PXD025238

PXD025238 is an original dataset announced via ProteomeXchange.

Title	Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer
Description	Triple negative breast cancer is an aggressive type of breast cancer with very little treatment options. TNBC is very heterogeneous with large alterations in the genomic, transcriptomic, and proteomic landscapes leading to various subtypes with differing responses to therapeutic treatments. We applied a multi-omics data integration method to evaluate the correlation of important regulatory features in TNBC BRCA1 wild-type MDA-MB-231 and TNBC BRCA1 5382insC mutated HCC1937 cells compared with normal epithelial breast MCF10A cells. The data includes DNA methylation, RNAseq, protein, phosphoproteomics, and histone post-translational modification. Data integration methods identified regulatory features from each omics method had greater than 80% positive correlation within each TNBC subtype. Key regulatory features at each omics level were identified distinguishing the three cell lines and were involved in important cancer related pathways such as TGFbeta signaling, PI3K/AKT/mTOR, and Wnt/beta-catenin signaling.
HostingRepository	PRIDE
AnnounceDate	2021-06-24
AnnouncementXML	Submission_2021-06-24_04:34:51.381.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025238
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Stephanie Byrum
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-04-06 19:49:15	ID requested
⏵ 1	2021-06-24 04:34:52	announced

Chappell K, Manna K, Washam CL, Graw S, Alkam D, Thompson MD, Zafar MK, Hazeslip L, Randolph C, Gies A, Bird JT, Byrd AK, Miah S, Byrum SD, Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer. Mol Omics, 17(5):677-691(2021) [pubmed]

submitter keyword: multi-omics data Integration, RNA-seq, phosphoproteomics, histone posttranslational modification, triple negative breast cancer

Stephanie D Byrum
contact affiliation	Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA
contact email	sbyrum@uams.edu
lab head
Stephanie Byrum
contact affiliation	UAMS
contact email	sbyrum@uams.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/06/PXD025238

PRIDE project URI

• PRIDE
  1. PXD025238
     1. Label: PRIDE project
     2. Name: Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer