README

==
f6_TCGA_atacseq_survival
==
TCGA survival top/bottom 50% patients -> differential ATAC score -> BART


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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



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f10_TF_condensates_top10k_TFBS
==

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


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f11_TF_condensates_KS_test
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NOTES: 
- only look at distance to down-stream region
- use KS test for TFMS/TFBS CP


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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