knitr::opts_chunk$set(
  echo = FALSE,
  message = FALSE,
  warning = FALSE,
  fig.width = 11,
  fig.height = 7,
  dpi = 160
)

suppressPackageStartupMessages({
  library(data.table)
  library(ggplot2)
})

candidate_project_dirs <- unique(normalizePath(
  c(getwd(), file.path(getwd(), ".."), file.path(getwd(), "..", "..")),
  mustWork = FALSE
))
project_dir <- candidate_project_dirs[
  file.exists(file.path(candidate_project_dirs, "AGENTS.md")) &
    dir.exists(file.path(candidate_project_dirs, "compartments_phased"))
][1]
if (is.na(project_dir)) {
  stop("Could not locate the ThreeD project root from ", getwd())
}

analysis_dir <- file.path(project_dir, "analysis", "tissue-DEGs-vs-compartments")
output_dir <- file.path(analysis_dir, "output")
table_dir <- file.path(output_dir, "tables")
fig_dir <- file.path(output_dir, "figures")
dir.create(table_dir, recursive = TRUE, showWarnings = FALSE)
dir.create(fig_dir, recursive = TRUE, showWarnings = FALSE)

knitr::opts_chunk$set(fig.path = file.path("output", "figures", ""))

1 Overview

This analysis asks whether genes that change expression between tissues also change their local phased A/B compartment signal between the same tissues. For each species and tissue pair, the report:

  1. estimates tissue log2 fold-change from RNA-seq counts using log2 CPM,
  2. assigns each annotated gene TSS to the phased compartment bin in each Hi-C tissue,
  3. computes delta_E1 in the same direction as the expression contrast, and
  4. compares DEGs with compartment switches and continuous E1 shifts.

Positive log2FC means higher expression in the first tissue of the contrast. Positive delta_E1 means the gene is more A-like in that same tissue.

The local R installation used for this report does not include edgeR, limma, or DESeq2, so the DEG calls are a self-contained screening analysis based on log2 CPM, Welch tests, BH FDR, and an absolute log2FC threshold. For publication-grade DEG calls, the same join and enrichment workflow can be rerun with the preferred count model.

2 Inputs

species species_label tissue tissue_label n_rna_samples compartment_label compartment_file
Eluc Northern pike Br Brain 4 brain ab_compartment_brain_El.tsv
Eluc Northern pike Gi Gill 4 gill ab_compartment_gill_El.tsv
Eluc Northern pike Li Liver 4 L11 mapped as liver ab_compartment_L11_El.tsv
Omyk Rainbow trout Br Brain 4 brain ab_compartment_brain_Om.tsv
Omyk Rainbow trout Gi Gill 4 gill ab_compartment_gill_Om.tsv
Omyk Rainbow trout Li Liver 4 liver ab_compartment_liver_Om.tsv
Salp Arctic char Br Brain 4 B34 mapped as brain ab_compartment_B34_Sa.tsv
Salp Arctic char Gi Gill 4 gill ab_compartment_gill_Sa.tsv
Salp Arctic char Li Liver 4 liver ab_compartment_liver_Sa.tsv
Ssal Atlantic salmon Br Brain 4 B35 mapped as brain ab_compartment_B35_Ss.tsv
Ssal Atlantic salmon Gi Gill 4 gill ab_compartment_gill_Ss.tsv
Ssal Atlantic salmon Li Liver 4 liver ab_compartment_liver_Ss.tsv
Tthy Grayling Br Brain 4 brain ab_compartment_brain_Tt.tsv
Tthy Grayling Li Liver 4 liver ab_compartment_liver_Tt.tsv
Upyg Eastern mudminnow Br Brain 4 B30 mapped as brain ab_compartment_B30_Up.tsv
Upyg Eastern mudminnow Gi Gill 2 gill ab_compartment_gill_Up.tsv
Upyg Eastern mudminnow Li Liver 4 liver ab_compartment_liver_Up.tsv

The DEG calls use padj < 0.05 and abs(log2FC) >= 1. Genes are tested when they have CPM >= 1 in at least 2 selected RNA-seq samples. A substantial compartment shift is defined as abs(delta_E1) >= 0.25; compartment switches are sign changes between phased A and B labels.

3 Run analysis

4 TSS compartment assignment

species tissue tissue_label n_annotated_genes n_genes_with_tss_compartment pct_annotated_assigned n_A n_B
Eluc Br Brain 25532 24708 96.8 18355 6353
Eluc Gi Gill 25532 24870 97.4 17660 7210
Eluc Li Liver 25532 24647 96.5 17448 7199
Omyk Br Brain 47152 43674 92.6 25670 18004
Omyk Gi Gill 47152 44220 93.8 30388 13832
Omyk Li Liver 47152 43796 92.9 27302 16494
Salp Br Brain 53864 50462 93.7 29848 20614
Salp Gi Gill 53864 51241 95.1 33278 17963
Salp Li Liver 53864 51683 96.0 30636 21047
Ssal Br Brain 44413 42193 95.0 27320 14873
Ssal Gi Gill 44413 42406 95.5 28973 13433
Ssal Li Liver 44413 42510 95.7 27153 15357
Tthy Br Brain 54402 52367 96.3 33472 18895
Tthy Li Liver 54402 52819 97.1 32362 20457
Upyg Br Brain 24391 24074 98.7 17393 6681
Upyg Gi Gill 24391 24085 98.7 18457 5628
Upyg Li Liver 24391 24033 98.5 15000 9033

5 Per-comparison summary

species contrast_label n_genes_with_compartments n_degs n_compartment_switches n_switching_degs spearman_rho spearman_padj prop_concordant_all_signed prop_concordant_degs_signed
Eluc Brain vs Gill 19886 8114 1483 714 0.129 0 0.563 0.597
Eluc Brain vs Liver 18774 12710 1753 1237 0.081 0 0.695 0.725
Eluc Gill vs Liver 17689 12758 1338 983 0.279 0 0.558 0.576
Omyk Brain vs Gill 29044 11090 8466 3457 0.257 0 0.541 0.615
Omyk Brain vs Liver 26831 18901 7617 5370 0.250 0 0.490 0.505
Omyk Gill vs Liver 24894 15465 5082 3212 0.245 0 0.613 0.639
Salp Brain vs Gill 31910 12822 7841 3540 0.263 0 0.572 0.637
Salp Brain vs Liver 29855 19486 8296 5422 0.282 0 0.558 0.591
Salp Gill vs Liver 28694 19217 5223 3662 0.254 0 0.661 0.689
Ssal Brain vs Gill 31324 12570 4590 1977 0.198 0 0.547 0.606
Ssal Brain vs Liver 29234 20454 4824 3457 0.229 0 0.580 0.604
Ssal Gill vs Liver 27617 17461 4202 2819 0.228 0 0.670 0.706
Tthy Brain vs Liver 30735 21356 7254 5136 0.240 0 0.579 0.605
Upyg Brain vs Gill 19344 5780 2977 1046 0.292 0 0.547 0.628
Upyg Brain vs Liver 18838 12141 4397 2978 0.245 0 0.642 0.683
Upyg Gill vs Liver 17212 6167 3575 1409 0.169 0 0.714 0.779

6 DEG enrichment in compartment changes

species contrast_label test n_deg_flagged n_deg_not_flagged odds_ratio conf_low conf_high padj
Eluc Brain vs Gill compartment_switch 714 7400 1.380 1.240 1.537 0.00e+00
Eluc Brain vs Liver compartment_switch 1237 11473 1.159 1.040 1.294 9.73e-03
Eluc Gill vs Liver compartment_switch 983 11775 1.076 0.947 1.224 3.05e-01
Omyk Brain vs Gill compartment_switch 3457 7633 1.170 1.111 1.233 0.00e+00
Omyk Brain vs Liver compartment_switch 5370 13531 1.004 0.947 1.064 9.06e-01
Omyk Gill vs Liver compartment_switch 3212 12253 1.060 0.994 1.130 9.51e-02
Salp Brain vs Gill compartment_switch 3540 9282 1.311 1.245 1.381 0.00e+00
Salp Brain vs Liver compartment_switch 5422 14064 1.005 0.953 1.061 9.06e-01
Salp Gill vs Liver compartment_switch 3662 15555 1.194 1.118 1.275 2.00e-07
Ssal Brain vs Gill compartment_switch 1977 10593 1.153 1.081 1.229 2.06e-05
Ssal Brain vs Liver compartment_switch 3457 16997 1.103 1.030 1.182 7.72e-03
Ssal Gill vs Liver compartment_switch 2819 14642 1.221 1.139 1.310 0.00e+00
Tthy Brain vs Liver compartment_switch 5136 16220 1.086 1.024 1.151 7.76e-03
Upyg Brain vs Gill compartment_switch 1046 4734 1.331 1.224 1.447 0.00e+00
Upyg Brain vs Liver compartment_switch 2978 9163 1.209 1.125 1.300 5.00e-07
Upyg Gill vs Liver compartment_switch 1409 4758 1.214 1.124 1.310 1.30e-06
Eluc Brain vs Gill substantial_e1_shift 1400 6714 0.877 0.814 0.945 6.13e-04
Eluc Brain vs Liver substantial_e1_shift 3358 9352 1.185 1.103 1.274 4.60e-06
Eluc Gill vs Liver substantial_e1_shift 1166 11592 1.293 1.141 1.467 5.30e-05
Omyk Brain vs Gill substantial_e1_shift 5623 5467 1.180 1.125 1.238 0.00e+00
Omyk Brain vs Liver substantial_e1_shift 9314 9587 1.016 0.963 1.071 5.65e-01
Omyk Gill vs Liver substantial_e1_shift 5243 10222 1.122 1.061 1.185 5.49e-05
Salp Brain vs Gill substantial_e1_shift 6631 6191 1.272 1.216 1.331 0.00e+00
Salp Brain vs Liver substantial_e1_shift 9958 9528 1.029 0.980 1.079 2.65e-01
Salp Gill vs Liver substantial_e1_shift 6689 12528 1.300 1.232 1.372 0.00e+00
Ssal Brain vs Gill substantial_e1_shift 3528 9042 1.168 1.110 1.230 0.00e+00
Ssal Brain vs Liver substantial_e1_shift 6302 14152 1.181 1.117 1.249 0.00e+00
Ssal Gill vs Liver substantial_e1_shift 5449 12012 1.219 1.154 1.287 0.00e+00
Tthy Brain vs Liver substantial_e1_shift 9235 12121 1.127 1.072 1.184 3.60e-06
Upyg Brain vs Gill substantial_e1_shift 2024 3756 1.378 1.290 1.472 0.00e+00
Upyg Brain vs Liver substantial_e1_shift 5528 6613 1.189 1.119 1.264 0.00e+00
Upyg Gill vs Liver substantial_e1_shift 3059 3108 1.055 0.991 1.123 1.09e-01

7 Plots

8 Top switching DEGs

species species_label contrast contrast_label gene_id biotype chrom tss0 log2FC padj delta_E1 compartment_a compartment_b transition expression_compartment_concordant
Tthy Grayling Br_vs_Li Brain vs Liver EPG42641 protein_coding Tth17A 9476295 8.224822 0.0e+00 0.3141024 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG11614 protein_coding Tth04A 44795920 8.557913 0.0e+00 0.6794915 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG36766 protein_coding Tth14B 9154168 7.175756 0.0e+00 0.4895467 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00276700 protein_coding CM082150.1 12355146 -13.992504 1.0e-07 -0.4420114 B A A_to_B TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000044291 protein_coding 10 26132329 11.007355 1.0e-07 0.2789533 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00292570 protein_coding CM082150.1 95685630 7.884446 1.0e-07 0.8267299 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00315420 protein_coding CM082151.1 35257637 -8.141164 3.0e-07 0.8598143 A B B_to_A FALSE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00090670 protein_coding CM082143.1 199453642 7.291744 3.0e-07 -0.1181660 B A A_to_B FALSE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00337970 protein_coding CM082152.1 30666967 6.641833 3.0e-07 0.9154507 A B B_to_A TRUE
Eluc Northern pike Br_vs_Gi Brain vs Gill ENSELUG00000000549 protein_coding 18 6822530 -8.478306 3.0e-07 -0.4099491 B A A_to_B TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000001248 protein_coding 6 20911997 -12.822903 4.0e-07 -0.1922760 B A A_to_B TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00019240 protein_coding CM082142.1 81537055 7.384034 4.0e-07 0.8400057 A B B_to_A TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000019887 protein_coding 21 22213502 5.129634 4.0e-07 0.0915599 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00345310 protein_coding CM082152.1 74424721 6.827877 4.0e-07 0.8680957 A B B_to_A TRUE
Ssal Atlantic salmon Br_vs_Li Brain vs Liver ENSSSAG00000054284 protein_coding 16 67666574 7.775331 5.0e-07 0.4637794 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00178580 protein_coding CM082146.1 90230173 -11.880528 5.0e-07 -0.6537743 B A A_to_B TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00014900 protein_coding CM082142.1 58604244 8.058629 6.0e-07 0.9799394 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00171850 protein_coding CM082146.1 47750082 7.986204 6.0e-07 0.1165670 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00339780 protein_coding CM082152.1 36883235 7.733816 6.0e-07 1.0754737 A B B_to_A TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000004967 protein_coding 24 2440880 -11.495967 7.0e-07 -0.2061881 B A A_to_B TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00202470 protein_coding CM082147.1 46559136 10.158864 8.0e-07 0.4077312 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00288680 protein_coding CM082150.1 74112240 -7.585044 8.0e-07 -0.8442155 B A A_to_B TRUE
Omyk Rainbow trout Br_vs_Li Brain vs Liver ENSOMYG00000010547 protein_coding 4 32121259 -15.075152 8.0e-07 -0.9591619 B A A_to_B TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000000601 protein_coding 5 20412339 1.939153 9.0e-07 0.2746076 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG10618 protein_coding Tth04A 8836087 10.177440 9.0e-07 0.4833653 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG33373 protein_coding Tth13A 7606452 8.065871 9.0e-07 1.0963018 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG50461 protein_coding Tth21A 17290994 7.909541 9.0e-07 0.7729369 A B B_to_A TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG07497 protein_coding Tth02B 37987840 5.892684 9.0e-07 -0.4554161 B A A_to_B FALSE
Tthy Grayling Br_vs_Li Brain vs Liver EPG31104 protein_coding Tth12A 19842321 5.071271 9.0e-07 0.5937725 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00194250 protein_coding CM082147.1 10282777 6.906729 9.0e-07 0.7069619 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00172280 protein_coding CM082146.1 50220679 -12.947361 9.0e-07 -0.5938696 B A A_to_B TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00008110 protein_coding CM082142.1 31337489 9.665362 9.0e-07 0.9506332 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00165140 protein_coding CM082146.1 22590412 7.320715 1.0e-06 0.5061200 A B B_to_A TRUE
Ssal Atlantic salmon Br_vs_Li Brain vs Liver ENSSSAG00000073185 protein_coding 26 522265 -10.400282 1.0e-06 -0.5371263 B A A_to_B TRUE
Tthy Grayling Br_vs_Li Brain vs Liver EPG56135 protein_coding Tth24A 4769891 11.344633 1.0e-06 0.0601409 A B B_to_A TRUE
Eluc Northern pike Gi_vs_Li Gill vs Liver ENSELUG00000024539 protein_coding 4 13745081 7.382778 1.1e-06 0.3590370 A B B_to_A TRUE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00176370 protein_coding CM082146.1 69456380 6.892884 1.1e-06 0.2206265 A B B_to_A TRUE
Omyk Rainbow trout Br_vs_Li Brain vs Liver ENSOMYG00000010955 protein_coding 21 31948778 8.237739 1.1e-06 -0.1844466 B A A_to_B FALSE
Omyk Rainbow trout Br_vs_Li Brain vs Liver ENSOMYG00000026529 protein_coding 30 2688661 4.366607 1.1e-06 -0.4352345 B A A_to_B FALSE
Upyg Eastern mudminnow Br_vs_Li Brain vs Liver UPYG_G00178160 protein_coding CM082146.1 87793767 4.119068 1.1e-06 -0.1993745 B A A_to_B FALSE

9 Output files

file
output/tables/input_summary.tsv
output/tables/annotation_biotype_summary.tsv
output/tables/gene_tss_compartment_assignment_summary.tsv
output/tables/gene_tss_phased_compartment_assignments.tsv
output/tables/gene_level_tissue_DE_vs_compartments.tsv
output/tables/comparison_summary.tsv
output/tables/deg_enrichment_in_compartment_changes.tsv
output/tables/transition_summary.tsv
output/tables/chromosome_spearman_summary.tsv
output/tables/top_switching_degs.tsv
output/figures/delta_E1_vs_log2FC_bin2d.png
output/figures/spearman_delta_E1_log2FC_heatmap.png
output/figures/chromosome_spearman_rho.png
output/figures/log2FC_by_compartment_transition.png
output/figures/deg_enrichment_compartment_switches.png