PXD025238 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-04-06 19:49:15 | ID requested | |
⏵ 1 | 2021-06-24 04:34:52 | announced | |
Publication List
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] |
Keyword List
submitter keyword: multi-omics data Integration, RNA-seq, phosphoproteomics, histone posttranslational modification, triple negative breast cancer |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025238
- Label: PRIDE project
- Name: Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer