{"doi":"10.1038/nature07385","title":"Comprehensive genomic characterization defines human glioblastoma genes and core pathways","abstract":"Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.","journal":"Nature","year":2008,"id":12093,"datarank":23.211885027308377,"base_score":8.939974177289633,"endowment":8.939974177289633,"self_citation_contribution":1.3409961265934451,"citation_network_contribution":21.87088890071493,"self_endowment_contribution":1.3409961265934451,"citer_contribution":21.87088890071493,"corpus_percentile":97.15215622457282,"corpus_rank":36,"citation_count":7782,"citer_count":196,"citers_with_citation_signal":196,"citers_with_endowment":196,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8226,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2008-09-04","fair_score":47.7083,"fair_percentile":44.415127528583994,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":70188,"name":"Roger E. McLendon","orcid":"0000-0001-6682-4588","position":1,"is_corresponding":false}],"reference_count":50,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"18772890","pmcid":"PMC2671642","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":0.2259,"fair_rationale":{"fair_score":47.71,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper states that data are deposited at the DCC and provides a URL, but does not describe machine-readable metadata or structured metadata formats."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The paper explicitly states that all TCGA data are deposited at the DCC for public access and provides a URL, but does not specify a formal authentication or authorization protocol."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper mentions standard common formats for data deposition and uses standard identifiers like gene names, but does not explicitly state use of standard vocabularies or ontologies."}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.5,"signal":null,"rationale":"The paper states data are deposited as a public resource and provides a URL, but lacks a formal data-availability statement, license, or explicit reproducibility details."}]}},"suggestions":["Include a machine-readable metadata file (e.g., JSON-LD) with structured descriptions of datasets and variables.","Provide a formal data access protocol with authentication requirements and download instructions.","Use standard ontologies (e.g., NCBI Gene, GO) and persistent identifiers (e.g., DOIs) for all referenced data.","Add a clear data-availability statement with a license (e.g., CC0) and specify how to reproduce the analyses."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:27:10.957306Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}