Notes

This repository contains all source code for analyzing the data and generating the results and figures in the paper:

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
Celestia Fang^*, Zhenjia Wang^*, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, Maria E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos^#, Chongzhi Zang^#. Genome Biology 21, 247 (2020)
A README file is attached to each folder/subfolder.
For scripts used to generate the figures, please refer to README_figure.rst.

Download

To download the processed data, including the union of all CTCF binding sites, the constitutive CTCF binding sites, the cancer-specific CTCF binding sites, etc., please check here.

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
f0_data_collection_new		f0_data_collection_new
f10_TF_binding		f10_TF_binding
f11_GSI_shCTCF		f11_GSI_shCTCF
f12_SWI_SNF		f12_SWI_SNF
f13_GSI_RNA_bw		f13_GSI_RNA_bw
f1_data_processing		f1_data_processing
f2_union_CTCFs		f2_union_CTCFs
f3_cancer_specific_CTCFs		f3_cancer_specific_CTCFs
f4_HiC_TADs		f4_HiC_TADs
f5_TCGA_ATAC		f5_TCGA_ATAC
f6_gene_expr		f6_gene_expr
f7_ICGC_mutation		f7_ICGC_mutation
f8_DNA_methylation		f8_DNA_methylation
f9_histone_modification		f9_histone_modification
fu_feature_combination		fu_feature_combination
fz_figures		fz_figures
utilities		utilities
.DS_Store		.DS_Store
LICENSE		LICENSE
README.md		README.md
README_figure.rst		README_figure.rst