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 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 is a table summarizing the track content of the hub (latest version).
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/a||klotz20||31601552|
|2||Ponnusamy 2019||ESR1, AR and FOXA1 ChIP-seq||50||SRP187889||GSE128018||Breast cancer xenografts||n/a||Vehicle and enobosarm-treated||ponnusamy19||31698248|
|3||Chi 2019||ESR1, GRHL2 and H3K27ac ChIP-seq||50||SRP108616||GSE99680||Normal breast cells, tumors and MCF7||n/a||n/a||chi19||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/a||severson18||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/a||severson18||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/a||maturi18||29744893|
|9||Guertin 2018||ESR1 (in parallel with CTCF) ChIP-seq||50||PRJNA434662||GSE110824||Patient-derived tumor xenografts (PDXs)||n/a||n/a||guertin18||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/a||ross12||22217937|
|12||T47D DNaseI from ENCODE 2012||DNase I hypersensitive sites||1||UCSC||n/a||T47D||n/a||n/a||UW-DNaseI-HS||22955617|