================================================================================ README — share/ Project : TaRGET II | Li_adt | BPA exposure — motif & TF gene expression analysis Updated : 2026-03-25 ================================================================================ OVERVIEW -------- This folder contains motif enrichment results from HOMER DAR (Differentially Accessible Region) analysis for adult liver (Li_adt) samples across multiple environmental exposures, with a focus on BPA (10mg and 10ug) female samples. Files progress from raw motif-gene lists through filtered subsets, pivot tables, and annotated TF gene expression tables. -------------------------------------------------------------------------------- SOURCE / INPUT FILES -------------------------------------------------------------------------------- 20240130_liver_blood_treatment_deg_after_PseudoCtrl_using_all_control.txt - Large reference DEG table (1,043,493 data rows) from pseudo-control corrected RNAseq across all TaRGET II treatment conditions. - Columns: baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, cond1, cond2, gene, lab, type, sig, direction, group, tissue, stage, sex - Used as the gene expression source for TF expression annotation. Li_adt_LESS_DAR_motif_gene.txt (86 data rows) Li_adt_MORE_DAR_motif_gene.txt (78 data rows) - HOMER motif enrichment results for LESS-accessible and MORE-accessible DARs in adult liver, across all treatment groups (AL_TCDD, BA_BPA10mg, BA_BPA10ug, BI_PM2.5, MU_PM2.5, WK_TBT, ZB_As) and both sexes (Li_F_adt, Li_M_adt). - Columns: Pvalue, logPvalue, _of_Targets, _of_background, Best_match_motif, Match_score, Rank, Gene, Type, Group, Open, Exp, Stage - Key columns: Rank : motif ID (e.g., motif1.info.html) Type : motif family/class label (e.g., Thrb;Rxr;Nr2f2;Hnf4) Open : LESS or MORE (DAR direction) Exp : treatment condition (e.g., BA_BPA10mg) Stage : tissue/stage (e.g., Li_F_adt) Li_adt_Motif_gene_list.txt (894 data rows) - Full list of TF genes associated with each motif type across all Li_adt conditions. - Columns: gene, motif, type, Open, Exp, Stage, Condition Li_adt_Motif_TF_gene_expression.txt (579 data rows) - TF gene expression (log2FoldChange, padj, sig, direction) joined to motif gene list. All Li_adt conditions included. - Columns: gene, Condition, motif, type, Open, Exp, Stage, log2FoldChange, padj, sig, direction Li_adt_Motif_TF_gene_expression_withMotif_score.txt (460 data rows) - Extended version of Li_adt_Motif_TF_gene_expression.txt with additional motif enrichment score columns (Pvalue, X_of_Targets). - Columns: Type, Exp, Open, Stage, Pvalue, X_of_Targets, gene, Condition, type, log2FoldChange, padj, sig, direction - Covers all treatment groups: AL_TCDD, BA_BPA10mg, BA_BPA10ug, BI_PM2.5, MU_PM2.5, WK_TBT, ZB_As; both sexes (Li_F_adt, Li_M_adt) -------------------------------------------------------------------------------- FILTERED / INTERMEDIATE FILES -------------------------------------------------------------------------------- LESS_filtered.txt (12 data rows) - Subset of LESS DAR motif results after filtering (criteria in upstream analysis script). Retains same columns as Li_adt_LESS_DAR_motif_gene.txt. MORE_filtered.txt (19 data rows) - Subset of MORE DAR motif results after filtering. Same structure as above. merged.txt (31 data rows) - Merged LESS + MORE filtered motif results for BPA female (Li_F_adt), both BA_BPA10mg and BA_BPA10ug conditions. - Columns: Pvalue, logPvalue, _of_Targets, _of_background, Best_match_motif, Match_score, Rank, Gene, Type, Group, Open, Exp, Stage merged_subset.txt (31 data rows) - Condensed version of merged.txt retaining only key columns. - Columns: _of_Targets, Rank, Type, Group, Open, Exp, Stage -------------------------------------------------------------------------------- OUTPUT / DERIVED FILES -------------------------------------------------------------------------------- merged_subset_pivot.txt (19 data rows + header) - Pivot table derived from merged_subset.txt. - Rows : motif Type (19 unique types) - Columns : _of_Targets value for each of 4 conditions: 10mg LESS _of_Targets (BA_BPA10mg, LESS DAR) 10ug LESS _of_Targets (BA_BPA10ug, LESS DAR) 10mg MORE _of_Targets (BA_BPA10mg, MORE DAR) 10ug MORE _of_Targets (BA_BPA10ug, MORE DAR) - Empty cells indicate the motif type was not present in that condition. TF_filtered.txt (19 data rows + header) - Pivot table of motif IDs (from the Rank column of merged.txt) for each Type under each of the 4 BPA female conditions. - Rows : motif Type (same 19 types as merged_subset_pivot.txt) - Columns : motif rank ID (e.g., motif1, motif6) for each condition: 10mg LESS _of_Targets (BA_BPA10mg, LESS DAR) 10ug LESS _of_Targets (BA_BPA10ug, LESS DAR) 10mg MORE _of_Targets (BA_BPA10mg, MORE DAR) 10ug MORE _of_Targets (BA_BPA10ug, MORE DAR) - Note: the same motif number can differ across conditions (e.g., Thrb;Rxr;Nr2f2;Hnf4 = motif1 in 10mg LESS, motif6 in 10ug LESS/10mg MORE). BPA_female_Motif_TF_expr.txt (85 data rows + header) - TF gene expression table filtered to BPA female samples only (Exp = BA_BPA10mg or BA_BPA10ug, Stage = Li_F_adt). - Source : Li_adt_Motif_TF_gene_expression_withMotif_score.txt - Breakdown: BA_BPA10mg = 50 rows | BA_BPA10ug = 35 rows - Added column motif_ID: motif rank ID annotated from TF_filtered.txt, matched on (Type, Exp, Open). - Columns: Type, Exp, Open, Stage, Pvalue, X_of_Targets, gene, Condition, type, log2FoldChange, padj, sig, direction, motif_ID -------------------------------------------------------------------------------- FILE RELATIONSHIPS / WORKFLOW -------------------------------------------------------------------------------- Li_adt_LESS_DAR_motif_gene.txt ──┐ ├─[filter]──> LESS_filtered.txt ──┐ Li_adt_MORE_DAR_motif_gene.txt ──┘ │ ├─[filter]──> MORE_filtered.txt ──┤ │ [merge, Exp=BA_BPA10mg/ug, Stage=Li_F_adt] │ merged.txt merged_subset.txt │ ┌───────────────────────────┤ │ │ [pivot _of_Targets] [pivot motif Rank ID] │ │ merged_subset_pivot.txt TF_filtered.txt │ Li_adt_Motif_TF_gene_expression_withMotif_score.txt │ │ │ ├─[filter Exp=BA_BPA10mg/ug, Stage=Li_F_adt] │ │ │ └──────────────────────────────────────────[join motif_ID] │ BPA_female_Motif_TF_expr.txt -------------------------------------------------------------------------------- NOTES -------------------------------------------------------------------------------- - Exp codes: BA = Bartolomei lab | BPA10mg / BPA10ug = dose levels - Stage codes: Li = Liver | F/M = Female/Male | adt = adult - Open: LESS = less accessible DARs (closed regions); MORE = more accessible - motif_ID values (e.g., motif1, motif13) refer to HOMER motif rank within each specific condition's enrichment output, NOT a universal motif index. ================================================================================