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
devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')
## ℹ Loading myUtilities
library(patchwork)
## Warning: package 'patchwork' was built under R version 4.2.3
wd <- "/Users/s-mitsutomi/My Drive (shuheimitsutomi@ric.u-tokyo.ac.jp)/Analysis/METTL2A/"
setwd(wd)
figdir <- paste0(wd, 'Figures/Espresso/Expression/')
tabledir <- paste0(wd, 'Tables/Espresso/Gprofiler/')
# # 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$signed_log10p |> abs() |> max(na.rm = TRUE)
p1 <-
df_source_simplified |>
select(query, signed_log10p, term_name, source) |>
#filter(source == 'GO:BP') |>
filter(query == 'down') |>
head(10) |>
ggplot(aes(x = reorder(term_name, -signed_log10p),
y = signed_log10p, label = term_name)) +
geom_bar(stat = 'identity', fill = 'blue', alpha = .2) +
geom_text(hjust = 1, colour = 'black', y = -0.2, size = 7 * 0.36) +
scale_y_continuous(limits = c(-yrange_max, 0)) +
labs(title = .source) +
coord_flip() +
dual_barplot_theme()
p2 <-
df_source_simplified |>
select(query, signed_log10p, term_name, source) |>
#filter(source == 'GO:BP') |>
filter(query == 'up') |>
head(10) |>
ggplot(aes(x = reorder(term_name, signed_log10p),
y = signed_log10p, label = term_name)) +
geom_bar(stat = 'identity', fill = 'red', alpha = 0.2) +
geom_text(hjust = 0, colour = 'black', y = 0.2, size = 7 * 0.36) +
scale_y_continuous(limits = c(0, yrange_max)) +
coord_flip() +
dual_barplot_theme()
dual_barplot <- p1 | p2
print(dual_barplot)
ggsave(
plot = dual_barplot,
filename = paste0(figdir, barplot_basename, '.pdf'),
width = 12, height = 6, units = 'cm',
)
}
gprofiler_gost <- function(ordered = TRUE) {
gostres <-
gprofiler2::gost(
query = list(
'up' = str_remove(espresso_deseq2_commonup$transcript_id,
'[.][0-9]+$'),
'down' = str_remove(espresso_deseq2_commondown$transcript_id,
'[.][0-9]+$')
),
organism = 'hsapiens',
ordered_query = ordered,
significant = TRUE,
#multi_query = TRUE
)
gostres$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(query == 'up') |>
filter(source == gp_source) |>
select(query, p_value, term_name, source) |>
head(20) |>
print()
df |>
filter(query == 'down') |>
filter(source == gp_source) |>
select(query, p_value, term_name, source) |>
head(20) |>
print()
}
}
Read DESeq2 result
espresso_deseq2 <-
read_tsv(
paste0(wd, 'Tables/Espresso/espresso_deseq2_genetype2_isDET_2024-04-01.tsv')
)
## Rows: 36717 Columns: 29
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (11): transcript_id, transcript_type, transcript_name, gene_id, gene_typ...
## 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.
espresso_deseq2
## # A tibble: 36,717 × 29
## transcript_id transcript_type transcript_name gene_id gene_type gene_name
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 ENST00000498442.1 retained_intron CRBN-212 ENSG00… protein_… CRBN
## 2 ENST00000459840.5 retained_intron CRBN-205 ENSG00… protein_… CRBN
## 3 ENST00000231948.9 protein_coding CRBN-201 ENSG00… protein_… CRBN
## 4 ENST00000432408.6 protein_coding CRBN-203 ENSG00… protein_… CRBN
## 5 ENST00000339437.… protein_coding TRNT1-203 ENSG00… protein_… TRNT1
## 6 ENST00000488263.5 retained_intron CRBN-209 ENSG00… protein_… CRBN
## 7 ENST00000420393.5 protein_coding TRNT1-207 ENSG00… protein_… TRNT1
## 8 ENST00000698415.1 retained_intron TRNT1-230 ENSG00… protein_… TRNT1
## 9 ENST00000450014.1 protein_coding CRBN-204 ENSG00… protein_… CRBN
## 10 ENST00000698416.1 retained_intron TRNT1-231 ENSG00… protein_… TRNT1
## # ℹ 36,707 more rows
## # ℹ 23 more variables: siMETTL2A_baseMean <dbl>,
## # siMETTL2A_log2FoldChange <dbl>, siMETTL2A_lfcSE <dbl>,
## # siMETTL2A_stat <dbl>, siMETTL2A_pvalue <dbl>, siMETTL2A_padj <dbl>,
## # siMETTL2A_I_baseMean <dbl>, siMETTL2A_I_log2FoldChange <dbl>,
## # siMETTL2A_I_lfcSE <dbl>, siMETTL2A_I_stat <dbl>, siMETTL2A_I_pvalue <dbl>,
## # siMETTL2A_I_padj <dbl>, siMETTL2A_G_baseMean <dbl>, …
espresso_deseq2_commonDETs <-
espresso_deseq2 |>
filter(common_DETs != 'other')
espresso_deseq2_commonDETs
## # A tibble: 978 × 29
## transcript_id transcript_type transcript_name gene_id gene_type gene_name
## <chr> <chr> <chr> <chr> <chr> <chr>
## 1 ENST00000301964.7 protein_coding TADA3-201 ENSG00… protein_… TADA3
## 2 ENST00000383817.5 protein_coding CIDEC-202 ENSG00… protein_… CIDEC
## 3 ENST00000344629.… protein_coding OGG1-205 ENSG00… protein_… OGG1
## 4 ENST00000306024.4 protein_coding LSM3-201 ENSG00… protein_… LSM3
## 5 ENST00000307839.… protein_coding RPL15-201 ENSG00… protein_… RPL15
## 6 ENST00000306627.8 protein_coding UBE2E1-201 ENSG00… protein_… UBE2E1
## 7 ENST00000479563.5 retained_intron RPL14-208 ENSG00… protein_… RPL14
## 8 ENST00000338970.… protein_coding RPL14-201 ENSG00… protein_… RPL14
## 9 ENST00000438607.2 protein_coding TMA7-201 ENSG00… protein_… TMA7
## 10 ENST00000477624.1 retained_intron TMA7-202 ENSG00… protein_… TMA7
## # ℹ 968 more rows
## # ℹ 23 more variables: siMETTL2A_baseMean <dbl>,
## # siMETTL2A_log2FoldChange <dbl>, siMETTL2A_lfcSE <dbl>,
## # siMETTL2A_stat <dbl>, siMETTL2A_pvalue <dbl>, siMETTL2A_padj <dbl>,
## # siMETTL2A_I_baseMean <dbl>, siMETTL2A_I_log2FoldChange <dbl>,
## # siMETTL2A_I_lfcSE <dbl>, siMETTL2A_I_stat <dbl>, siMETTL2A_I_pvalue <dbl>,
## # siMETTL2A_I_padj <dbl>, siMETTL2A_G_baseMean <dbl>, …
espresso_deseq2_commonup <-
espresso_deseq2_commonDETs |>
filter(common_DETs == 'up')
espresso_deseq2_commondown <-
espresso_deseq2_commonDETs |>
filter(common_DETs == 'down')
# Enrichment analyses -----------------------------------------------------
gprofiler_result_ordered <-
gprofiler_gost(ordered = TRUE) |>
calc_signed_log10p()
gprofiler_result_ordered |>
export_tsv(outdir = tabledir, compression = 'gz')
##
## Exported to: /Users/s-mitsutomi/My Drive (shuheimitsutomi@ric.u-tokyo.ac.jp)/Analysis/METTL2A/Tables/Espresso/Gprofiler/gprofiler_result_ordered_2024-04-17.tsv.gz
## # A tibble: 1,259 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 4.57e-26 635 475 71 0.149
## 2 down TRUE 7.55e-25 402 475 54 0.114
## 3 up TRUE 1.47e-24 2133 356 106 0.298
## 4 up TRUE 1.53e-24 2134 356 106 0.298
## 5 up TRUE 1.53e-24 2134 356 106 0.298
## 6 up TRUE 2.42e-24 2109 356 105 0.295
## 7 down TRUE 1.44e-23 12345 478 376 0.787
## 8 up TRUE 3.34e-23 4004 357 149 0.417
## 9 down TRUE 3.39e-23 4220 475 188 0.396
## 10 down TRUE 7.43e-22 5487 478 220 0.460
## # ℹ 1,249 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: /Users/s-mitsutomi/My Drive (shuheimitsutomi@ric.u-tokyo.ac.jp)/Analysis/METTL2A/Tables/Espresso/Gprofiler/gprofiler_result_notordered_2024-04-17.tsv.gz
## # A tibble: 1,744 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 down TRUE 1.22e-27 635 449 71 0.158
## 2 down TRUE 1.20e-26 547 333 75 0.225
## 3 down TRUE 2.21e-26 677 333 83 0.249
## 4 down TRUE 3.02e-26 12345 470 376 0.8
## 5 up TRUE 3.46e-26 12345 348 291 0.836
## 6 up TRUE 4.21e-26 2133 348 107 0.307
## 7 up TRUE 4.38e-26 2134 348 107 0.307
## 8 up TRUE 4.38e-26 2134 348 107 0.307
## 9 up TRUE 7.09e-26 2109 348 106 0.305
## 10 up TRUE 3.88e-25 4004 348 150 0.431
## # ℹ 1,734 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 sources
quickview_gprofiler_result(gprofiler_result_ordered)
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 5.53e-18 cytoplasmic translation GO:BP
## 2 up 9.88e-18 aerobic electron transport chain GO:BP
## 3 up 3.73e-17 mitochondrial ATP synthesis coupled electron transport GO:BP
## 4 up 3.73e-17 ATP synthesis coupled electron transport GO:BP
## 5 up 3.03e-16 oxidative phosphorylation GO:BP
## 6 up 8.53e-16 respiratory electron transport chain GO:BP
## 7 up 4.11e-14 aerobic respiration GO:BP
## 8 up 2.18e-13 electron transport chain GO:BP
## 9 up 1.04e-12 cellular respiration GO:BP
## 10 up 6.26e-11 energy derivation by oxidation of organic compounds GO:BP
## 11 up 9.28e-10 generation of precursor metabolites and energy GO:BP
## 12 up 1.27e- 9 organonitrogen compound biosynthetic process GO:BP
## 13 up 1.29e- 9 peptide metabolic process GO:BP
## 14 up 1.81e- 9 translation GO:BP
## 15 up 3.97e- 9 organonitrogen compound metabolic process GO:BP
## 16 up 6.51e- 9 peptide biosynthetic process GO:BP
## 17 up 1.21e- 8 purine ribonucleoside triphosphate biosynthetic process GO:BP
## 18 up 1.40e- 8 purine nucleoside triphosphate biosynthetic process GO:BP
## 19 up 1.59e- 8 amide metabolic process GO:BP
## 20 up 1.97e- 8 proton motive force-driven mitochondrial ATP synthesis GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 4.57e-26 chromosome organization GO:BP
## 2 down 2.18e-21 cell cycle GO:BP
## 3 down 1.99e-20 mitotic cell cycle GO:BP
## 4 down 4.85e-20 chromosome segregation GO:BP
## 5 down 9.98e-19 mitotic sister chromatid segregation GO:BP
## 6 down 1.11e-18 sister chromatid segregation GO:BP
## 7 down 2.23e-18 DNA metabolic process GO:BP
## 8 down 2.56e-18 mitotic cell cycle process GO:BP
## 9 down 7.59e-18 cell cycle process GO:BP
## 10 down 4.75e-17 nuclear chromosome segregation GO:BP
## 11 down 5.49e-17 cell division GO:BP
## 12 down 1.13e-15 mitotic nuclear division GO:BP
## 13 down 9.98e-15 DNA replication GO:BP
## 14 down 4.96e-13 nuclear division GO:BP
## 15 down 2.30e-12 chromosome separation GO:BP
## 16 down 2.74e-12 mitotic sister chromatid separation GO:BP
## 17 down 3.15e-12 regulation of chromosome segregation GO:BP
## 18 down 3.78e-12 DNA-templated DNA replication GO:BP
## 19 down 4.36e-12 organelle fission GO:BP
## 20 down 5.48e-12 regulation of chromosome separation GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 1.47e-24 extracellular vesicle GO:CC
## 2 up 1.53e-24 extracellular organelle GO:CC
## 3 up 1.53e-24 extracellular membrane-bounded organelle GO:CC
## 4 up 2.42e-24 extracellular exosome GO:CC
## 5 up 3.34e-23 vesicle GO:CC
## 6 up 5.75e-21 cytosolic ribosome GO:CC
## 7 up 1.25e-19 cytoplasm GO:CC
## 8 up 1.39e-17 inner mitochondrial membrane protein complex GO:CC
## 9 up 1.98e-17 ribosomal subunit GO:CC
## 10 up 2.19e-17 respiratory chain complex GO:CC
## 11 up 3.28e-17 mitochondrial respirasome GO:CC
## 12 up 4.27e-17 extracellular space GO:CC
## 13 up 5.54e-17 organelle membrane GO:CC
## 14 up 8.99e-17 respirasome GO:CC
## 15 up 2.58e-16 mitochondrial protein-containing complex GO:CC
## 16 up 1.01e-14 cytoplasmic vesicle GO:CC
## 17 up 1.15e-14 intracellular vesicle GO:CC
## 18 up 3.58e-14 extracellular region GO:CC
## 19 up 6.36e-14 secretory granule GO:CC
## 20 up 8.65e-14 focal adhesion GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 7.55e-25 chromosomal region GO:CC
## 2 down 1.44e-23 cytoplasm GO:CC
## 3 down 3.39e-23 nucleoplasm GO:CC
## 4 down 7.43e-22 cytosol GO:CC
## 5 down 1.61e-20 organelle lumen GO:CC
## 6 down 1.61e-20 intracellular organelle lumen GO:CC
## 7 down 1.61e-20 membrane-enclosed lumen GO:CC
## 8 down 1.53e-16 chromosome, centromeric region GO:CC
## 9 down 2.55e-16 nuclear lumen GO:CC
## 10 down 2.59e-15 condensed chromosome GO:CC
## 11 down 4.63e-15 chromosome GO:CC
## 12 down 5.58e-15 spindle GO:CC
## 13 down 9.61e-14 condensed chromosome, centromeric region GO:CC
## 14 down 1.68e-13 kinetochore GO:CC
## 15 down 2.13e-12 nuclear chromosome GO:CC
## 16 down 3.03e-11 membrane-bounded organelle GO:CC
## 17 down 3.33e-11 intracellular membrane-bounded organelle GO:CC
## 18 down 4.14e-11 intracellular anatomical structure GO:CC
## 19 down 2.60e-10 microtubule cytoskeleton GO:CC
## 20 down 3.19e-10 catalytic complex GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 4.17e-17 oxidoreduction-driven active transmembrane transporter… GO:MF
## 2 up 1.77e-15 electron transfer activity GO:MF
## 3 up 1.64e-12 primary active transmembrane transporter activity GO:MF
## 4 up 2.09e- 9 cell adhesion molecule binding GO:MF
## 5 up 1.92e- 8 NADH dehydrogenase (ubiquinone) activity GO:MF
## 6 up 2.23e- 8 NADH dehydrogenase (quinone) activity GO:MF
## 7 up 2.32e- 8 cadherin binding GO:MF
## 8 up 3.00e- 8 NADH dehydrogenase activity GO:MF
## 9 up 3.45e- 8 NAD(P)H dehydrogenase (quinone) activity GO:MF
## 10 up 9.28e- 8 active transmembrane transporter activity GO:MF
## 11 up 1.52e- 7 oxidoreductase activity, acting on NAD(P)H, quinone or… GO:MF
## 12 up 6.98e- 7 structural constituent of ribosome GO:MF
## 13 up 2.20e- 6 oxidoreductase activity, acting on NAD(P)H GO:MF
## 14 up 1.61e- 5 oxidoreductase activity GO:MF
## 15 up 3.91e- 5 transmembrane transporter activity GO:MF
## 16 up 4.84e- 5 proton transmembrane transporter activity GO:MF
## 17 up 1.18e- 4 transporter activity GO:MF
## 18 up 1.54e- 4 cytochrome-c oxidase activity GO:MF
## 19 up 1.54e- 4 oxidoreductase activity, acting on a heme group of don… GO:MF
## 20 up 2.03e- 4 cadherin binding involved in cell-cell adhesion GO:MF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.10e-10 protein binding GO:MF
## 2 down 4.21e- 9 single-stranded DNA helicase activity GO:MF
## 3 down 2.01e- 7 catalytic activity GO:MF
## 4 down 9.95e- 7 heterocyclic compound binding GO:MF
## 5 down 1.55e- 6 single-stranded DNA binding GO:MF
## 6 down 2.78e- 6 DNA helicase activity GO:MF
## 7 down 2.88e- 6 cadherin binding GO:MF
## 8 down 3.35e- 6 nucleotide binding GO:MF
## 9 down 3.42e- 6 nucleoside phosphate binding GO:MF
## 10 down 4.29e- 5 purine nucleotide binding GO:MF
## 11 down 4.62e- 5 DNA polymerase binding GO:MF
## 12 down 5.87e- 5 anion binding GO:MF
## 13 down 7.39e- 5 adenyl nucleotide binding GO:MF
## 14 down 9.18e- 5 identical protein binding GO:MF
## 15 down 1.36e- 4 chromatin binding GO:MF
## 16 down 2.23e- 4 cell adhesion molecule binding GO:MF
## 17 down 2.83e- 4 ribonucleotide binding GO:MF
## 18 down 3.77e- 4 enzyme binding GO:MF
## 19 down 5.73e- 4 carbohydrate derivative binding GO:MF
## 20 down 8.18e- 4 purine ribonucleotide binding GO:MF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 7.27e-16 Eukaryotic Translation Elongation REAC
## 2 up 3.02e-15 Peptide chain elongation REAC
## 3 up 9.66e-15 SRP-dependent cotranslational protein targeting to mem… REAC
## 4 up 3.98e-14 Viral mRNA Translation REAC
## 5 up 8.01e-14 Formation of a pool of free 40S subunits REAC
## 6 up 8.01e-14 Response of EIF2AK4 (GCN2) to amino acid deficiency REAC
## 7 up 1.19e-13 Eukaryotic Translation Termination REAC
## 8 up 1.19e-13 Selenocysteine synthesis REAC
## 9 up 2.00e-13 Nonsense Mediated Decay (NMD) independent of the Exon … REAC
## 10 up 6.52e-13 Cellular response to starvation REAC
## 11 up 8.63e-13 L13a-mediated translational silencing of Ceruloplasmin… REAC
## 12 up 1.08e-12 GTP hydrolysis and joining of the 60S ribosomal subunit REAC
## 13 up 4.80e-12 Cap-dependent Translation Initiation REAC
## 14 up 4.80e-12 Eukaryotic Translation Initiation REAC
## 15 up 7.06e-12 Respiratory electron transport, ATP synthesis by chemi… REAC
## 16 up 1.96e-11 Nonsense Mediated Decay (NMD) enhanced by the Exon Jun… REAC
## 17 up 1.96e-11 Nonsense-Mediated Decay (NMD) REAC
## 18 up 2.40e-11 Selenoamino acid metabolism REAC
## 19 up 2.57e-11 Respiratory electron transport REAC
## 20 up 5.84e-11 Influenza Viral RNA Transcription and Replication REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 9.11e-17 Cell Cycle, Mitotic REAC
## 2 down 3.44e-16 Cell Cycle REAC
## 3 down 2.02e- 9 DNA strand elongation REAC
## 4 down 7.49e- 9 Resolution of Sister Chromatid Cohesion REAC
## 5 down 9.17e- 9 Mitotic Metaphase and Anaphase REAC
## 6 down 3.09e- 8 Mitotic G1 phase and G1/S transition REAC
## 7 down 3.51e- 8 Mitotic Anaphase REAC
## 8 down 6.79e- 8 G1/S Transition REAC
## 9 down 7.72e- 8 Mitotic Prometaphase REAC
## 10 down 2.08e- 7 Synthesis of DNA REAC
## 11 down 4.94e- 7 S Phase REAC
## 12 down 5.38e- 7 Cell Cycle Checkpoints REAC
## 13 down 1.41e- 6 Separation of Sister Chromatids REAC
## 14 down 2.08e- 6 EML4 and NUDC in mitotic spindle formation REAC
## 15 down 4.77e- 6 Lagging Strand Synthesis REAC
## 16 down 6.22e- 6 Leading Strand Synthesis REAC
## 17 down 6.22e- 6 Polymerase switching REAC
## 18 down 1.09e- 5 RHO GTPases Activate Formins REAC
## 19 down 1.10e- 5 Activation of the pre-replicative complex REAC
## 20 down 1.27e- 5 M Phase REAC
## # A tibble: 11 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.00000180 hsa-let-7c-5p MIRNA
## 2 up 0.000342 hsa-let-7e-5p MIRNA
## 3 up 0.00242 hsa-miR-296-3p MIRNA
## 4 up 0.00827 hsa-miR-17-5p MIRNA
## 5 up 0.00984 hsa-miR-4460 MIRNA
## 6 up 0.0138 hsa-miR-652-3p MIRNA
## 7 up 0.0188 hsa-miR-140-5p MIRNA
## 8 up 0.0286 hsa-miR-744-5p MIRNA
## 9 up 0.0372 hsa-miR-30a-5p MIRNA
## 10 up 0.0396 hsa-let-7a-5p MIRNA
## 11 up 0.0444 hsa-miR-186-5p MIRNA
## # A tibble: 9 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 2.27e-16 hsa-miR-193b-3p MIRNA
## 2 down 4.82e- 4 hsa-miR-744-5p MIRNA
## 3 down 1.09e- 3 hsa-miR-615-3p MIRNA
## 4 down 5.00e- 3 hsa-miR-484 MIRNA
## 5 down 1.07e- 2 hsa-miR-34a-5p MIRNA
## 6 down 2.36e- 2 hsa-miR-4758-3p MIRNA
## 7 down 2.95e- 2 hsa-miR-4721 MIRNA
## 8 down 3.21e- 2 hsa-miR-4669 MIRNA
## 9 down 4.17e- 2 hsa-miR-497-3p MIRNA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 5.08e-16 Mitochondrial inheritance HP
## 2 up 9.43e-15 Centrocecal scotoma HP
## 3 up 1.19e-13 Leber optic atrophy HP
## 4 up 1.20e-12 Ventricular preexcitation HP
## 5 up 1.29e-12 Retinal arterial tortuosity HP
## 6 up 1.29e-12 Central retinal vessel vascular tortuosity HP
## 7 up 2.15e-12 Mitochondrial respiratory chain defects HP
## 8 up 5.82e-11 Retinal telangiectasia HP
## 9 up 6.31e-10 Slow decrease in visual acuity HP
## 10 up 8.62e-10 Episodic vomiting HP
## 11 up 1.29e- 9 Mitochondrial myopathy HP
## 12 up 1.29e- 9 Ragged-red muscle fibers HP
## 13 up 2.49e- 9 Abnormal mitochondria in muscle tissue HP
## 14 up 5.42e- 9 Arterial tortuosity HP
## 15 up 8.16e- 9 Blurred vision HP
## 16 up 1.57e- 8 Mixed demyelinating and axonal polyneuropathy HP
## 17 up 1.89e- 8 Vascular tortuosity HP
## 18 up 1.91e- 8 Multiple glomerular cysts HP
## 19 up 3.40e- 8 Central scotoma HP
## 20 up 4.36e- 8 Stroke-like episode HP
## # A tibble: 0 × 4
## # ℹ 4 variables: query <chr>, p_value <dbl>, term_name <chr>, source <chr>
## # A tibble: 7 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 1.63e-13 Electron transport chain OXPHOS system in mitochondria WP
## 2 up 3.83e-11 Cytoplasmic ribosomal proteins WP
## 3 up 5.42e- 7 Oxidative phosphorylation WP
## 4 up 3.52e- 4 Mitochondrial complex I assembly model OXPHOS system WP
## 5 up 1.13e- 2 Mitochondrial complex III assembly WP
## 6 up 1.66e- 2 Nonalcoholic fatty liver disease WP
## 7 up 3.41e- 2 Mitochondrial complex IV assembly WP
## # A tibble: 8 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 4.95e-11 Retinoblastoma gene in cancer WP
## 2 down 1.31e- 8 DNA replication WP
## 3 down 1.59e- 3 Gastric cancer network 1 WP
## 4 down 2.42e- 3 G1 to S cell cycle control WP
## 5 down 6.25e- 3 DNA mismatch repair WP
## 6 down 3.10e- 2 Gastric cancer network 2 WP
## 7 down 3.27e- 2 Cell cycle WP
## 8 down 4.69e- 2 Cohesin complex Cornelia de Lange syndrome WP
## # A tibble: 16 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 1.81e-12 Oxidative phosphorylation KEGG
## 2 up 3.77e-10 Diabetic cardiomyopathy KEGG
## 3 up 1.19e- 9 Chemical carcinogenesis - reactive oxygen species KEGG
## 4 up 2.08e- 9 Ribosome KEGG
## 5 up 2.20e- 9 Thermogenesis KEGG
## 6 up 3.62e- 9 Parkinson disease KEGG
## 7 up 4.59e- 9 Huntington disease KEGG
## 8 up 1.55e- 8 Prion disease KEGG
## 9 up 5.63e- 7 Amyotrophic lateral sclerosis KEGG
## 10 up 9.70e- 7 Pathways of neurodegeneration - multiple diseases KEGG
## 11 up 1.00e- 6 Alzheimer disease KEGG
## 12 up 7.68e- 5 Coronavirus disease - COVID-19 KEGG
## 13 up 1.18e- 4 Cardiac muscle contraction KEGG
## 14 up 1.34e- 3 Retrograde endocannabinoid signaling KEGG
## 15 up 7.68e- 3 Non-alcoholic fatty liver disease KEGG
## 16 up 4.98e- 2 Ubiquitin mediated proteolysis KEGG
## # A tibble: 4 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.00000000196 DNA replication KEGG
## 2 down 0.000133 Cell cycle KEGG
## 3 down 0.00532 Mismatch repair KEGG
## 4 down 0.00643 Base excision repair KEGG
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.0000360 Factor: ER71; motif: ACCGGAARYN; match class: 1 TF
## 2 up 0.000220 Factor: MYBL1; motif: ACCGTTAACSGY TF
## 3 up 0.000290 Factor: SAP-1; motif: NRNCGGAWRYN TF
## 4 up 0.000354 Factor: Kaiso; motif: TCTCGCGAG; match class: 1 TF
## 5 up 0.000494 Factor: Cdx-2; motif: NRTCGTAANNNN; match class: 1 TF
## 6 up 0.000510 Factor: Fli-1; motif: ACCGGAAGYN TF
## 7 up 0.000518 Factor: GABPalpha; motif: RCCGGAWRYN; match class: 1 TF
## 8 up 0.000553 Factor: E2F; motif: GGCGSG TF
## 9 up 0.000566 Factor: E2F1; motif: NNNNNGCGSSAAAN TF
## 10 up 0.000780 Factor: FLI1; motif: ACCGGAARTN; match class: 1 TF
## 11 up 0.00100 Factor: LRF; motif: NCGACCACCGN; match class: 1 TF
## 12 up 0.00120 Factor: Erg; motif: NACCGGAARYN; match class: 1 TF
## 13 up 0.00123 Factor: E2F-4:DP-1; motif: TTTSGCGC TF
## 14 up 0.00133 Factor: Erg; motif: ACCGGAAGTN; match class: 1 TF
## 15 up 0.00181 Factor: E2F; motif: GGCGSG; match class: 1 TF
## 16 up 0.00184 Factor: FLI-1; motif: NAYTTCCGGT; match class: 1 TF
## 17 up 0.00261 Factor: Kaiso; motif: TCTCGCGAG TF
## 18 up 0.00308 Factor: c-ets-2; motif: ACCGGAWRTN TF
## 19 up 0.00340 Factor: Fli-1; motif: NACCGGAARTN; match class: 1 TF
## 20 up 0.00344 Factor: GCMb:FOXI1; motif: RTAAATANGGGNN TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.12e-12 Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 TF
## 2 down 1.21e-11 Factor: E2F-1; motif: NNNSSCGCSAANN TF
## 3 down 3.60e-11 Factor: E2F-4; motif: SNGGGCGGGAANN; match class: 1 TF
## 4 down 6.56e-11 Factor: E2F; motif: TTTSGCGSG TF
## 5 down 7.03e-11 Factor: E2F; motif: NKCGCGCSAAAN TF
## 6 down 1.23e-10 Factor: E2F-1; motif: NGGGCGGGARV; match class: 1 TF
## 7 down 1.38e-10 Factor: E2F; motif: NCSCGCSAAAN TF
## 8 down 2.21e-10 Factor: ZF5; motif: NRNGNGCGCGCWN; match class: 1 TF
## 9 down 1.40e- 9 Factor: ER81; motif: RCCGGAARYN; match class: 1 TF
## 10 down 2.97e- 9 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 11 down 3.20e- 9 Factor: E2F-1; motif: TTTSGCGCGMNR TF
## 12 down 1.43e- 8 Factor: E2F; motif: TTTSGCGSG TF
## 13 down 1.72e- 8 Factor: ZF5; motif: NRNGNGCGCGCWN TF
## 14 down 3.65e- 8 Factor: E2F-1; motif: NNNSSCGCSAANN; match class: 1 TF
## 15 down 5.84e- 8 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN; match class: 1 TF
## 16 down 8.57e- 8 Factor: E2F-1; motif: TTTSGCGS TF
## 17 down 1.26e- 7 Factor: E2F1; motif: GSGCGGGAAN TF
## 18 down 1.71e- 7 Factor: E2F-4; motif: NTTTCSCGCC TF
## 19 down 1.76e- 7 Factor: ZF5; motif: GSGCGCGR; match class: 1 TF
## 20 down 1.98e- 7 Factor: ZF5; motif: GGSGCGCGS TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.000194 skin 2; fibrohistiocytic cells[≥Medium] HPA
## 2 up 0.000245 skin 1; fibrohistiocytic cells[≥Low] HPA
## 3 up 0.000991 skin 2; fibrohistiocytic cells[≥Low] HPA
## 4 up 0.00253 skin 1; fibrohistiocytic cells[≥Medium] HPA
## 5 up 0.00286 skin 1; endothelial cells[≥Low] HPA
## 6 up 0.00312 skin 1; cells in basal layer[≥Low] HPA
## 7 up 0.00390 skin 2; endothelial cells[≥Low] HPA
## 8 up 0.00402 skin 1; lymphocytes[≥Low] HPA
## 9 up 0.00447 skin 2; cells in basal layer[≥Low] HPA
## 10 up 0.00745 skin 2; endothelial cells[≥Medium] HPA
## 11 up 0.00762 skin 2; cells in basal layer[≥Medium] HPA
## 12 up 0.0101 skin 1; langerhans cells[≥Low] HPA
## 13 up 0.0110 skin 2; langerhans cells[≥Low] HPA
## 14 up 0.0164 skin 2; lymphocytes[≥Low] HPA
## 15 up 0.0165 skin 1; endothelial cells[≥Medium] HPA
## 16 up 0.0172 skin 2; lymphocytes[≥Medium] HPA
## 17 up 0.0303 skin 1; lymphocytes[High] HPA
## 18 up 0.0360 skin 2; langerhans cells[≥Medium] HPA
## 19 up 0.0401 skin 1; lymphocytes[≥Medium] HPA
## 20 up 0.0421 skin 1; cells in basal layer[≥Medium] HPA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.00000000661 skin 2; cells in spinous layer[≥Low] HPA
## 2 down 0.0000000296 skin 1; cells in basal layer[≥Low] HPA
## 3 down 0.0000000451 skin 1; cells in spinous layer[≥Low] HPA
## 4 down 0.000000160 skin 2; cells in basal layer[≥Low] HPA
## 5 down 0.000000235 skin 2; cells in spinous layer[≥Medium] HPA
## 6 down 0.00000263 skin 1; cells in spinous layer[≥Medium] HPA
## 7 down 0.00000295 skin 1; cells in basal layer[≥Medium] HPA
## 8 down 0.00000305 skin 2; cells in basal layer[≥Medium] HPA
## 9 down 0.0000240 skin 2; cells in basal layer[High] HPA
## 10 down 0.000338 skin 1; langerhans cells[≥Low] HPA
## 11 down 0.00113 skin 1; lymphocytes[≥Medium] HPA
## 12 down 0.00129 skin 1; fibrohistiocytic cells[High] HPA
## 13 down 0.00137 skin 1; langerhans cells[≥Medium] HPA
## 14 down 0.00147 skin 2; lymphocytes[≥Low] HPA
## 15 down 0.00149 skin 2; lymphocytes[≥Medium] HPA
## 16 down 0.00151 skin 1; cells in basal layer[High] HPA
## 17 down 0.00184 bone marrow; hematopoietic cells[High] HPA
## 18 down 0.00226 skin 1; lymphocytes[High] HPA
## 19 down 0.00228 skin 1; hair follicles[≥Low] HPA
## 20 down 0.00245 skin 1; endothelial cells[High] HPA
## # A tibble: 6 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.000845 Respiratory chain complex I (incomplete intermediate ND… CORUM
## 2 up 0.000955 Ribosome, cytoplasmic CORUM
## 3 up 0.00119 Respiratory chain complex I (gamma subunit) mitochondri… CORUM
## 4 up 0.0119 Respiratory chain complex I (holoenzyme), mitochondrial CORUM
## 5 up 0.0487 Cytochrome c oxidase, mitochondrial CORUM
## 6 up 0.0491 40S ribosomal subunit, cytoplasmic CORUM
## # A tibble: 1 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.0333 RC complex (Replication competent complex) CORUM
quickview_gprofiler_result(gprofiler_result_notordered)
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 2.09e-18 cytoplasmic translation GO:BP
## 2 up 9.40e-16 oxidative phosphorylation GO:BP
## 3 up 1.52e-15 aerobic electron transport chain GO:BP
## 4 up 9.66e-15 mitochondrial ATP synthesis coupled electron transport GO:BP
## 5 up 9.66e-15 ATP synthesis coupled electron transport GO:BP
## 6 up 3.16e-13 organonitrogen compound metabolic process GO:BP
## 7 up 7.11e-13 respiratory electron transport chain GO:BP
## 8 up 1.56e-12 aerobic respiration GO:BP
## 9 up 5.25e-12 organonitrogen compound biosynthetic process GO:BP
## 10 up 1.21e-11 electron transport chain GO:BP
## 11 up 8.20e-11 peptide metabolic process GO:BP
## 12 up 1.21e-10 translation GO:BP
## 13 up 2.63e-10 cellular respiration GO:BP
## 14 up 4.61e-10 peptide biosynthetic process GO:BP
## 15 up 1.09e- 9 amide metabolic process GO:BP
## 16 up 1.98e- 9 amide biosynthetic process GO:BP
## 17 up 4.93e- 9 purine ribonucleoside triphosphate biosynthetic process GO:BP
## 18 up 5.71e- 9 purine nucleoside triphosphate biosynthetic process GO:BP
## 19 up 1.17e- 8 ribonucleoside triphosphate biosynthetic process GO:BP
## 20 up 1.55e- 8 protein metabolic process GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.22e-27 chromosome organization GO:BP
## 2 down 8.08e-24 cell cycle GO:BP
## 3 down 5.28e-22 mitotic cell cycle GO:BP
## 4 down 2.86e-21 chromosome segregation GO:BP
## 5 down 6.65e-20 DNA metabolic process GO:BP
## 6 down 1.07e-19 cell cycle process GO:BP
## 7 down 1.10e-19 mitotic cell cycle process GO:BP
## 8 down 1.51e-19 sister chromatid segregation GO:BP
## 9 down 1.56e-19 mitotic sister chromatid segregation GO:BP
## 10 down 2.53e-18 cell division GO:BP
## 11 down 5.62e-18 nuclear chromosome segregation GO:BP
## 12 down 1.63e-16 mitotic nuclear division GO:BP
## 13 down 1.21e-14 DNA replication GO:BP
## 14 down 6.08e-14 nuclear division GO:BP
## 15 down 3.56e-13 organelle organization GO:BP
## 16 down 5.33e-13 organelle fission GO:BP
## 17 down 7.83e-13 chromosome separation GO:BP
## 18 down 8.94e-13 regulation of chromosome segregation GO:BP
## 19 down 1.03e-12 mitotic sister chromatid separation GO:BP
## 20 down 1.96e-12 regulation of chromosome separation GO:BP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 8.49e-19 Eukaryotic Translation Elongation REAC
## 2 up 4.62e-18 Peptide chain elongation REAC
## 3 up 9.55e-18 SRP-dependent cotranslational protein targeting to mem… REAC
## 4 up 6.41e-17 Cellular response to starvation REAC
## 5 up 8.17e-17 Viral mRNA Translation REAC
## 6 up 1.33e-16 Response of EIF2AK4 (GCN2) to amino acid deficiency REAC
## 7 up 1.33e-16 Formation of a pool of free 40S subunits REAC
## 8 up 2.51e-16 Eukaryotic Translation Termination REAC
## 9 up 2.51e-16 Selenocysteine synthesis REAC
## 10 up 4.29e-16 Nonsense Mediated Decay (NMD) independent of the Exon … REAC
## 11 up 1.54e-15 L13a-mediated translational silencing of Ceruloplasmin… REAC
## 12 up 1.93e-15 GTP hydrolysis and joining of the 60S ribosomal subunit REAC
## 13 up 9.03e-15 Eukaryotic Translation Initiation REAC
## 14 up 9.03e-15 Cap-dependent Translation Initiation REAC
## 15 up 4.81e-14 Nonsense-Mediated Decay (NMD) REAC
## 16 up 4.81e-14 Nonsense Mediated Decay (NMD) enhanced by the Exon Jun… REAC
## 17 up 5.93e-14 Selenoamino acid metabolism REAC
## 18 up 1.20e-13 Influenza Viral RNA Transcription and Replication REAC
## 19 up 3.31e-13 Influenza Infection REAC
## 20 up 6.27e-12 Regulation of expression of SLITs and ROBOs REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.20e-26 Cell Cycle, Mitotic REAC
## 2 down 2.21e-26 Cell Cycle REAC
## 3 down 1.82e-13 Mitotic Metaphase and Anaphase REAC
## 4 down 1.02e-12 Mitotic Anaphase REAC
## 5 down 1.91e-12 Resolution of Sister Chromatid Cohesion REAC
## 6 down 4.54e-12 Mitotic Prometaphase REAC
## 7 down 1.06e-11 Cell Cycle Checkpoints REAC
## 8 down 2.18e-11 Mitotic G1 phase and G1/S transition REAC
## 9 down 6.59e-11 G1/S Transition REAC
## 10 down 9.34e-11 M Phase REAC
## 11 down 2.60e-10 Separation of Sister Chromatids REAC
## 12 down 1.80e- 9 DNA strand elongation REAC
## 13 down 2.26e- 9 EML4 and NUDC in mitotic spindle formation REAC
## 14 down 6.57e- 9 Synthesis of DNA REAC
## 15 down 1.05e- 8 RHO GTPases Activate Formins REAC
## 16 down 1.11e- 8 S Phase REAC
## 17 down 4.84e- 8 Mitotic Spindle Checkpoint REAC
## 18 down 1.42e- 7 Amplification of signal from unattached kinetochores… REAC
## 19 down 1.42e- 7 Amplification of signal from the kinetochores REAC
## 20 down 7.97e- 7 Mitotic G2-G2/M phases REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 3.46e-26 cytoplasm GO:CC
## 2 up 4.21e-26 extracellular vesicle GO:CC
## 3 up 4.38e-26 extracellular membrane-bounded organelle GO:CC
## 4 up 4.38e-26 extracellular organelle GO:CC
## 5 up 7.09e-26 extracellular exosome GO:CC
## 6 up 3.88e-25 vesicle GO:CC
## 7 up 3.07e-20 cytosolic ribosome GO:CC
## 8 up 1.63e-18 extracellular space GO:CC
## 9 up 1.39e-17 inner mitochondrial membrane protein complex GO:CC
## 10 up 5.45e-17 organelle membrane GO:CC
## 11 up 1.06e-16 mitochondrial protein-containing complex GO:CC
## 12 up 1.13e-16 ribosomal subunit GO:CC
## 13 up 1.97e-16 respirasome GO:CC
## 14 up 5.66e-16 extracellular region GO:CC
## 15 up 5.95e-16 mitochondrial respirasome GO:CC
## 16 up 1.53e-15 cytoplasmic vesicle GO:CC
## 17 up 1.75e-15 intracellular vesicle GO:CC
## 18 up 5.60e-15 respiratory chain complex GO:CC
## 19 up 5.60e-15 endomembrane system GO:CC
## 20 up 2.35e-14 secretory granule GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 3.02e-26 cytoplasm GO:CC
## 2 down 4.46e-25 chromosomal region GO:CC
## 3 down 7.48e-24 nucleoplasm GO:CC
## 4 down 4.66e-23 cytosol GO:CC
## 5 down 9.20e-22 intracellular organelle lumen GO:CC
## 6 down 9.20e-22 membrane-enclosed lumen GO:CC
## 7 down 9.20e-22 organelle lumen GO:CC
## 8 down 2.44e-17 nuclear lumen GO:CC
## 9 down 1.08e-16 chromosome, centromeric region GO:CC
## 10 down 1.84e-15 condensed chromosome GO:CC
## 11 down 2.13e-15 chromosome GO:CC
## 12 down 3.20e-15 spindle GO:CC
## 13 down 5.98e-14 intracellular anatomical structure GO:CC
## 14 down 7.33e-14 condensed chromosome, centromeric region GO:CC
## 15 down 1.29e-13 kinetochore GO:CC
## 16 down 3.06e-13 membrane-bounded organelle GO:CC
## 17 down 1.81e-12 nuclear chromosome GO:CC
## 18 down 3.08e-12 intracellular membrane-bounded organelle GO:CC
## 19 down 4.58e-12 intracellular organelle GO:CC
## 20 down 1.11e-11 organelle GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 8.18e-11 protein binding GO:MF
## 2 up 3.56e-10 electron transfer activity GO:MF
## 3 up 5.11e-10 cell adhesion molecule binding GO:MF
## 4 up 1.82e- 9 oxidoreduction-driven active transmembrane transporter… GO:MF
## 5 up 7.94e- 9 cadherin binding GO:MF
## 6 up 2.38e- 8 primary active transmembrane transporter activity GO:MF
## 7 up 1.29e- 6 structural constituent of ribosome GO:MF
## 8 up 1.77e- 4 NADH dehydrogenase (ubiquinone) activity GO:MF
## 9 up 1.77e- 4 cadherin binding involved in cell-cell adhesion GO:MF
## 10 up 2.15e- 4 NADH dehydrogenase (quinone) activity GO:MF
## 11 up 3.14e- 4 NADH dehydrogenase activity GO:MF
## 12 up 3.76e- 4 NAD(P)H dehydrogenase (quinone) activity GO:MF
## 13 up 4.81e- 4 proton transmembrane transporter activity GO:MF
## 14 up 2.43e- 3 oxidoreductase activity, acting on NAD(P)H, quinone or… GO:MF
## 15 up 2.80e- 3 peroxiredoxin activity GO:MF
## 16 up 8.29e- 3 cell adhesion mediator activity GO:MF
## 17 up 8.72e- 3 oxidoreductase activity, acting on NAD(P)H GO:MF
## 18 up 1.06e- 2 oxidoreductase activity GO:MF
## 19 up 1.29e- 2 cell-cell adhesion mediator activity GO:MF
## 20 up 1.88e- 2 protein tag activity GO:MF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 7.26e-20 protein binding GO:MF
## 2 down 1.82e- 8 catalytic activity GO:MF
## 3 down 8.59e- 8 heterocyclic compound binding GO:MF
## 4 down 3.84e- 7 nucleotide binding GO:MF
## 5 down 3.85e- 7 single-stranded DNA helicase activity GO:MF
## 6 down 3.93e- 7 nucleoside phosphate binding GO:MF
## 7 down 8.40e- 7 single-stranded DNA binding GO:MF
## 8 down 5.34e- 6 cadherin binding GO:MF
## 9 down 6.50e- 6 anion binding GO:MF
## 10 down 8.80e- 6 purine nucleotide binding GO:MF
## 11 down 9.91e- 6 identical protein binding GO:MF
## 12 down 2.15e- 5 adenyl nucleotide binding GO:MF
## 13 down 4.97e- 5 chromatin binding GO:MF
## 14 down 5.54e- 5 ribonucleotide binding GO:MF
## 15 down 1.03e- 4 enzyme binding GO:MF
## 16 down 1.13e- 4 DNA polymerase binding GO:MF
## 17 down 1.62e- 4 purine ribonucleotide binding GO:MF
## 18 down 1.70e- 4 purine ribonucleoside triphosphate binding GO:MF
## 19 down 1.73e- 4 carbohydrate derivative binding GO:MF
## 20 down 3.22e- 4 DNA helicase activity GO:MF
## # A tibble: 8 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.000105 hsa-let-7c-5p MIRNA
## 2 up 0.00335 hsa-let-7e-5p MIRNA
## 3 up 0.00407 hsa-miR-30a-5p MIRNA
## 4 up 0.00411 hsa-miR-17-5p MIRNA
## 5 up 0.00576 hsa-miR-4460 MIRNA
## 6 up 0.00951 hsa-miR-140-5p MIRNA
## 7 up 0.00992 hsa-let-7a-5p MIRNA
## 8 up 0.0109 hsa-miR-652-3p MIRNA
## # A tibble: 11 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 9.79e-20 hsa-miR-193b-3p MIRNA
## 2 down 2.20e- 4 hsa-miR-744-5p MIRNA
## 3 down 5.95e- 4 hsa-miR-34a-5p MIRNA
## 4 down 1.04e- 3 hsa-miR-484 MIRNA
## 5 down 1.10e- 3 hsa-miR-16-5p MIRNA
## 6 down 1.09e- 2 hsa-miR-615-3p MIRNA
## 7 down 1.78e- 2 hsa-miR-215-5p MIRNA
## 8 down 1.85e- 2 hsa-miR-1226-3p MIRNA
## 9 down 2.61e- 2 hsa-miR-1-3p MIRNA
## 10 down 2.68e- 2 hsa-miR-6090 MIRNA
## 11 down 3.06e- 2 hsa-miR-103a-3p MIRNA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 1.28e-15 seminal vesicle; glandular cells[≥Low] HPA
## 2 up 1.28e-15 seminal vesicle HPA
## 3 up 3.36e-15 endometrium 1 HPA
## 4 up 1.78e-14 pancreas; exocrine glandular cells[≥Low] HPA
## 5 up 3.20e-14 pancreas HPA
## 6 up 3.74e-14 skin 2 HPA
## 7 up 3.79e-14 prostate; glandular cells[≥Low] HPA
## 8 up 3.79e-14 prostate HPA
## 9 up 3.99e-14 endometrium 2 HPA
## 10 up 6.27e-14 skin 1 HPA
## 11 up 1.16e-13 epididymis; glandular cells[≥Low] HPA
## 12 up 1.16e-13 epididymis HPA
## 13 up 2.13e-13 colon HPA
## 14 up 2.37e-13 endometrium 1; glandular cells[≥Low] HPA
## 15 up 3.11e-13 thyroid gland; glandular cells[≥Low] HPA
## 16 up 3.11e-13 thyroid gland HPA
## 17 up 1.33e-12 cervix; glandular cells[≥Low] HPA
## 18 up 1.34e-12 endometrium 2; glandular cells[≥Low] HPA
## 19 up 2.16e-12 gallbladder HPA
## 20 up 2.16e-12 gallbladder; glandular cells[≥Low] HPA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 1.32e-17 duodenum HPA
## 2 down 9.60e-16 skin 2; cells in spinous layer[≥Low] HPA
## 3 down 6.77e-15 skin 1; cells in basal layer[≥Low] HPA
## 4 down 7.47e-15 rectum HPA
## 5 down 1.79e-14 small intestine HPA
## 6 down 3.24e-14 skin 2; cells in basal layer[≥Low] HPA
## 7 down 4.02e-14 skin 1; cells in spinous layer[≥Low] HPA
## 8 down 2.58e-13 esophagus; squamous epithelial cells[≥Low] HPA
## 9 down 2.58e-13 esophagus HPA
## 10 down 1.28e-12 stomach 1; glandular cells[≥Low] HPA
## 11 down 1.28e-12 stomach 1 HPA
## 12 down 1.30e-12 skin 2; cells in spinous layer[≥Medium] HPA
## 13 down 1.37e-12 tonsil; germinal center cells[≥Low] HPA
## 14 down 1.67e-12 appendix HPA
## 15 down 2.22e-12 tonsil; squamous epithelial cells[≥Low] HPA
## 16 down 3.01e-12 esophagus; squamous epithelial cells[≥Medium] HPA
## 17 down 4.55e-12 tonsil HPA
## 18 down 1.01e-11 tonsil; squamous epithelial cells[≥Medium] HPA
## 19 down 1.34e-11 skin 2; cells in basal layer[≥Medium] HPA
## 20 down 1.73e-11 lymph node; germinal center cells[≥Low] HPA
## # A tibble: 6 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 8.48e-15 Cytoplasmic ribosomal proteins WP
## 2 up 3.85e-14 Electron transport chain OXPHOS system in mitochondria WP
## 3 up 9.22e- 6 Oxidative phosphorylation WP
## 4 up 7.29e- 4 VEGFA VEGFR2 signaling WP
## 5 up 2.77e- 3 Nonalcoholic fatty liver disease WP
## 6 up 5.00e- 2 Mitochondrial complex IV assembly WP
## # A tibble: 9 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 6.31e-17 Retinoblastoma gene in cancer WP
## 2 down 2.49e-11 DNA replication WP
## 3 down 2.90e- 5 G1 to S cell cycle control WP
## 4 down 3.74e- 5 Gastric cancer network 1 WP
## 5 down 8.80e- 5 Cell cycle WP
## 6 down 1.18e- 3 Gastric cancer network 2 WP
## 7 down 1.38e- 3 DNA mismatch repair WP
## 8 down 2.48e- 3 Cohesin complex Cornelia de Lange syndrome WP
## 9 down 3.33e- 2 DNA repair pathways full network WP
## # A tibble: 16 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 2.97e-16 Oxidative phosphorylation KEGG
## 2 up 1.06e-14 Ribosome KEGG
## 3 up 3.53e-10 Coronavirus disease - COVID-19 KEGG
## 4 up 1.61e- 9 Parkinson disease KEGG
## 5 up 4.37e- 9 Diabetic cardiomyopathy KEGG
## 6 up 4.92e- 9 Chemical carcinogenesis - reactive oxygen species KEGG
## 7 up 4.49e- 8 Huntington disease KEGG
## 8 up 7.73e- 8 Prion disease KEGG
## 9 up 7.97e- 8 Thermogenesis KEGG
## 10 up 9.70e- 8 Pathways of neurodegeneration - multiple diseases KEGG
## 11 up 5.49e- 7 Amyotrophic lateral sclerosis KEGG
## 12 up 1.74e- 6 Alzheimer disease KEGG
## 13 up 7.76e- 5 Cardiac muscle contraction KEGG
## 14 up 3.04e- 4 Non-alcoholic fatty liver disease KEGG
## 15 up 1.46e- 2 Mitophagy - animal KEGG
## 16 up 2.51e- 2 Lysosome KEGG
## # A tibble: 12 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 7.74e-11 DNA replication KEGG
## 2 down 5.87e-10 Cell cycle KEGG
## 3 down 5.24e- 4 Base excision repair KEGG
## 4 down 3.89e- 3 Oocyte meiosis KEGG
## 5 down 4.87e- 3 Mismatch repair KEGG
## 6 down 5.85e- 3 Fructose and mannose metabolism KEGG
## 7 down 7.00e- 3 Spliceosome KEGG
## 8 down 8.21e- 3 Nucleotide excision repair KEGG
## 9 down 1.04e- 2 Biosynthesis of nucleotide sugars KEGG
## 10 down 1.33e- 2 Metabolic pathways KEGG
## 11 down 2.91e- 2 Pentose phosphate pathway KEGG
## 12 down 3.72e- 2 Biosynthesis of amino acids KEGG
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 0.0000000135 Factor: Kaiso; motif: TCTCGCGAG TF
## 2 up 0.0000000554 Factor: E2F; motif: GGCGSG TF
## 3 up 0.000000565 Factor: E2F-2; motif: GCGCGCGCNCS; match class: 1 TF
## 4 up 0.000000642 Factor: E2F-1:HES-7; motif: GGCRCGTGSYNNWNGGCGCSM;… TF
## 5 up 0.000000703 Factor: CHD2; motif: TCTCGCGAG TF
## 6 up 0.000000728 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN TF
## 7 up 0.000000808 Factor: ZF5; motif: GSGCGCGR TF
## 8 up 0.000000903 Factor: Kaiso; motif: TCTCGCGAG; match class: 1 TF
## 9 up 0.00000171 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 10 up 0.00000233 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN; match cla… TF
## 11 up 0.00000433 Factor: E2F-4:DP-1; motif: TTTSGCGC TF
## 12 up 0.00000491 Factor: ZF5; motif: GGSGCGCGS TF
## 13 up 0.00000517 Factor: E2F; motif: GGCGSG; match class: 1 TF
## 14 up 0.00000569 Factor: IRX-1; motif: NACRYNNNNNNNNRYGNN; match cl… TF
## 15 up 0.00000601 Factor: p300; motif: ACNTCCG; match class: 1 TF
## 16 up 0.00000613 Factor: Churchill; motif: CGGGNN TF
## 17 up 0.00000637 Factor: c-ets-2; motif: ACCGGAWRTN TF
## 18 up 0.00000657 Factor: E2F-3:HES-7; motif: NNNSGCGCSNNNNNCRCGYGNN… TF
## 19 up 0.00000784 Factor: TCF-1; motif: ACATCGRGRCGCTGW TF
## 20 up 0.00000909 Factor: E2F-1; motif: NGGGCGGGARV TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 4.19e-14 Factor: E2F-4; motif: SNGGGCGGGAANN; match class: 1 TF
## 2 down 1.55e-12 Factor: E2F-1; motif: NNNSSCGCSAANN TF
## 3 down 2.19e-12 Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 TF
## 4 down 5.19e-12 Factor: E2F4; motif: YCCCGCCNCNNSSNNSNN; match class: 1 TF
## 5 down 7.69e-12 Factor: ZF5; motif: NRNGNGCGCGCWN; match class: 1 TF
## 6 down 1.15e-11 Factor: E2F; motif: TTTSGCGSG TF
## 7 down 1.31e-11 Factor: ZF5; motif: GGSGCGCGS; match class: 1 TF
## 8 down 3.46e-11 Factor: E2F-1; motif: NGGGCGGGARV; match class: 1 TF
## 9 down 3.99e-11 Factor: E2F; motif: NCSCGCSAAAN TF
## 10 down 4.60e-11 Factor: ZF5; motif: NRNGNGCGCGCWN TF
## 11 down 1.14e-10 Factor: ZF5; motif: GSGCGCGR TF
## 12 down 1.18e-10 Factor: ZF5; motif: GGSGCGCGS TF
## 13 down 2.12e-10 Factor: E2F; motif: NKCGCGCSAAAN TF
## 14 down 3.29e-10 Factor: E2F-2; motif: GCGCGCGCNCS TF
## 15 down 3.81e-10 Factor: ZF5; motif: GSGCGCGR; match class: 1 TF
## 16 down 7.08e-10 Factor: E2F-3:HES-7; motif: NNNSGCGCSNNNNNCRCGYGNN; ma… TF
## 17 down 8.56e-10 Factor: ER81; motif: RCCGGAARYN; match class: 1 TF
## 18 down 8.69e-10 Factor: E2F1; motif: GSGCGGGAAN TF
## 19 down 8.71e-10 Factor: E2F-4; motif: NTTTCSCGCC TF
## 20 down 1.04e- 9 Factor: E2F-1; motif: TTTSGCGCGMNR TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 6.43e-11 Mitochondrial inheritance HP
## 2 up 3.33e-10 Centrocecal scotoma HP
## 3 up 1.21e- 9 Leber optic atrophy HP
## 4 up 1.28e- 8 Central retinal vessel vascular tortuosity HP
## 5 up 1.28e- 8 Retinal arterial tortuosity HP
## 6 up 5.67e- 8 Arterial tortuosity HP
## 7 up 7.00e- 8 Mitochondrial respiratory chain defects HP
## 8 up 1.30e- 7 Ventricular preexcitation HP
## 9 up 1.66e- 7 Normochromic anemia HP
## 10 up 2.80e- 7 Vascular tortuosity HP
## 11 up 2.80e- 7 Erythroid hypoplasia HP
## 12 up 1.18e- 6 Abnormal radial artery morphology HP
## 13 up 1.18e- 6 Elevated red cell adenosine deaminase activity HP
## 14 up 1.18e- 6 Radial artery aplasia HP
## 15 up 1.74e- 6 Abnormal erythrocyte adenosine deaminase activity HP
## 16 up 1.74e- 6 Retinal telangiectasia HP
## 17 up 2.37e- 6 Distal peripheral sensory neuropathy HP
## 18 up 2.53e- 6 Macrocytic dyserythropoietic anemia HP
## 19 up 2.66e- 6 Malignant genitourinary tract tumor HP
## 20 up 3.89e- 6 Abnormal number of erythroid precursors HP
## # A tibble: 0 × 4
## # ℹ 4 variables: query <chr>, p_value <dbl>, term_name <chr>, source <chr>
## # A tibble: 6 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 up 1.08e-10 Ribosome, cytoplasmic CORUM
## 2 up 2.90e- 5 40S ribosomal subunit, cytoplasmic CORUM
## 3 up 5.99e- 5 40S ribosomal subunit, cytoplasmic CORUM
## 4 up 1.95e- 4 Nop56p-associated pre-rRNA complex CORUM
## 5 up 2.00e- 4 60S ribosomal subunit, cytoplasmic CORUM
## 6 up 4.12e- 2 TRBP containing complex (DICER, RPL7A, EIF6, MOV10 and … CORUM
## # A tibble: 2 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 down 0.00630 RC complex (Replication competent complex) CORUM
## 2 down 0.0497 Importin alpha-CAS-RanGTP complex CORUM
TF
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)
