Transciptional_condensates

f6_TCGA_atacseq_survival

TCGA survival top/bottom 50% patients -> differential ATAC score -> BART

f7_TF_condensates_test

-- Hypothesis test -- TF clusters/condensates are associated with SE check if the clustered TFs, either from motif matching data, or chip-seq data in a cell type, have any association/correlation with IDR and SE

NOTES: focus on cell-type specific, or differential ATAC-seq regions

f8_TF_condensates_V2

NOTES: use TFBS data from all cell types

cluster potential (CP) of

• TF motif sites (TFMS)
• ChIP-seq TF binding sites (TFBS) with motif
• TFBS without motif

Correlation among

• TF cluster potential
• TF protein AICAP score
• TF enrichment at SEs

Clinical outcomes by

• ATAC-seq signals at cancer-specific TFs
• ATAC-seq signals at SEs with cancer-specific TFs

f9_TF_condensates_V3

NOTES: only look at distance to down-stream region

cluster potential (CP) of

• TF motif sites (TFMS) vs. random
• TFBS vs. TFMS

only look at distance to down-stream region in bedtools closest for

• TFMS, TFBS, and
• randomly selected TFMS as control for TFBS

f10_TF_condensates_top10k_TFBS

NOTES: only use top10K peaks from each dataset only look at distance to down-stream region

f11_TF_condensates_KS_test

NOTES:

• only look at distance to down-stream region
• use KS test for TFMS/TFBS CP

f12_KS_test_with_rename

• only look at distance to down-stream region
• use KS test for TFMS/TFBS CP
• Jurkat and CUTLL1 as T-ALL
• RBPJ as NOTCH1