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Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

ABSTRACT: Patient tissue samples raw data: ERBB2 positive and ERBB2 negative

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: william hancock

PROVIDER: MSV000079211 | MassIVE | Wed Aug 05 16:41:00 BST 2015

SECONDARY ACCESSION(S): PXD002674

REPOSITORIES: MassIVE

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Publications

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

Yan Julia Fangfei JF Kim Hoguen H Jeong Seul-Ki SK Lee Hyoung-Joo HJ Sethi Manveen K MK Lee Ling Y LY Beavis Ronald C RC Im Hogune H Snyder Michael P MP Hofree Matan M Ideker Trey T Wu Shiaw-Lin SL Paik Young-Ki YK Fanayan Susan S Hancock William S WS

Journal of proteome research 20151020 12

V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative ...[more]

PMID: 26435392

Similar Datasets

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

Project description:V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative is the amplification mechanism that typically results in overexpression of a set of genes adjacent to ERBB2, which provides evidence of a linkage between gene location and expression. In this report we studied patient samples from ERBB2-positive together with adjacent control nontumor tissues. In addition, non-ERBB2-expressing patient samples were selected as comparison to study the effect of expression of this oncogene. We detected 196 proteins in ERBB2-positive patient tumor samples that had minimal overlap (29 proteins) with the non-ERBB2 tumor samples. Interaction and pathway analysis identified extracellular signal regulated kinase (ERK) cascade and actin polymerization and actinmyosin assembly contraction as pathways of importance in ERBB2+ and ERBB2- gastric cancer samples, respectively. The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.

| S-EPMC5706558 | biostudies-literature

Methylation analysis of STAT3 targets in gastric cancer patient samples

Project description:To investigate the differences of STAT3-mediated DNA methylation in gastric cancer patient samples, genome wide DNA methylation profiling for STAT3-positive/negative patient samples

2023-12-05 | GSE162731 | GEO

Integrated transcriptomic-genomic tool Texomer profiles cancer tissues.

Project description:Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data. Texomer results in substantially improved accuracy in sample categorization and functional variant prioritization.

| S-EPMC7337246 | biostudies-literature

Site-specific glycan analysis of ErbB2 in breast cancer cell SKBR-3

2024-05-24 | PXD039837 | Pride

Site-specific glycan analysis of ErbB2 in breast cancer cell BT474

Project description:This study provides site-specific profiles of asparagine-linked and serine/threonine-linked glycosylations on ErbB2, a therapeutic target RTK for ErbB2-positive cancer, through structural analysis of recombinant ErbB2 extracellular region and endogenous ErbB2 from ErbB2-positive breast cancer cells. Furthermore, comparison of the N-glycosylated structures of the extracellular regions of ErbB2 and its homologue, the epidermal growth factor receptor (EGFR), showed differences in the distribution and density of N-glycans on both molecules, providing new insights into the different activation mechanisms of ErbB2 and EGFR from a glycan perspective.

2024-05-24 | PXD039838 | Pride

Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive breast cancer [RPPA-Longterm-BT474]

Project description:EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer. Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

2014-08-13 | GSE50107 | GEO

Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive breast cancer [RPPA-Shortterm-BT474]

Project description:EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer. Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

2014-08-13 | GSE50104 | GEO

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-SKBR3]

Project description:EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer. Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

2012-10-22 | GSE36326 | GEO

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-Longterm]

Project description:EGFR-inhibition is required for targeted therapies of EGFR high/ERBB2 positive breast cancer. Approximately 30% of human ERBB2 positive breast tumors also express EGFR.

2012-10-22 | GSE36325 | GEO

Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-HCC1954]

Project description:EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer. Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

2012-10-22 | GSE36324 | GEO

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