nanoporeDRS_m3Csites_middleC_gprofiler.R
shuheimitsutomi
2024-07-30
suppressPackageStartupMessages(library(tidyverse))
devtools::load_all('~/Google Drive/My Drive/Scripts/R_packages/myUtilities/')## ℹ Loading myUtilitieswd <- "~/Google Drive/My Drive/Analysis/METTL2A/"
setwd(wd)
tabledir <- paste0(wd, 'Tables/DRS_m3C_sites/Gprofiler/')
figdir <- paste0(wd, 'Figures/DRS_m3C_sites/Gprofiler/')
theme_set(
theme_classic(base_size = 7) +
theme(legend.position = 'bottom')
)Functions
gprofiler_gost <- function() {
gostres <-
gprofiler2::gost(
query = list(
'methylated' = str_remove(
num_sites_in_transcripts$transcript_id,
'[.][0-9]+$')
),
organism = 'hsapiens',
ordered_query = TRUE,
significant = TRUE,
#multi_query = TRUE
)
gostres$result |>
as_tibble()
}
simplify_terms <- function(df) {
term_ranks <-
df |>
arrange(p_value) |>
select(rank, query, term_id) |>
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) |>
rename(parent_term_id = parents) |>
left_join(term_ranks) |>
filter(is.na(parent_term_rank) | rank < parent_term_rank) |>
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()
)
}Read data
num_sites_in_transcripts <-
read_tsv(
paste0(wd, 'Tables/DRS/Positions/common_sig_seqs_in_intensity_up_2024-04-10.tsv.gz')
) |>
filter(middle_isC == 'C')## Rows: 605 Columns: 65
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (30): transcript_id, transcript_name, ref_kmer, GMM_cov_type_G, cluster_...
## dbl (35): position, GMM_logit_pvalue_G, KS_dwell_pvalue_G, KS_intensity_pval...
##
## 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.num_sites_in_transcripts## # A tibble: 489 × 65
## transcript_id transcript_name position ref_kmer GMM_logit_pvalue_G
## <chr> <chr> <dbl> <chr> <dbl>
## 1 ENST00000429711.7 RPL32-204 422 GCCCA 1
## 2 ENST00000647248.2 RPL35A-211 380 ACCCC 1
## 3 ENST00000647248.2 RPL35A-211 381 CCCCT 1
## 4 ENST00000389680.2 MT-RNR1-201 57 CCCCG 1
## 5 ENST00000389680.2 MT-RNR1-201 75 ACCCT 0.777
## 6 ENST00000389680.2 MT-RNR1-201 93 ATCAA 1
## 7 ENST00000389680.2 MT-RNR1-201 148 GCCAC 1
## 8 ENST00000389680.2 MT-RNR1-201 153 ACCCC 1
## 9 ENST00000389680.2 MT-RNR1-201 154 CCCCC 1
## 10 ENST00000389680.2 MT-RNR1-201 155 CCCCA 1
## # ℹ 479 more rows
## # ℹ 60 more variables: KS_dwell_pvalue_G <dbl>, KS_intensity_pvalue_G <dbl>,
## # GMM_cov_type_G <chr>, GMM_n_clust_G <dbl>, cluster_counts_G <chr>,
## # Logit_LOR_G <dbl>, c1_mean_intensity_G <dbl>, c2_mean_intensity_G <dbl>,
## # c1_median_intensity_G <dbl>, c2_median_intensity_G <dbl>,
## # c1_sd_intensity_G <dbl>, c2_sd_intensity_G <dbl>, c1_mean_dwell_G <dbl>,
## # c2_mean_dwell_G <dbl>, c1_median_dwell_G <dbl>, c2_median_dwell_G <dbl>, …Gprofile
gprofiler_result <-
gprofiler_gost() |>
mutate(
signed_log10p = -log10(p_value)
) |>
arrange(p_value)
gprofiler_result## # A tibble: 537 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 methyl… TRUE 3.51e-50 117 64 30 0.469
## 2 methyl… TRUE 8.34e-45 90 64 30 0.469
## 3 methyl… TRUE 3.95e-44 94 64 30 0.469
## 4 methyl… TRUE 1.26e-42 90 64 29 0.453
## 5 methyl… TRUE 2.30e-42 156 64 29 0.453
## 6 methyl… TRUE 5.59e-42 94 64 29 0.453
## 7 methyl… TRUE 5.59e-42 94 64 29 0.453
## 8 methyl… TRUE 1.15e-41 96 64 29 0.453
## 9 methyl… TRUE 5.53e-41 192 64 29 0.453
## 10 methyl… TRUE 8.89e-41 102 64 29 0.453
## # ℹ 527 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_GOBP_simplified <-
gprofiler_result |>
filter(source == 'GO:BP') |>
rownames_to_column(var = 'rank')
gprofiler_result_GOBP_simplified |>
export_tsv(outdir = tabledir)##
## Exported to: ~/Google Drive/My Drive/Analysis/METTL2A/Tables/DRS_m3C_sites/Gprofiler/gprofiler_result_GOBP_simplified_2024-07-30.tsv## # A tibble: 71 × 16
## rank query significant p_value term_size query_size intersection_size
## <chr> <chr> <lgl> <dbl> <int> <int> <int>
## 1 1 methylated TRUE 2.30e-42 156 64 29
## 2 2 methylated TRUE 2.53e-25 723 64 31
## 3 3 methylated TRUE 8.39e-25 752 64 31
## 4 4 methylated TRUE 1.20e-22 887 59 30
## 5 5 methylated TRUE 1.42e-22 1761 65 39
## 6 6 methylated TRUE 2.61e-22 911 59 30
## 7 7 methylated TRUE 6.59e-19 1194 59 30
## 8 8 methylated TRUE 9.86e-14 145 14 9
## 9 9 methylated TRUE 5.35e-13 92 14 8
## 10 10 methylated TRUE 1.07e-12 100 14 8
## # ℹ 61 more rows
## # ℹ 9 more variables: precision <dbl>, recall <dbl>, term_id <chr>,
## # source <chr>, term_name <chr>, effective_domain_size <int>,
## # source_order <int>, parents <list>, signed_log10p <dbl>methylated_genes_GOBP_barplot <-
gprofiler_result_GOBP_simplified |>
select(query, signed_log10p, term_name, source) |>
filter(source == 'GO:BP') |>
head(10) |>
ggplot(aes(x = reorder(term_name, signed_log10p),
y = signed_log10p, label = term_name)) +
geom_bar(stat = 'identity', fill = 'grey20', alpha = .2) +
geom_text(hjust = 0, colour = 'black', y = 0.2, size = 2.5) +
coord_flip() +
dual_barplot_theme()
methylated_genes_GOBP_barplot
ggsave(
plot = methylated_genes_GOBP_barplot,
filename = paste0(
wd, 'Figures/DRS_m3C_sites/Gprofiler/2024-04-15_methylated_genes_GOBP_barplot.pdf'
),
width = 4, height = 6, units = 'cm'
)
gprofiler_result_GOBP_simplified |>
#select(query, signed_log10p, term_name, source) |>
filter(source == 'GO:BP') |>
head(10) |>
ggplot(aes(
x = reorder(term_name, signed_log10p),
y = 'query',
fill = signed_log10p
)) +
geom_tile() +
coord_flip() +
scale_fill_gradient(limits = c(0, 100), low = 'gray', high = 'red') +
theme_minimal()
for (gp_source in unique(gprofiler_result$source)) {
filtered_resuls <-
gprofiler_result |>
filter(source == gp_source) |>
select(query, p_value, term_name, source) |>
head(20)
filtered_resuls |>
print()
plot_bar <-
filtered_resuls |>
ggplot(aes(
x = reorder(term_name, -p_value),
y = p_value |> log10())) +
geom_bar(stat = 'identity') +
labs(title = gp_source) +
coord_flip()
print(plot_bar)
}## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 3.51e-50 cytosolic ribosome GO:CC
## 2 methylated 5.53e-41 ribosomal subunit GO:CC
## 3 methylated 3.25e-31 ribosome GO:CC
## 4 methylated 4.97e-29 cytosolic large ribosomal subunit GO:CC
## 5 methylated 3.82e-23 large ribosomal subunit GO:CC
## 6 methylated 6.29e-19 cytosolic small ribosomal subunit GO:CC
## 7 methylated 1.42e-15 small ribosomal subunit GO:CC
## 8 methylated 2.61e-14 inner mitochondrial membrane protein complex GO:CC
## 9 methylated 5.85e-14 respiratory chain complex GO:CC
## 10 methylated 7.61e-14 mitochondrial respirasome GO:CC
## 11 methylated 1.47e-13 respirasome GO:CC
## 12 methylated 1.59e-13 focal adhesion GO:CC
## 13 methylated 2.34e-13 cell-substrate junction GO:CC
## 14 methylated 6.98e-13 extracellular exosome GO:CC
## 15 methylated 9.56e-13 extracellular vesicle GO:CC
## 16 methylated 9.68e-13 extracellular membrane-bounded organelle GO:CC
## 17 methylated 9.68e-13 extracellular organelle GO:CC
## 18 methylated 8.62e-12 mitochondrial protein-containing complex GO:CC
## 19 methylated 1.43e-11 protein-containing complex GO:CC
## 20 methylated 2.91e-10 anchoring junction GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 8.34e-45 Peptide chain elongation REAC
## 2 methylated 3.95e-44 Eukaryotic Translation Elongation REAC
## 3 methylated 1.26e-42 Viral mRNA Translation REAC
## 4 methylated 5.59e-42 Eukaryotic Translation Termination REAC
## 5 methylated 5.59e-42 Selenocysteine synthesis REAC
## 6 methylated 1.15e-41 Nonsense Mediated Decay (NMD) independent of the … REAC
## 7 methylated 8.89e-41 Formation of a pool of free 40S subunits REAC
## 8 methylated 8.89e-41 Response of EIF2AK4 (GCN2) to amino acid deficien… REAC
## 9 methylated 2.00e-39 L13a-mediated translational silencing of Cerulopl… REAC
## 10 methylated 2.69e-39 GTP hydrolysis and joining of the 60S ribosomal s… REAC
## 11 methylated 2.69e-39 SRP-dependent cotranslational protein targeting t… REAC
## 12 methylated 6.36e-39 Nonsense Mediated Decay (NMD) enhanced by the Exo… REAC
## 13 methylated 6.36e-39 Nonsense-Mediated Decay (NMD) REAC
## 14 methylated 8.44e-39 Selenoamino acid metabolism REAC
## 15 methylated 1.93e-38 Eukaryotic Translation Initiation REAC
## 16 methylated 1.93e-38 Cap-dependent Translation Initiation REAC
## 17 methylated 5.41e-37 Influenza Viral RNA Transcription and Replication REAC
## 18 methylated 3.81e-35 Influenza Infection REAC
## 19 methylated 1.06e-34 Cellular response to starvation REAC
## 20 methylated 1.53e-33 Regulation of expression of SLITs and ROBOs REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 2.30e-42 cytoplasmic translation GO:BP
## 2 methylated 2.53e-25 translation GO:BP
## 3 methylated 8.39e-25 peptide biosynthetic process GO:BP
## 4 methylated 1.20e-22 amide biosynthetic process GO:BP
## 5 methylated 1.42e-22 organonitrogen compound biosynthetic process GO:BP
## 6 methylated 2.61e-22 peptide metabolic process GO:BP
## 7 methylated 6.59e-19 amide metabolic process GO:BP
## 8 methylated 9.86e-14 oxidative phosphorylation GO:BP
## 9 methylated 5.35e-13 aerobic electron transport chain GO:BP
## 10 methylated 1.07e-12 mitochondrial ATP synthesis coupled electron tran… GO:BP
## 11 methylated 1.07e-12 ATP synthesis coupled electron transport GO:BP
## 12 methylated 1.57e-12 aerobic respiration GO:BP
## 13 methylated 5.49e-12 respiratory electron transport chain GO:BP
## 14 methylated 1.16e-11 cellular respiration GO:BP
## 15 methylated 1.04e-10 electron transport chain GO:BP
## 16 methylated 2.05e-10 energy derivation by oxidation of organic compoun… GO:BP
## 17 methylated 1.31e- 9 ribosome biogenesis GO:BP
## 18 methylated 1.72e- 9 cellular nitrogen compound biosynthetic process GO:BP
## 19 methylated 4.83e- 9 generation of precursor metabolites and energy GO:BP
## 20 methylated 1.10e- 7 organonitrogen compound metabolic process GO:BP
## # A tibble: 7 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 5.63e-40 Cytoplasmic ribosomal proteins WP
## 2 methylated 1.63e-12 Electron transport chain OXPHOS system in mitochon… WP
## 3 methylated 3.26e- 6 Oxidative phosphorylation WP
## 4 methylated 1.61e- 3 Mitochondrial complex IV assembly WP
## 5 methylated 9.98e- 3 Neuroinflammation WP
## 6 methylated 1.26e- 2 Mitochondrial complex I assembly model OXPHOS syst… WP
## 7 methylated 1.53e- 2 Nonalcoholic fatty liver disease WP
## # A tibble: 16 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 1.18e-32 Ribosome KEGG
## 2 methylated 3.61e-27 Coronavirus disease - COVID-19 KEGG
## 3 methylated 7.46e-12 Oxidative phosphorylation KEGG
## 4 methylated 1.48e-10 Diabetic cardiomyopathy KEGG
## 5 methylated 7.17e-10 Chemical carcinogenesis - reactive oxygen species KEGG
## 6 methylated 1.11e- 9 Thermogenesis KEGG
## 7 methylated 3.69e- 9 Parkinson disease KEGG
## 8 methylated 4.51e- 9 Prion disease KEGG
## 9 methylated 1.30e- 8 Huntington disease KEGG
## 10 methylated 6.16e- 8 Amyotrophic lateral sclerosis KEGG
## 11 methylated 8.24e- 8 Alzheimer disease KEGG
## 12 methylated 6.55e- 7 Pathways of neurodegeneration - multiple diseases KEGG
## 13 methylated 8.15e- 4 Cardiac muscle contraction KEGG
## 14 methylated 1.56e- 3 Metabolic pathways KEGG
## 15 methylated 4.80e- 3 Retrograde endocannabinoid signaling KEGG
## 16 methylated 7.74e- 3 Non-alcoholic fatty liver disease KEGG
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 4.17e-30 structural constituent of ribosome GO:MF
## 2 methylated 1.34e-22 structural molecule activity GO:MF
## 3 methylated 1.24e-14 oxidoreduction-driven active transmembrane transp… GO:MF
## 4 methylated 1.26e-12 electron transfer activity GO:MF
## 5 methylated 2.54e-11 primary active transmembrane transporter activity GO:MF
## 6 methylated 1.59e- 8 RNA binding GO:MF
## 7 methylated 8.07e- 8 active transmembrane transporter activity GO:MF
## 8 methylated 1.06e- 6 oxidoreductase activity GO:MF
## 9 methylated 3.96e- 6 transmembrane transporter activity GO:MF
## 10 methylated 5.12e- 6 cytochrome-c oxidase activity GO:MF
## 11 methylated 5.12e- 6 oxidoreductase activity, acting on a heme group o… GO:MF
## 12 methylated 5.19e- 6 NADH dehydrogenase (ubiquinone) activity GO:MF
## 13 methylated 5.74e- 6 NADH dehydrogenase (quinone) activity GO:MF
## 14 methylated 6.95e- 6 NADH dehydrogenase activity GO:MF
## 15 methylated 7.63e- 6 NAD(P)H dehydrogenase (quinone) activity GO:MF
## 16 methylated 9.08e- 6 transporter activity GO:MF
## 17 methylated 9.88e- 6 proton transmembrane transporter activity GO:MF
## 18 methylated 2.01e- 5 oxidoreductase activity, acting on NAD(P)H, quino… GO:MF
## 19 methylated 1.18e- 4 oxidoreductase activity, acting on NAD(P)H GO:MF
## 20 methylated 7.34e- 3 heparan sulfate binding GO:MF
## # A tibble: 11 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 1.14e-22 Ribosome, cytoplasmic CORUM
## 2 methylated 6.70e-14 Nop56p-associated pre-rRNA complex CORUM
## 3 methylated 8.75e-13 60S ribosomal subunit, cytoplasmic CORUM
## 4 methylated 3.21e- 8 40S ribosomal subunit, cytoplasmic CORUM
## 5 methylated 1.80e- 7 40S ribosomal subunit, cytoplasmic CORUM
## 6 methylated 2.58e- 5 Respiratory chain complex I (incomplete intermedi… CORUM
## 7 methylated 1.95e- 4 TRBP containing complex (DICER, RPL7A, EIF6, MOV1… CORUM
## 8 methylated 1.82e- 3 Respiratory chain complex I (gamma subunit) mitoc… CORUM
## 9 methylated 1.92e- 3 Cytochrome c oxidase, mitochondrial CORUM
## 10 methylated 2.54e- 2 Ecsit complex (ECSIT, MT-CO2, NDUFA1, MT-ND1, TRA… CORUM
## 11 methylated 3.41e- 2 Ferritin complex CORUM
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 6.26e-15 Mitochondrial inheritance HP
## 2 methylated 5.91e-13 Centrocecal scotoma HP
## 3 methylated 2.06e-12 Ventricular preexcitation HP
## 4 methylated 2.10e-12 Episodic vomiting HP
## 5 methylated 3.03e-12 Mitochondrial myopathy HP
## 6 methylated 3.03e-12 Ragged-red muscle fibers HP
## 7 methylated 1.26e-11 Abnormal mitochondria in muscle tissue HP
## 8 methylated 2.65e-11 Mitochondrial respiratory chain defects HP
## 9 methylated 4.48e-11 Leber optic atrophy HP
## 10 methylated 1.83e-10 Muscle abnormality related to mitochondrial dysfu… HP
## 11 methylated 1.97e-10 Retinal arterial tortuosity HP
## 12 methylated 1.97e-10 Central retinal vessel vascular tortuosity HP
## 13 methylated 3.00e-10 Retinal telangiectasia HP
## 14 methylated 1.80e- 9 Slow decrease in visual acuity HP
## 15 methylated 1.14e- 8 Stroke-like episode HP
## 16 methylated 1.27e- 8 Blurred vision HP
## 17 methylated 1.65e- 8 Proximal tubulopathy HP
## 18 methylated 1.81e- 8 Sensorimotor neuropathy HP
## 19 methylated 1.90e- 8 Multiple glomerular cysts HP
## 20 methylated 1.90e- 8 Mixed demyelinating and axonal polyneuropathy HP
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.000000543 Factor: GCMa:HOXB13; motif: RTGCGGGTMATAAAN TF
## 2 methylated 0.000133 Factor: GCMa:HOXA13; motif: RTGCGGGTAATAAA TF
## 3 methylated 0.000618 Factor: GCMa:HOXB13; motif: RTGCGGGTMATAAAN; m… TF
## 4 methylated 0.000734 Factor: GCMb:Prrxl1; motif: ATRCGGGTNATTAN TF
## 5 methylated 0.000955 Factor: GCMb:FOXI1; motif: RTAAATANGGGNN TF
## 6 methylated 0.00122 Factor: MYBL1; motif: ACCGTTAACSGY TF
## 7 methylated 0.00450 Factor: ZNF647; motif: NTAGGCCTAN; match class… TF
## 8 methylated 0.00585 Factor: GCMa:HOXA2; motif: RTRNGGGYNTAATNN TF
## 9 methylated 0.00967 Factor: Barhl-1; motif: NTAAACGN; match class:… TF
## 10 methylated 0.0103 Factor: ZNF286; motif: NTTGGCGGATGM TF
## 11 methylated 0.0103 Factor: ZNF286B; motif: NTTGGCGGATGM TF
## 12 methylated 0.0115 Factor: HOXB2:PEA3; motif: ACCGGAAATGRN TF
## 13 methylated 0.0120 Factor: Oct-1; motif: NNNRTAATNANNN; match cla… TF
## 14 methylated 0.0125 Factor: GCMa:HOXA2; motif: RTRNGGGYNTAATNN; ma… TF
## 15 methylated 0.0141 Factor: Bcl-6; motif: NTTYCTAGRA; match class:… TF
## 16 methylated 0.0162 Factor: SAP-1; motif: NTCGTAAATGCN TF
## 17 methylated 0.0163 Factor: E2F2; motif: AAAATGGCGCCATTTT TF
## 18 methylated 0.0213 Factor: HOXA5; motif: TGCNHNCWYCCYCATTAKTGNDCN… TF
## 19 methylated 0.0354 Factor: meis1:Elf-1; motif: NTGCCGGAAGTN; matc… TF
## 20 methylated 0.0365 Factor: GCMa; motif: ATGNGGGYR TF
## # A tibble: 14 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.00000239 hsa-miR-652-3p MIRNA
## 2 methylated 0.00000791 hsa-miR-744-5p MIRNA
## 3 methylated 0.0000462 hsa-let-7c-5p MIRNA
## 4 methylated 0.0000680 hsa-miR-100-5p MIRNA
## 5 methylated 0.0000731 hsa-miR-320a MIRNA
## 6 methylated 0.000137 hsa-let-7e-5p MIRNA
## 7 methylated 0.000210 hsa-miR-296-3p MIRNA
## 8 methylated 0.000255 hsa-let-7a-5p MIRNA
## 9 methylated 0.00309 hsa-miR-760 MIRNA
## 10 methylated 0.0131 hsa-miR-16-5p MIRNA
## 11 methylated 0.0138 hsa-miR-615-3p MIRNA
## 12 methylated 0.0144 hsa-let-7b-5p MIRNA
## 13 methylated 0.0209 hsa-miR-99a-5p MIRNA
## 14 methylated 0.0457 hsa-miR-320c MIRNA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.00219 duodenum; paneth cells[High] HPA
## 2 methylated 0.00315 appendix; goblet cells[High] HPA
## 3 methylated 0.00399 appendix; enterocytes[High] HPA
## 4 methylated 0.00517 small intestine; goblet cells[≥Medium] HPA
## 5 methylated 0.00590 colon; goblet cells[High] HPA
## 6 methylated 0.00633 small intestine; goblet cells[High] HPA
## 7 methylated 0.00633 duodenum; goblet cells[High] HPA
## 8 methylated 0.00694 rectum; goblet cells[High] HPA
## 9 methylated 0.00727 duodenum; glands of Brunner[High] HPA
## 10 methylated 0.00776 colon; enterocytes[High] HPA
## 11 methylated 0.00923 duodenum; paneth cells[≥Medium] HPA
## 12 methylated 0.00963 rectum; enterocytes[High] HPA
## 13 methylated 0.00993 appendix; goblet cells[≥Low] HPA
## 14 methylated 0.0105 appendix; endocrine cells[High] HPA
## 15 methylated 0.0111 duodenum; enterocytes[High] HPA
## 16 methylated 0.0134 duodenum; goblet cells[≥Low] HPA
## 17 methylated 0.0136 small intestine; enterocytes[High] HPA
## 18 methylated 0.0145 small intestine; goblet cells[≥Low] HPA
## 19 methylated 0.0161 colon; endocrine cells[High] HPA
## 20 methylated 0.0168 appendix; endocrine cells[≥Low] HPA