{"doi":"10.1038/srep24799","title":"Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues","abstract":"The central dogma of molecular biology describes the translation of genetic information from mRNA to protein, but does not specify the quantitation or timing of this process across the genome. We have analyzed protein and gene expression in a diverse set of human tissues. To study concordance and discordance of gene and protein expression, we integrated mass spectrometry data from the Human Proteome Map project and RNA-Seq measurements from the Genotype-Tissue Expression project. We analyzed 16,561 genes and the corresponding proteins in 14 tissue types across nearly 200 samples. A comprehensive tissue- and gene-specific analysis revealed that across the 14 tissues, correlation between mRNA and protein expression was positive and ranged from 0.36 to 0.5. We also identified 1,012 genes whose RNA and protein expression was correlated across all the tissues and examined genes and proteins that were concordantly and discordantly expressed for each tissue of interest. We extended our analysis to look for genes and proteins that were differentially correlated in cancer compared to normal tissues, showing higher levels of correlation in normal tissues. Finally, we explored the implications of these findings in the context of biomarker and drug target discovery.","journal":"Scientific Reports","year":2016,"id":10100,"datarank":5.154179156653189,"base_score":5.389071729816501,"endowment":5.389071729816501,"self_citation_contribution":0.8083607594724752,"citation_network_contribution":4.345818397180714,"self_endowment_contribution":0.8083607594724752,"citer_contribution":4.345818397180714,"corpus_percentile":95.94646863154638,"corpus_rank":525,"citation_count":218,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.737,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-05-04","fair_score":39.375,"fair_percentile":22.516556291390728,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":85788,"name":"Nishant Jain","orcid":"0000-0003-3260-2543","position":1,"is_corresponding":false},{"id":3381,"name":"Dvir Aran","orcid":"0000-0001-6334-5039","position":2,"is_corresponding":false},{"id":51,"name":"Atul Janardhan Butte","orcid":"0000-0002-7433-2740","position":3,"is_corresponding":false},{"id":2824,"name":"Marina Sirota","orcid":"0000-0002-7246-6083","position":4,"is_corresponding":false},{"id":52431,"name":"Idit Kosti","orcid":"0000-0003-2212-5472","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"27142790","pmcid":"PMC4855174","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":55.0,"fair_i":25.0,"fair_r":25.0,"fair_zscore":-0.7354,"fair_rationale":{"fair_score":39.38,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"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":0.25,"signal":null,"rationale":"The paper does not describe any machine-readable metadata or structured metadata provision; only human-readable figures and tables are present."}]},"A":{"name":"Accessible","score":55.0,"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":0.5,"signal":null,"rationale":"Data sources (GTEx, HPM, TCPA) are named with URLs/accessions, but the paper does not provide a clear, direct link or protocol to access the exact dataset or code used in the analysis."}]},"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 uses standard file formats (e.g., RPKM) and common identifiers (gene symbols), but does not specify use of formal ontologies or standardized vocabularies for tissue types or assays."}]},"R":{"name":"Reusable","score":25.0,"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":0.333,"signal":null,"rationale":"A CC-BY 4.0 license is provided, but there is no explicit data availability statement for the derived dataset, no sharing of analysis code, and insufficient detail to fully reproduce the analysis without accessing external sources."}]}},"suggestions":["Publish the processed per-tissue gene and protein expression matrix in a structured, machine-readable format (e.g., CSV or JSON) in a public repository.","Provide a direct DOI or stable URL to the exact derived dataset and analysis scripts (e.g., R code) used in the study.","Use standard ontology terms for tissues (e.g., UBERON) and assays (e.g., OBI) to improve interoperability and semantic clarity.","Add a formal data availability statement in the paper specifying where and how to access all supporting data and code.","Include metadata annotations (e.g., schema.org or DataCite) to improve findability in automated systems."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:37:00.924502Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}