H3k27ac-HiChIP in LNCaP

The repository contains the intermediate files reported in H3k27ac-HiChIP in prostate cell lines identifies risk genes for prostate cancer susceptibility Claudia Giambartolomei* and Ji-Heui Seo*, Tommer Schwarz, Malika Kumar Freund, Ruth Dolly Johnson, Sandor Spisak, Sylvan C. Baca, Alexander Gusev, Nicholas Mancuso, Bogdan Pasaniuc and Matthew L. Freedman. bioRxiv 2020.

Results

epigenome_browser Files reported and downloadable from http://epigenomegateway.wustl.edu/legacy/?genome=hg19&session=bC3sBcUfeX&statusId=1396228268.

additional Other intermediate files used in the paper.

• LNCaP_back0_loops_longrange.txt.gz HiChIP loops in longrange format viewable in https://epigenomegateway.readthedocs.io/en/latest/tracks.html#hic.

• credsets95_paintor_1causals_137regions.txt.gz contains the results from fine-mapping using Paintor (1 causal) across 137 regions. In the analyses we removed regions that did not reach P < 5*10^-8, and we replaced the fine-mapped results in two regions in the 8q24 (127.6–129.0Mb, "chr8.127849659.128199916.rs16901979,rs183373024,rs10086908,rs12543663", "chr8.128260673.128560038.rs1447295,rs620861,rs6983267") with 174 JAM fine-mapping (Supplementary Data 3 of Matejcic et al.) in region chr8.127600000.129000000.rs77541621

• PrCa_GeneList_Used.csv contains the list of genes somatically mutated in prostate cancer were extracted from three publications.

• paintor_genes_small_pad5000.csv contains the overlaps of HiChIP looing data with TSS and fine-mapped SNPs.

• Thib_eqtl_sig_bonf_bestSNP.txt.gz unique SNP-gene pair tested in Thibodeau (only 1 SNP per eGene).

• TCGA_eqtl_sig_bonf_bestSNP.txt.gz unique SNP-gene pair tested in TCGA (only 1 SNP per eGene).

• ALL_TCGA_sig_thresh_bonferroni.txt.gz all associations at a Bonferroni threshold.

• ALL_Thibodeau_sig_thresh_bonferroni.txt.gz all associations at a Bonferroni threshold.

code Code used in the paper to annotate HiChIP loops with data (GWAS, eQTLs, etc).

Software and support

Dependencies: Packages in R: source("myfunctions.R") library(diffloop) library(data.table) library(GenomicRanges) library(tidyr) library(stringr) library(dplyr)

If you have any questions or comments please contact claudia.giambartolomei@gmail.com