title: Consolidation of proteomics data in the Cancer Proteomics database.
abstract: Cancer is a class of diseases characterized by abnormal cell growth and one of the major reasons for human deaths. Proteins are involved in the molecular mechanisms leading to cancer, furthermore they are affected by anti-cancer drugs, and protein biomarkers can be used to diagnose certain cancer types. Therefore, it is important to explore the proteomics background of cancer. In this report, we developed the Cancer Proteomics database to re-interrogate published proteome studies investigating cancer. The database is divided in three sections related to cancer processes, cancer types, and anti-cancer drugs. Currently, the Cancer Proteomics database contains 9778 entries of 4118 proteins extracted from 143 scientific articles covering all three sections: cell death (cancer process), prostate cancer (cancer type) and platinum-based anti-cancer drugs including carboplatin, cisplatin, and oxaliplatin (anti-cancer drugs). The detailed information extracted from the literature includes basic information about the articles (e.g., PubMed ID, authors, journal name, publication year), information about the samples (type, study/reference, prognosis factor), and the proteomics workflow (Subcellular fractionation, protein, and peptide separation, mass spectrometry, quantification). Useful annotations such as hyperlinks to UniProt and PubMed were included. In addition, many filtering options were established as well as export functions. The database is freely available at http://cancerproteomics.uio.no.
authors: Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.|Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, Ås, Norway.
authors: Magnus Ø
authors: MØ
authors: Arntzen
authors: Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.
authors: Paul
authors: P
authors: Boddie
authors: Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.
authors: Rahel
authors: R
authors: Frick
authors: Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.|Department of Biosciences, University of Oslo, Oslo, Norway.
authors: Christian J
authors: CJ
authors: Koehler
authors: Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway.|Department of Biosciences, University of Oslo, Oslo, Norway.
authors: Bernd
authors: B
authors: Thiede
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology / Q000627:therapeutic use; D016923:Cell Death; D030562:Databases, Protein; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins; D009369:Neoplasms / Q000188:drug therapy / Q000378:metabolism* / Q000473:pathology; D011471:Prostatic Neoplasms / Q000188:drug therapy / Q000378:metabolism / Q000473:pathology; D020543:Proteome; D040901:Proteomics
chemical_list: D000970:Antineoplastic Agents; D009363:Neoplasm Proteins; D020543:Proteome
keywords: Bioinformatics; Cancer; Cell death; Cisplatin; Database; Prostate cancer