ChIP-Seq

The Breast Cancer Epigenomics Track Hub

The Breast Cancer (BC) hub provides a new way to view and analyze cancer-related epigenetic data using the UCSC genome browser as a visualization platform and data integration hub. The data may come from different studies aimed at understanding the molecular mechanisms driving cancer growth or may be generated by large-scale genomics projects such as ENCODE. The UCSC cancer hub is available for the human genome assembly hg19.

The browser is a collection of public high-resolution tracks from different sources such as research groups at EPFL, native UCSC data tracks and reprocessed public data from GEO. They can be combined for joint data analysis to identify patterns in genomic data gathered in large-scale cancer studies.

The cancer hub can be easily customized via the selection of the tracks of interest.

The prospective user community are biologists interested in a specific gene regulatory region. The BC hub is designed to make it easier to users to find and assemble relevant data for visual inspection of such regions.

Access to the Hub

Access to the genome browser is provided through UCSC session links posted here below.

This first set of sessions are customized views focusing on ESR1 binding sites at classical estrogen-regulated genes such as GREB1, TFF1, PGR, CCND1, and MYC:

Here below are two more interesting examples of ESR1 binding around CHD1 (E-cadherin) and ZEB1, which are two key genes involved in epithelial-to-mesenchymal transition (EMT) during the initial stages of tumor invasion. We also show PGR and AR binding in the ZEB1 promoter region, indicating possible hormone receptors cross-talk with each other in hormone-driven cancers.

... and below an example of a PGR/AR binding enhancer region upstream of the KLK3 gene:

GREB1 promoter region shown above

Hub data tracks

Here below is a table summarizing the track content of the hub (latest version).

Breast Cancer (BC) Hub viewer for H. sapiens (Feb 2009 GRCh37/hg19), version 1.0

The Breast Cancer Hub Viewer for H. sapiens is made of the tracks given in the table below. Note that when strand is n/a, it means that signal applies to both strands.

UCSC track name Track description Track resolution [bp] Original dataset GEO Tissue Tumor Grade Condition MGA series name PMID
1 Klotz 2020 ATAC-seq 1 SRP139038 GSE112852 Breast cancer CTC lines and CTC-derived metastases in mouse n/a n/aklotz20 31601552
2 Ponnusamy 2019 ESR1, AR and FOXA1 ChIP-seq 50 SRP187889 GSE128018 Breast cancer xenografts n/a Vehicle and enobosarm-treatedponnusamy19 31698248
3 Chi 2019 ESR1, GRHL2 and H3K27ac ChIP-seq 50 SRP108616 GSE99680 Normal breast cells, tumors and MCF7 n/a n/achi19 31110002
track subset: ChIP-seq and CNV
4 Severson 2018 ESR1, AR, PGR, NR3C1, FOXA1, GATA3, and H3K4me1 ChIP-seq 50 SRP119087 GSE104399 Male and female breast tumors, and MCF7 n/a n/aseverson18 29396493
5 Severson 2018 Genome-wide log2-transformed, normalized (ratios of) read counts (CopywriteR from Bioconductor) 50 SRP119087 GSE104399 Male and female breast tumors, and MCF7 n/a n/aseverson18 29396493
track subset: ChIP-seq and ATAC-seq
6 Takaku 2018 GATA3 and mutated (ZnFn2) GATA3, ESR1, PGR, FOXA1, and PolII ChIP-seq 50 SRP108337 GSE99479 T47D and GATA3 mutant cell line (CR3) n/a Vehicle and P4 takaku18 29535312
7 Takaku 2018 ATAC-seq 1 SRP108337 GSE99479 T47D and GATA3 mutant cell line (CR3) n/a n/a takaku18 29535312
8 Maturi 2018 ZEB1 ChIP-seq 50 E-MTAB-5241 n/a Triple-negative breast cancer cell line Hs578T n/a n/amaturi18 29744893
9 Guertin 2018 ESR1 (in parallel with CTCF) ChIP-seq 50 PRJNA434662 GSE110824 Patient-derived tumor xenografts (PDXs) n/a n/aguertin18 29672735
10 Mohammed 2015 ESR1, PGR, and p300 ChIP-seq 50 SRP057755, SRP057756, SRP057757 GSE68359 MCF7, T47D, and xenografted MCF7 n/a Estrogen-treated and with/without progestins (Progesterone/R5020)mohammed15 26153859
11 Ross-Inness 2012 ESR1 and FOXA1 ChIP-seq 50 SRP032421 GSE32222 Primary ER-positive breast tumors from patients, distant ER-positive metastases, and cancer cell lines (MCF7, T47D, ZR75, BT474) n/a n/aross12 22217937
12 T47D DNaseI from ENCODE 2012 DNase I hypersensitive sites 1 UCSC n/a T47D n/a n/aUW-DNaseI-HS 22955617

Last update October 2021