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
wd <- "/Users/s-mitsutomi/My Drive (shuheimitsutomi@ric.u-tokyo.ac.jp)/Analysis/METTL2A/"
setwd(wd)
tabledir <- paste0(wd, 'Tables/DRS_m3C_sites/Gprofiler/')
figdir <- paste0(wd, 'Figures/DRS_m3C_sites/Gprofiler/')
num_sites_in_transcripts <-
read_tsv(
paste0(wd, 'Tables/DRS/Positions/common_sig_seqs_in_intensity_up_2024-04-10.tsv.gz')
)
## 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: 605 × 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 43 ACACA 1
## 5 ENST00000389680.2 MT-RNR1-201 57 CCCCG 1
## 6 ENST00000389680.2 MT-RNR1-201 71 GTTCA 1
## 7 ENST00000389680.2 MT-RNR1-201 73 TCACC 1
## 8 ENST00000389680.2 MT-RNR1-201 75 ACCCT 0.777
## 9 ENST00000389680.2 MT-RNR1-201 93 ATCAA 1
## 10 ENST00000389680.2 MT-RNR1-201 138 GCTTA 1
## # ℹ 595 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>, …
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()
)
}
gprofiler_result <-
gprofiler_gost() |>
mutate(
signed_log10p = -log10(p_value)
) |>
arrange(p_value)
gprofiler_result
## # A tibble: 576 × 15
## query significant p_value term_size query_size intersection_size precision
## <chr> <lgl> <dbl> <int> <int> <int> <dbl>
## 1 methyl… TRUE 1.65e-49 117 76 31 0.408
## 2 methyl… TRUE 5.94e-44 90 76 31 0.408
## 3 methyl… TRUE 2.99e-43 94 76 31 0.408
## 4 methyl… TRUE 4.05e-42 192 76 31 0.408
## 5 methyl… TRUE 7.14e-42 90 76 30 0.395
## 6 methyl… TRUE 1.26e-41 156 76 30 0.395
## 7 methyl… TRUE 3.37e-41 94 76 30 0.395
## 8 methyl… TRUE 3.37e-41 94 76 30 0.395
## 9 methyl… TRUE 7.11e-41 96 76 30 0.395
## 10 methyl… TRUE 5.98e-40 102 76 30 0.395
## # ℹ 566 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') |>
simplify_terms()
## Joining with `by = join_by(query, parent_term_id)`
gprofiler_result_GOBP_simplified
## # A tibble: 66 × 7
## rank query signed_log10p source term_name term_id source_order
## <chr> <chr> <dbl> <chr> <chr> <chr> <int>
## 1 1 methylated 40.9 GO:BP cytoplasmic trans… GO:000… 736
## 2 2 methylated 25.8 GO:BP translation GO:000… 2194
## 3 3 methylated 25.3 GO:BP peptide biosynthe… GO:004… 10843
## 4 4 methylated 23.0 GO:BP amide biosyntheti… GO:004… 11153
## 5 5 methylated 22.6 GO:BP peptide metabolic… GO:000… 2266
## 6 6 methylated 22.6 GO:BP organonitrogen co… GO:190… 22100
## 7 7 methylated 20.1 GO:BP amide metabolic p… GO:004… 11152
## 8 10 methylated 12.0 GO:BP mitochondrial ATP… GO:004… 10709
## 9 11 methylated 12.0 GO:BP ATP synthesis cou… GO:004… 10707
## 10 12 methylated 11.8 GO:BP aerobic respirati… GO:000… 3273
## # ℹ 56 more rows
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()
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 1.65e-49 cytosolic ribosome GO:CC
## 2 methylated 4.05e-42 ribosomal subunit GO:CC
## 3 methylated 2.72e-31 ribosome GO:CC
## 4 methylated 7.75e-30 cytosolic large ribosomal subunit GO:CC
## 5 methylated 1.79e-25 large ribosomal subunit GO:CC
## 6 methylated 6.12e-18 cytosolic small ribosomal subunit GO:CC
## 7 methylated 2.03e-16 small ribosomal subunit GO:CC
## 8 methylated 5.16e-16 focal adhesion GO:CC
## 9 methylated 8.15e-16 cell-substrate junction GO:CC
## 10 methylated 2.73e-14 inner mitochondrial membrane protein complex GO:CC
## 11 methylated 6.01e-14 cytosol GO:CC
## 12 methylated 6.11e-14 respiratory chain complex GO:CC
## 13 methylated 7.78e-14 extracellular exosome GO:CC
## 14 methylated 7.96e-14 mitochondrial respirasome GO:CC
## 15 methylated 1.11e-13 extracellular vesicle GO:CC
## 16 methylated 1.12e-13 extracellular organelle GO:CC
## 17 methylated 1.12e-13 extracellular membrane-bounded organelle GO:CC
## 18 methylated 1.54e-13 respirasome GO:CC
## 19 methylated 5.08e-12 cytoplasm GO:CC
## 20 methylated 8.78e-12 anchoring junction GO:CC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 5.94e-44 Peptide chain elongation REAC
## 2 methylated 2.99e-43 Eukaryotic Translation Elongation REAC
## 3 methylated 7.14e-42 Viral mRNA Translation REAC
## 4 methylated 3.37e-41 Selenocysteine synthesis REAC
## 5 methylated 3.37e-41 Eukaryotic Translation Termination REAC
## 6 methylated 7.11e-41 Nonsense Mediated Decay (NMD) independent of the … REAC
## 7 methylated 5.98e-40 Response of EIF2AK4 (GCN2) to amino acid deficien… REAC
## 8 methylated 5.98e-40 Formation of a pool of free 40S subunits REAC
## 9 methylated 1.52e-38 L13a-mediated translational silencing of Cerulopl… REAC
## 10 methylated 2.06e-38 SRP-dependent cotranslational protein targeting t… REAC
## 11 methylated 2.06e-38 GTP hydrolysis and joining of the 60S ribosomal s… REAC
## 12 methylated 5.03e-38 Nonsense Mediated Decay (NMD) enhanced by the Exo… REAC
## 13 methylated 5.03e-38 Nonsense-Mediated Decay (NMD) REAC
## 14 methylated 6.74e-38 Selenoamino acid metabolism REAC
## 15 methylated 1.59e-37 Cap-dependent Translation Initiation REAC
## 16 methylated 1.59e-37 Eukaryotic Translation Initiation REAC
## 17 methylated 5.02e-36 Influenza Viral RNA Transcription and Replication REAC
## 18 methylated 4.10e-34 Influenza Infection REAC
## 19 methylated 1.18e-33 Cellular response to starvation REAC
## 20 methylated 1.87e-32 Regulation of expression of SLITs and ROBOs REAC
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 1.26e-41 cytoplasmic translation GO:BP
## 2 methylated 1.41e-26 translation GO:BP
## 3 methylated 5.06e-26 peptide biosynthetic process GO:BP
## 4 methylated 1.03e-23 amide biosynthetic process GO:BP
## 5 methylated 2.43e-23 peptide metabolic process GO:BP
## 6 methylated 2.77e-23 organonitrogen compound biosynthetic process GO:BP
## 7 methylated 8.05e-21 amide metabolic process GO:BP
## 8 methylated 1.02e-13 oxidative phosphorylation GO:BP
## 9 methylated 5.55e-13 aerobic electron transport chain GO:BP
## 10 methylated 1.11e-12 mitochondrial ATP synthesis coupled electron tran… GO:BP
## 11 methylated 1.11e-12 ATP synthesis coupled electron transport GO:BP
## 12 methylated 1.63e-12 aerobic respiration GO:BP
## 13 methylated 5.70e-12 respiratory electron transport chain GO:BP
## 14 methylated 1.20e-11 cellular respiration GO:BP
## 15 methylated 1.08e-10 electron transport chain GO:BP
## 16 methylated 2.13e-10 energy derivation by oxidation of organic compoun… GO:BP
## 17 methylated 3.19e-10 cellular nitrogen compound biosynthetic process GO:BP
## 18 methylated 1.01e- 9 ribosome biogenesis GO:BP
## 19 methylated 1.29e- 9 organonitrogen compound metabolic process GO:BP
## 20 methylated 3.92e- 9 generation of precursor metabolites and energy GO:BP
## # A tibble: 8 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 3.54e-39 Cytoplasmic ribosomal proteins WP
## 2 methylated 1.66e-12 Electron transport chain OXPHOS system in mitochon… WP
## 3 methylated 3.31e- 6 Oxidative phosphorylation WP
## 4 methylated 5.44e- 5 Mitochondrial complex IV assembly WP
## 5 methylated 8.34e- 3 Nonalcoholic fatty liver disease WP
## 6 methylated 1.01e- 2 Neuroinflammation WP
## 7 methylated 1.28e- 2 Mitochondrial complex I assembly model OXPHOS syst… WP
## 8 methylated 1.52e- 2 5q35 copy number variation WP
## # A tibble: 16 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 1.31e-31 Ribosome KEGG
## 2 methylated 5.88e-26 Coronavirus disease - COVID-19 KEGG
## 3 methylated 7.05e-12 Oxidative phosphorylation KEGG
## 4 methylated 1.40e-10 Diabetic cardiomyopathy KEGG
## 5 methylated 6.77e-10 Chemical carcinogenesis - reactive oxygen species KEGG
## 6 methylated 1.05e- 9 Thermogenesis KEGG
## 7 methylated 3.49e- 9 Parkinson disease KEGG
## 8 methylated 4.26e- 9 Prion disease KEGG
## 9 methylated 1.23e- 8 Huntington disease KEGG
## 10 methylated 5.82e- 8 Amyotrophic lateral sclerosis KEGG
## 11 methylated 7.79e- 8 Alzheimer disease KEGG
## 12 methylated 6.19e- 7 Pathways of neurodegeneration - multiple diseases KEGG
## 13 methylated 1.42e- 4 Cardiac muscle contraction KEGG
## 14 methylated 1.47e- 3 Metabolic pathways KEGG
## 15 methylated 3.82e- 3 Non-alcoholic fatty liver disease KEGG
## 16 methylated 4.54e- 3 Retrograde endocannabinoid signaling KEGG
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 9.69e-29 structural constituent of ribosome GO:MF
## 2 methylated 3.56e-23 structural molecule activity GO:MF
## 3 methylated 1.47e-14 oxidoreduction-driven active transmembrane transp… GO:MF
## 4 methylated 1.49e-12 electron transfer activity GO:MF
## 5 methylated 2.99e-11 primary active transmembrane transporter activity GO:MF
## 6 methylated 1.90e- 9 RNA binding GO:MF
## 7 methylated 9.51e- 8 active transmembrane transporter activity GO:MF
## 8 methylated 1.86e- 7 oxidoreductase activity GO:MF
## 9 methylated 4.67e- 6 transmembrane transporter activity GO:MF
## 10 methylated 6.12e- 6 NADH dehydrogenase (ubiquinone) activity GO:MF
## 11 methylated 6.76e- 6 NADH dehydrogenase (quinone) activity GO:MF
## 12 methylated 7.61e- 6 oxidoreductase activity, acting on a heme group o… GO:MF
## 13 methylated 7.61e- 6 cytochrome-c oxidase activity GO:MF
## 14 methylated 8.19e- 6 NADH dehydrogenase activity GO:MF
## 15 methylated 8.99e- 6 NAD(P)H dehydrogenase (quinone) activity GO:MF
## 16 methylated 1.07e- 5 transporter activity GO:MF
## 17 methylated 1.94e- 5 proton transmembrane transporter activity GO:MF
## 18 methylated 2.37e- 5 oxidoreductase activity, acting on NAD(P)H, quino… GO:MF
## 19 methylated 3.02e- 5 rRNA binding GO:MF
## 20 methylated 1.39e- 4 oxidoreductase activity, acting on NAD(P)H GO:MF
## # A tibble: 11 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 3.79e-22 Ribosome, cytoplasmic CORUM
## 2 methylated 6.17e-15 Nop56p-associated pre-rRNA complex CORUM
## 3 methylated 3.16e-13 60S ribosomal subunit, cytoplasmic CORUM
## 4 methylated 1.56e- 7 40S ribosomal subunit, cytoplasmic CORUM
## 5 methylated 5.69e- 7 40S ribosomal subunit, cytoplasmic CORUM
## 6 methylated 2.14e- 5 Respiratory chain complex I (incomplete intermedi… CORUM
## 7 methylated 3.73e- 4 TRBP containing complex (DICER, RPL7A, EIF6, MOV1… CORUM
## 8 methylated 1.51e- 3 Respiratory chain complex I (gamma subunit) mitoc… CORUM
## 9 methylated 1.59e- 3 Cytochrome c oxidase, mitochondrial CORUM
## 10 methylated 2.10e- 2 Ecsit complex (ECSIT, MT-CO2, NDUFA1, MT-ND1, TRA… CORUM
## 11 methylated 3.16e- 2 Ferritin complex CORUM
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 5.46e-15 Mitochondrial inheritance HP
## 2 methylated 5.15e-13 Centrocecal scotoma HP
## 3 methylated 1.79e-12 Ventricular preexcitation HP
## 4 methylated 1.83e-12 Episodic vomiting HP
## 5 methylated 2.64e-12 Ragged-red muscle fibers HP
## 6 methylated 2.64e-12 Mitochondrial myopathy HP
## 7 methylated 1.10e-11 Abnormal mitochondria in muscle tissue HP
## 8 methylated 2.31e-11 Mitochondrial respiratory chain defects HP
## 9 methylated 3.91e-11 Leber optic atrophy HP
## 10 methylated 1.59e-10 Muscle abnormality related to mitochondrial dysfu… HP
## 11 methylated 1.72e-10 Central retinal vessel vascular tortuosity HP
## 12 methylated 1.72e-10 Retinal arterial tortuosity HP
## 13 methylated 2.62e-10 Retinal telangiectasia HP
## 14 methylated 1.57e- 9 Slow decrease in visual acuity HP
## 15 methylated 9.95e- 9 Stroke-like episode HP
## 16 methylated 1.11e- 8 Blurred vision HP
## 17 methylated 1.44e- 8 Proximal tubulopathy HP
## 18 methylated 1.58e- 8 Sensorimotor neuropathy HP
## 19 methylated 1.66e- 8 Mixed demyelinating and axonal polyneuropathy HP
## 20 methylated 1.66e- 8 Multiple glomerular cysts HP
## # A tibble: 17 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.000000303 hsa-miR-320a MIRNA
## 2 methylated 0.00000244 hsa-miR-652-3p MIRNA
## 3 methylated 0.0000284 hsa-miR-744-5p MIRNA
## 4 methylated 0.0000473 hsa-let-7c-5p MIRNA
## 5 methylated 0.0000718 hsa-miR-296-3p MIRNA
## 6 methylated 0.000140 hsa-let-7e-5p MIRNA
## 7 methylated 0.000260 hsa-let-7a-5p MIRNA
## 8 methylated 0.000357 hsa-miR-100-5p MIRNA
## 9 methylated 0.00108 hsa-miR-615-3p MIRNA
## 10 methylated 0.00316 hsa-miR-760 MIRNA
## 11 methylated 0.00337 hsa-miR-186-5p MIRNA
## 12 methylated 0.00456 hsa-miR-1301-3p MIRNA
## 13 methylated 0.0147 hsa-let-7b-5p MIRNA
## 14 methylated 0.0162 hsa-miR-16-5p MIRNA
## 15 methylated 0.0332 hsa-miR-99a-5p MIRNA
## 16 methylated 0.0360 hsa-miR-7150 MIRNA
## 17 methylated 0.0454 hsa-miR-96-5p MIRNA
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.000000572 Factor: GCMa:HOXB13; motif: RTGCGGGTMATAAAN TF
## 2 methylated 0.000141 Factor: GCMa:HOXA13; motif: RTGCGGGTAATAAA TF
## 3 methylated 0.000651 Factor: GCMa:HOXB13; motif: RTGCGGGTMATAAAN; m… TF
## 4 methylated 0.000773 Factor: GCMb:Prrxl1; motif: ATRCGGGTNATTAN TF
## 5 methylated 0.00128 Factor: MYBL1; motif: ACCGTTAACSGY TF
## 6 methylated 0.00137 Factor: GCMb:FOXI1; motif: RTAAATANGGGNN TF
## 7 methylated 0.00207 Factor: E2F2; motif: AAAATGGCGCCATTTT TF
## 8 methylated 0.00232 Factor: Cdx-2; motif: NRTCGTAANNNN; match clas… TF
## 9 methylated 0.00474 Factor: ZNF647; motif: NTAGGCCTAN; match class… TF
## 10 methylated 0.00615 Factor: GCMa:HOXA2; motif: RTRNGGGYNTAATNN TF
## 11 methylated 0.00665 Factor: SAP-1; motif: NTCGTAAATGCN TF
## 12 methylated 0.00908 Factor: Barhl-1; motif: NTAAACGN; match class:… TF
## 13 methylated 0.0108 Factor: ZNF286B; motif: NTTGGCGGATGM TF
## 14 methylated 0.0108 Factor: ZNF286; motif: NTTGGCGGATGM TF
## 15 methylated 0.0121 Factor: meis1:Elf-1; motif: NTGCCGGAAGTN; matc… TF
## 16 methylated 0.0127 Factor: Oct-1; motif: NNNRTAATNANNN; match cla… TF
## 17 methylated 0.0132 Factor: GCMa:HOXA2; motif: RTRNGGGYNTAATNN; ma… TF
## 18 methylated 0.0142 Factor: PU.1; motif: ACTTCCTCT TF
## 19 methylated 0.0224 Factor: HOXA5; motif: TGCNHNCWYCCYCATTAKTGNDCN… TF
## 20 methylated 0.0243 Factor: PU.1; motif: NRAAAGAGGAAGTGARA TF
## # A tibble: 20 × 4
## query p_value term_name source
## <chr> <dbl> <chr> <chr>
## 1 methylated 0.000466 duodenum; paneth cells[High] HPA
## 2 methylated 0.000816 appendix; goblet cells[High] HPA
## 3 methylated 0.00101 appendix; enterocytes[High] HPA
## 4 methylated 0.00115 duodenum; paneth cells[≥Medium] HPA
## 5 methylated 0.00193 small intestine; goblet cells[≥Medium] HPA
## 6 methylated 0.00196 colon; goblet cells[High] HPA
## 7 methylated 0.00237 duodenum; goblet cells[High] HPA
## 8 methylated 0.00255 duodenum; paneth cells[≥Low] HPA
## 9 methylated 0.00257 rectum; goblet cells[High] HPA
## 10 methylated 0.00310 colon; enterocytes[High] HPA
## 11 methylated 0.00444 rectum; enterocytes[High] HPA
## 12 methylated 0.00467 pancreas; exocrine glandular cells[High] HPA
## 13 methylated 0.00488 appendix; endocrine cells[≥Low] HPA
## 14 methylated 0.00507 appendix; endocrine cells[High] HPA
## 15 methylated 0.00528 appendix; goblet cells[≥Low] HPA
## 16 methylated 0.00557 duodenum; enterocytes[High] HPA
## 17 methylated 0.00608 appendix; enterocytes[≥Medium] HPA
## 18 methylated 0.00633 small intestine; goblet cells[High] HPA
## 19 methylated 0.00655 appendix; goblet cells[≥Medium] HPA
## 20 methylated 0.00670 skin 2; cells in basal layer[High] HPA
