP
## 18 down 2.93e-28 regulation of cell cycle GO:BP
## 19 down 8.07e-27 organelle fission GO:BP
## 20 down 9.33e-27 double-strand break repair GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 7.13e-56 duodenum HPA
## 2 down 5.43e-46 small intestine HPA
## 3 down 3.11e-45 rectum HPA
## 4 down 1.84e-43 stomach 2; glandular cells[≥Low] HPA
## 5 down 1.84e-43 stomach 2 HPA
## 6 down 2.09e-41 gallbladder HPA
## 7 down 2.09e-41 gallbladder; glandular cells[≥Low] HPA
## 8 down 5.75e-41 colon HPA
## 9 down 1.09e-40 appendix HPA
## 10 down 1.65e-39 stomach 1; glandular cells[≥Low] HPA
## 11 down 1.65e-39 stomach 1 HPA
## 12 down 5.97e-37 urinary bladder HPA
## 13 down 5.97e-37 urinary bladder; urothelial cells[≥Low] HPA
## 14 down 1.52e-36 duodenum; glandular cells[≥Low] HPA
## 15 down 4.04e-35 esophagus; squamous epithelial cells[≥Low] HPA
## 16 down 4.04e-35 esophagus HPA
## 17 down 2.05e-34 pancreas; exocrine glandular cells[≥Low] HPA
## 18 down 2.24e-34 colon; glandular cells[≥Low] HPA
## 19 down 3.57e-33 rectum; glandular cells[≥Low] HPA
## 20 down 4.03e-33 tonsil HPA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.24e-53 Cell Cycle REAC
## 2 down 2.00e-47 Cell Cycle, Mitotic REAC
## 3 down 1.17e-25 Cell Cycle Checkpoints REAC
## 4 down 8.11e-23 M Phase REAC
## 5 down 2.96e-22 Mitotic Prometaphase REAC
## 6 down 4.08e-22 Mitotic Metaphase and Anaphase REAC
## 7 down 1.49e-21 Mitotic Anaphase REAC
## 8 down 3.85e-19 S Phase REAC
## 9 down 5.92e-19 Resolution of Sister Chromatid Cohesion REAC
## 10 down 8.53e-18 Mitotic G1 phase and G1/S transition REAC
## 11 down 8.21e-17 G1/S Transition REAC
## 12 down 3.21e-16 Activation of the pre-replicative complex REAC
## 13 down 8.18e-16 Mitotic Spindle Checkpoint REAC
## 14 down 2.46e-15 DNA strand elongation REAC
## 15 down 2.49e-15 Separation of Sister Chromatids REAC
## 16 down 3.14e-15 Synthesis of DNA REAC
## 17 down 4.97e-15 RHO GTPases Activate Formins REAC
## 18 down 5.60e-15 Amplification of signal from unattached kinetochores… REAC
## 19 down 5.60e-15 Amplification of signal from the kinetochores REAC
## 20 down 1.05e-14 EML4 and NUDC in mitotic spindle formation REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.06e-52 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN; match class: 1 TF
## 2 down 2.10e-47 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 3 down 3.26e-45 Factor: ZF5; motif: GSGCGCGR; match class: 1 TF
## 4 down 4.34e-44 Factor: E2F-4; motif: NTTTCSCGCC TF
## 5 down 2.11e-41 Factor: E2F-4; motif: SNGGGCGGGAANN; match class: 1 TF
## 6 down 3.17e-41 Factor: ZF5; motif: GGSGCGCGS TF
## 7 down 4.16e-41 Factor: E2F-3:HES-7; motif: NNNSGCGCSNNNNNCRCGYGNN; ma… TF
## 8 down 5.75e-41 Factor: ZF5; motif: GSGCGCGR TF
## 9 up 3.61e-39 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 10 down 4.97e-39 Factor: E2F-2; motif: GCGCGCGCGYW TF
## 11 up 6.89e-38 Factor: E2F-3:HES-7; motif: NNNSGCGCSNNNNNCRCGYGNN; ma… TF
## 12 down 9.05e-38 Factor: E2F-1; motif: NGGGCGGGARV TF
## 13 down 1.81e-37 Factor: E2F; motif: GGCGSG TF
## 14 up 2.22e-37 Factor: E2F-3; motif: GGCGGGN TF
## 15 down 3.76e-37 Factor: E2F-1; motif: NNNNGGCGGGAARN TF
## 16 up 3.83e-37 Factor: ZF5; motif: GSGCGCGR; match class: 1 TF
## 17 up 5.88e-37 Factor: Sp1; motif: NNGGGGCGGGGNN TF
## 18 up 8.13e-37 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN; match class: 1 TF
## 19 up 9.41e-37 Factor: E2F-4; motif: SNGGGCGGGAANN; match class: 1 TF
## 20 down 4.89e-36 Factor: E2F-4; motif: SNGGGCGGGAANN TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 6.91e-44 protein binding GO:MF
## 2 up 5.08e-36 protein binding GO:MF
## 3 down 4.97e-25 catalytic activity GO:MF
## 4 down 3.52e-21 catalytic activity, acting on a nucleic acid GO:MF
## 5 down 9.21e-16 heterocyclic compound binding GO:MF
## 6 down 1.01e-15 nucleotide binding GO:MF
## 7 down 1.08e-15 nucleoside phosphate binding GO:MF
## 8 down 1.64e-13 transferase activity GO:MF
## 9 down 3.20e-13 single-stranded DNA binding GO:MF
## 10 down 8.73e-13 adenyl nucleotide binding GO:MF
## 11 down 2.22e-12 purine nucleotide binding GO:MF
## 12 down 7.92e-12 ATP binding GO:MF
## 13 down 1.51e-11 purine ribonucleoside triphosphate binding GO:MF
## 14 down 2.51e-11 enzyme binding GO:MF
## 15 down 2.58e-11 anion binding GO:MF
## 16 down 3.27e-11 ribonucleotide binding GO:MF
## 17 down 5.31e-11 catalytic activity, acting on DNA GO:MF
## 18 down 6.19e-11 adenyl ribonucleotide binding GO:MF
## 19 down 1.25e-10 purine ribonucleotide binding GO:MF
## 20 down 7.78e-10 catalytic activity, acting on RNA GO:MF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 2.70e-24 "Retinoblastoma gene in cancer" WP
## 2 down 3.71e-19 "DNA replication" WP
## 3 down 1.73e-12 "DNA repair pathways full network" WP
## 4 down 2.44e-12 "Cell cycle" WP
## 5 down 5.21e-11 "G1 to S cell cycle control" WP
## 6 down 3.03e- 7 "DNA IR damage and cellular response via ATR" WP
## 7 down 8.50e- 6 "DNA mismatch repair" WP
## 8 down 9.85e- 5 "Base excision repair" WP
## 9 up 7.07e- 3 "Primary focal segmental glomerulosclerosis FSGS " WP
## 10 up 8.60e- 3 "Glycosaminoglycan degradation" WP
## 11 down 1.36e- 2 "Cohesin complex Cornelia de Lange syndrome" WP
## 12 up 1.59e- 2 "Electron transport chain OXPHOS system in mitochondri… WP
## 13 up 1.79e- 2 "IL 26 signaling pathways" WP
## 14 up 1.93e- 2 "Ciliary landscape" WP
## 15 up 2.10e- 2 "Ebola virus infection in host" WP
## 16 down 2.17e- 2 "DNA damage response" WP
## 17 down 2.63e- 2 "Gastric cancer network 2" WP
## 18 up 2.80e- 2 "Apoptosis related network due to altered Notch3 in ov… WP
## 19 up 3.32e- 2 "VEGFA VEGFR2 signaling" WP
## 20 down 3.99e- 2 "Regulation of sister chromatid separation at the meta… WP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 9.15e-22 hsa-miR-193b-3p MIRNA
## 2 down 4.16e-18 hsa-miR-215-5p MIRNA
## 3 down 8.67e-14 hsa-miR-192-5p MIRNA
## 4 up 2.27e- 6 hsa-miR-17-5p MIRNA
## 5 up 1.47e- 4 hsa-miR-93-5p MIRNA
## 6 up 2.18e- 4 hsa-miR-106a-5p MIRNA
## 7 up 3.76e- 4 hsa-miR-20b-5p MIRNA
## 8 down 7.32e- 4 hsa-miR-484 MIRNA
## 9 up 8.34e- 4 hsa-miR-20a-5p MIRNA
## 10 up 1.71e- 3 hsa-miR-519d-3p MIRNA
## 11 up 2.58e- 3 hsa-miR-106b-5p MIRNA
## 12 up 3.21e- 3 hsa-let-7e-5p MIRNA
## 13 up 1.15e- 2 hsa-miR-526b-3p MIRNA
## 14 up 1.24e- 2 hsa-miR-519b-3p MIRNA
## 15 up 1.29e- 2 hsa-miR-98-5p MIRNA
## 16 up 1.42e- 2 hsa-miR-30a-5p MIRNA
## 17 up 1.47e- 2 hsa-let-7a-5p MIRNA
## 18 down 1.60e- 2 hsa-miR-186-5p MIRNA
## 19 down 1.70e- 2 hsa-miR-16-5p MIRNA
## 20 up 1.89e- 2 hsa-miR-519a-3p MIRNA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 5.68e-18 Cell cycle KEGG
## 2 down 2.55e-13 DNA replication KEGG
## 3 up 3.50e-13 Lysosome KEGG
## 4 down 1.56e- 7 Fanconi anemia pathway KEGG
## 5 down 1.22e- 6 Homologous recombination KEGG
## 6 down 4.71e- 6 Base excision repair KEGG
## 7 down 8.73e- 5 Nucleocytoplasmic transport KEGG
## 8 up 1.50e- 4 Oxidative phosphorylation KEGG
## 9 up 3.46e- 4 Alzheimer disease KEGG
## 10 down 3.50e- 4 Mismatch repair KEGG
## 11 down 7.88e- 4 Biosynthesis of cofactors KEGG
## 12 up 1.00e- 3 Phagosome KEGG
## 13 down 1.82e- 3 Pentose phosphate pathway KEGG
## 14 up 5.82e- 3 Glycosaminoglycan degradation KEGG
## 15 down 6.22e- 3 Biosynthesis of amino acids KEGG
## 16 down 7.13e- 3 Cellular senescence KEGG
## 17 up 1.06e- 2 Parkinson disease KEGG
## 18 up 1.12e- 2 Diabetic cardiomyopathy KEGG
## 19 down 1.26e- 2 Nucleotide metabolism KEGG
## 20 down 1.62e- 2 RNA degradation KEGG
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.0000000863 Decreased head circumference HP
## 2 down 0.000000121 Microcephaly HP
## 3 down 0.000000440 Aplasia/Hypoplasia of the cerebrum HP
## 4 down 0.000000711 Abnormal cerebral morphology HP
## 5 down 0.000000821 Abnormal forebrain morphology HP
## 6 up 0.00000504 Distal peripheral sensory neuropathy HP
## 7 down 0.00000576 Aplasia/Hypoplasia involving the central nervous s… HP
## 8 down 0.00000720 Pyridoxine-responsive sideroblastic anemia HP
## 9 down 0.0000133 Abnormality of skull size HP
## 10 down 0.0000221 Duodenal stenosis HP
## 11 down 0.0000221 Small intestinal stenosis HP
## 12 down 0.0000324 Absent testis HP
## 13 up 0.0000437 Dementia HP
## 14 down 0.0000579 Abnormality of chromosome stability HP
## 15 down 0.0000791 Sideroblastic anemia HP
## 16 down 0.000247 Multiple cafe-au-lait spots HP
## 17 down 0.000258 Global developmental delay HP
## 18 up 0.000272 Recurrent paroxysmal headache HP
## 19 down 0.00166 Abnormal brain morphology HP
## 20 down 0.00186 Aplasia/Hypoplasia of the uvula HP
## # A tibble: 19 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.00140 CENP-A NAC-CAD complex CORUM
## 2 down 0.00671 BRAFT complex CORUM
## 3 down 0.00671 BASC complex (BRCA1-associated genome surveillance comp… CORUM
## 4 down 0.00676 CTF18-cohesion-RFC complex CORUM
## 5 down 0.00676 FA core complex (Fanconi anemia core complex) CORUM
## 6 down 0.00754 PCNA-CHL12-RFC2-5 complex CORUM
## 7 down 0.00754 CHTF18-RFC2-5 complex CORUM
## 8 down 0.00754 CHTF18-RFC2-5 complex CORUM
## 9 up 0.00925 Oligosaccharyltransferase complex (Stt3A variant) CORUM
## 10 down 0.0129 Fanconi anemia FAAP100 complex CORUM
## 11 down 0.0237 CTF18-cohesion-RFC-POLH complex CORUM
## 12 down 0.0237 FA complex (Fanconi anemia complex) CORUM
## 13 down 0.0237 RC complex (Replication competent complex) CORUM
## 14 down 0.0237 BASC (Ab 80) complex (BRCA1-associated genome surveilla… CORUM
## 15 up 0.0296 Oligosaccharyltransferase complex (Stt3B variant) CORUM
## 16 down 0.0309 CENP-H-I complex CORUM
## 17 down 0.0309 FA complex (Fanconi anemia complex) CORUM
## 18 down 0.0397 Condensin I-PARP-1-XRCC1 complex CORUM
## 19 down 0.0397 CENP-A NAC complex CORUM
quickview_gprofiler_result(gprofiler_result_highlighted)
## # A tibble: 12 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.14e-79 nucleoplasm GO:CC
## 2 up 5.16e-68 cytoplasm GO:CC
## 3 down 1.29e-20 spindle GO:CC
## 4 down 1.42e-18 envelope GO:CC
## 5 down 1.26e- 5 Fanconi anaemia nuclear complex GO:CC
## 6 down 1.14e- 3 spliceosomal complex GO:CC
## 7 down 2.43e- 3 aminoacyl-tRNA synthetase multienzyme complex GO:CC
## 8 down 4.42e- 3 BRCA1-C complex GO:CC
## 9 down 2.79e- 2 cyclin-dependent protein kinase holoenzyme complex GO:CC
## 10 up 3.70e- 2 laminin complex GO:CC
## 11 up 4.84e- 2 neuromuscular junction GO:CC
## 12 down 5.00e- 2 FANCM-MHF complex GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.91e-56 cell cycle GO:BP
## 2 down 4.13e-53 DNA metabolic process GO:BP
## 3 down 7.13e-31 cell division GO:BP
## 4 up 2.43e-23 protein metabolic process GO:BP
## 5 up 6.64e-12 vesicle-mediated transport GO:BP
## 6 up 7.42e-10 organelle organization GO:BP
## 7 down 1.37e- 9 small molecule metabolic process GO:BP
## 8 down 1.92e- 9 ncRNA metabolic process GO:BP
## 9 up 2.13e- 6 biological process involved in symbiotic interaction GO:BP
## 10 down 2.31e- 6 protein localization to chromosome GO:BP
## 11 down 1.70e- 5 nucleobase-containing compound transport GO:BP
## 12 up 6.83e- 5 oxidative phosphorylation GO:BP
## 13 down 9.99e- 4 response to ionizing radiation GO:BP
## 14 up 1.62e- 3 cellular component disassembly GO:BP
## 15 down 1.65e- 3 RNA modification GO:BP
## 16 down 1.78e- 3 cellular component organization or biogenesis GO:BP
## 17 down 2.87e- 3 apoptotic process GO:BP
## 18 up 2.87e- 3 protein localization to Golgi apparatus GO:BP
## 19 up 7.77e- 3 phosphorus metabolic process GO:BP
## 20 up 8.49e- 3 extracellular matrix organization GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 6.91e-44 protein binding GO:MF
## 2 up 5.08e-36 protein binding GO:MF
## 3 down 4.97e-25 catalytic activity GO:MF
## 4 down 3.20e-13 single-stranded DNA binding GO:MF
## 5 down 1.94e- 8 damaged DNA binding GO:MF
## 6 down 2.33e- 8 DNA secondary structure binding GO:MF
## 7 up 2.21e- 7 enzyme regulator activity GO:MF
## 8 down 5.91e- 4 chromatin binding GO:MF
## 9 down 6.34e- 4 magnesium ion binding GO:MF
## 10 down 2.74e- 3 oxidoreductase activity, acting on CH-OH group of dono… GO:MF
## 11 down 3.27e- 3 mismatch repair complex binding GO:MF
## 12 down 9.70e- 3 tubulin binding GO:MF
## 13 down 1.12e- 2 anaphase-promoting complex binding GO:MF
## 14 up 1.16e- 2 metalloendopeptidase activity involved in amyloid prec… GO:MF
## 15 up 2.47e- 2 insulin-like growth factor receptor binding GO:MF
## 16 down 2.74e- 2 DNA replication origin binding GO:MF
## 17 up 3.16e- 2 catalytic activity GO:MF
## 18 up 3.44e- 2 molecular adaptor activity GO:MF
## 19 up 3.52e- 2 cyclin-dependent protein serine/threonine kinase inhib… GO:MF
## 20 up 3.75e- 2 insulin-like growth factor II binding GO:MF
Apoptosis
gprofiler_result_ordered |>
filter(query == 'up' & source == 'GO:BP') |>
arrange(p_value) |>
select(term_name, p_value) |>
head(n = 20)
## # A tibble: 20 × 2
## term_name p_value
## <chr> <dbl>
## 1 protein maturation 0.00000545
## 2 endoderm formation 0.0000158
## 3 endoderm development 0.000237
## 4 protein catabolic process 0.000592
## 5 formation of primary germ layer 0.000788
## 6 protein metabolic process 0.000932
## 7 organonitrogen compound catabolic process 0.000988
## 8 vesicle-mediated transport 0.00133
## 9 amyloid precursor protein catabolic process 0.00136
## 10 macromolecule catabolic process 0.00155
## 11 gastrulation 0.00167
## 12 Golgi vesicle transport 0.00192
## 13 protein processing 0.00215
## 14 embryonic placenta morphogenesis 0.00227
## 15 proteolysis 0.00271
## 16 positive regulation of apoptotic process 0.00351
## 17 positive regulation of programmed cell death 0.00355
## 18 amyloid precursor protein metabolic process 0.00367
## 19 biological process involved in symbiotic interaction 0.00395
## 20 regulation of plasminogen activation 0.00499
gprofiler_result_notordered |>
filter(query == 'up' & source == 'GO:BP') |>
arrange(p_value) |>
select(term_name, p_value) |>
head(n = 20)
## # A tibble: 20 × 2
## term_name p_value
## <chr> <dbl>
## 1 protein metabolic process 2.43e-23
## 2 organonitrogen compound metabolic process 3.92e-23
## 3 catabolic process 6.00e-13
## 4 vesicle-mediated transport 6.64e-12
## 5 organonitrogen compound catabolic process 2.01e-11
## 6 regulation of response to stimulus 3.00e-11
## 7 proteolysis 3.17e-11
## 8 protein maturation 3.29e-11
## 9 macromolecule catabolic process 7.79e-11
## 10 regulation of signal transduction 1.07e-10
## 11 tissue development 1.72e-10
## 12 organic substance catabolic process 1.81e-10
## 13 cell death 2.01e-10
## 14 programmed cell death 3.09e-10
## 15 protein catabolic process 3.16e-10
## 16 organelle organization 7.42e-10
## 17 anatomical structure development 7.77e-10
## 18 positive regulation of cellular process 9.85e-10
## 19 positive regulation of biological process 1.15e- 9
## 20 apoptotic process 1.35e- 9
TF (to remove –)
TF_remove_patterns <- 'Factor: |; match class: [0-9]+'
gprofiler_result_ordered_TF <-
gprofiler_result_ordered |>
filter(source == 'TF') |>
mutate(
term_name = paste0(
term_name |>
str_remove_all(TF_remove_patterns) |>
str_replace('; motif: ', ' (') |>
str_remove(';'),
')'
)
)
plot_dual_barplot_each_source('TF', gprofiler_result_ordered_TF)
## Warning: Removed 1 row containing missing values or values outside the scale range
## (`geom_bar()`).
## Removed 1 row containing missing values or values outside the scale range
## (`geom_bar()`).
