{"corpus_id":1582696,"paper_sha":"eb960b5d56ed1368991eaa4f40cb7afee66edb1f","doi":"10.1016/S1476-5586(04)80047-2","arxiv_id":null,"pmid":15068665,"pmcid":"PMC1635162","mag_id":1977918192,"dblp_id":null,"acl_id":null,"title":"ONCOMINE: a cancer microarray database and integrated data-mining platform.","year":2004,"publication_date":null,"venue":"Neoplasia","journal":{"name":"Neoplasia","pages":"\n          1-6\n        ","volume":"6 1"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle","Study"],"pubmed_pub_types":["Comparative Study","Journal Article","Research Support, Non-U.S. Gov't","Research Support, U.S. Gov't, Non-P.H.S."],"s2_fields_of_study":["Biology","Medicine","Computer Science"],"reference_count":47,"citation_count":3442,"influential_citation_count":138,"is_open_access":false,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Databases, Genetic","mj":true,"ui":"D030541"},{"d":"Gene Expression Profiling","mj":true,"ui":"D020869"},{"d":"Neoplasms","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"}],"ui":"D009369"},{"d":"Oligonucleotide Array Sequence Analysis","mj":true,"ui":"D020411"},{"d":"Software","mj":false,"ui":"D012984"}],"chemicals":null,"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":null,"s2_open_access_landing_url":null,"s2_open_access_license":null,"s2_open_access_status":null,"pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"DNA microarray technology has led to an explosion of oncogenomic analyses, generating a wealth of data and uncovering the complex gene expression patterns of cancer. Unfortunately, due to the lack of a unifying bioinformatic resource, the majority of these data sit stagnant and disjointed following publication, massively underutilized by the cancer research community. Here, we present ONCOMINE, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses. To date, ONCOMINE contains 65 gene expression datasets comprising nearly 48 million gene expression measurements form over 4700 microarray experiments. Differential expression analyses comparing most major types of cancer with respective normal tissues as well as a variety of cancer subtypes and clinical-based and pathology-based analyses are available for exploration. Data can be queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets.","claims":[{"public_id":"cl_810a364c040a4d4cea73cfd9ef05d4ee","status":"active","text":"Differential expression analyses are available for comparisons of major cancer types with normal tissues, cancer subtypes, and clinical-based and pathology-based analyses.","confidence":0.97,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_810a364c040a4d4cea73cfd9ef05d4ee"},{"public_id":"cl_2fa2dc29c69ec83f7961f015aa5a40cf","status":"active","text":"Gene sets can be restricted to clinically important annotations, including secreted, kinase, membrane, and known gene-drug target pairs, to support discovery of novel biomarkers and therapeutic targets.","confidence":0.96,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_2fa2dc29c69ec83f7961f015aa5a40cf"},{"public_id":"cl_7939988b863f71b92c7452495e504367","status":"active","text":"ONCOMINE is presented as a cancer microarray database and web-based data-mining platform for discovery from genome-wide expression analyses.","confidence":0.99,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_7939988b863f71b92c7452495e504367"},{"public_id":"cl_3cb4d59f83ff01fd7e9a7651c2b04c5f","status":"active","text":"Queries and visualizations can be performed for a selected gene across all analyses or for multiple genes in a selected analysis.","confidence":0.95,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_3cb4d59f83ff01fd7e9a7651c2b04c5f"},{"public_id":"cl_c5880bbb7c1aba8f2eaccd97be654523","status":"active","text":"The resource contains 65 gene expression datasets with nearly 48 million gene expression measurements from over 4700 microarray experiments.","confidence":0.99,"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous (12632b8b5f)","roles":["extraction"],"url":"https://sah.borca.ai/u/12632b8b5f"}],"url":"https://sah.borca.ai/claims/cl_c5880bbb7c1aba8f2eaccd97be654523"}],"concepts":[{"public_id":"co_2388561e50bd20dd6ecd05303ce81575","status":"active","name":"gene sets","description":"Collections of genes grouped for filtering or analysis.","types":["set"],"aliases":[],"contributors":[{"id":1,"public_id":"12632b8b5f","public_label":"Anonymous 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