Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26435392", "kind": "science-record", "revision": 5, "content_hash": "sha256:1e5ee09122e6516b752062fddca5bd2a76a36c06d7d5ffeca37bf9d8c080e9b3", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T18:47:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.", "doi": "10.1021/acs.jproteome.5b00827", "pmid": "26435392", "authors": ["Julia Fangfei Yan", "Hoguen Kim", "Seul-Ki Jeong", "Hyoung-Joo Lee", "Manveen K Sethi", "Ling Y Lee", "Ronald C Beavis", "Hogune Im", "Michael P Snyder", "Matan Hofree", "Trey Ideker", "Shiaw-Lin Wu", "Young-Ki Paik", "Susan Fanayan", "William S Hancock"], "journal": "Journal of proteome research", "year": 2015, "abstract": "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.", "claims": [{"id": "claim-target-result", "statement": "Headline result: “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 statistical method is not stated in the specified sections, so there is no numerical result for that registered target; the raw-data route is ProteomeXchange and GPMDB: “The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.”", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26435392", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "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."}, {"asset": "source:pmid:26435392", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Headline result: “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 statistical method is not stated in the specified sections, so there is no numerical result for that registered target; the raw-data route is ProteomeXchange and GPMDB: “The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.”", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26435392"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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A total of 150 samples were examined by immunohistochemistry and FISH, and eight ERBB2-positive samples a"], "order_basis": "paper_text_order:2300", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nd location, spectral counts, as well as the RNA-Seq values for two gastric cancer cell lines (SN", "the genes listed in the KEGG pathway and the RNA-Seq values for the two gastric cancer cell lines", "focus on overexpressed genes as measured by transcriptomic and proteomic measurements.32 Supplementary", "xamined for integration of the proteomic and transcriptomic data and are listed in Supplementary Figure"], "order_basis": "paper_text_order:7186", "id": "assay:2"}]}