{"doi":"10.1038/ncomms8973","title":"Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type","abstract":"Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.","journal":"Nature Communications","year":2015,"id":8832,"datarank":2.7666230060052235,"base_score":4.394449154672439,"endowment":4.394449154672439,"self_citation_contribution":0.6591673732008659,"citation_network_contribution":2.1074556328043577,"self_endowment_contribution":0.6591673732008659,"citer_contribution":2.1074556328043577,"corpus_percentile":92.1482169103427,"corpus_rank":1016,"citation_count":80,"citer_count":72,"citers_with_citation_signal":59,"citers_with_endowment":59,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5405,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-08-18","fair_score":44.5833,"fair_percentile":32.89183222958057,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":14693,"name":"Sharon L. 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Kardia","orcid":"0000-0002-9853-3379","position":1,"is_corresponding":false},{"id":4558,"name":"Angela Yen","orcid":"0000-0002-9802-7679","position":0,"is_corresponding":true}],"reference_count":70,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"26282110","pmcid":"PMC4557131","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":52.5,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.4132,"fair_rationale":{"fair_score":44.58,"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 provide machine-readable metadata; it only describes the data and methods in prose."}]},"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 states that code and data are available at a URL under a GPL 3 license, but does not specify a formal data repository or persistent identifier for the data."}]},"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 formats (e.g., ChromHMM annotations, GENCODE gene annotations) and standard identifiers (e.g., gene symbols), but does not mention use of standard vocabularies or ontologies for metadata."}]},"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 includes a data-availability statement and a license (CC BY 4.0 for the article, GPL 3 for code), but does not provide a formal reproducibility package or detailed provenance for all data used."}]}},"suggestions":["Provide machine-readable metadata (e.g., as JSON-LD or RDF) describing the dataset, methods, and results.","Deposit the data in a persistent repository with a DOI and include the DOI in the paper.","Use standard ontologies (e.g., OBI, EDAM) to describe the data and methods.","Include a formal reproducibility statement with exact software versions and parameters used.","Provide a complete list of all input data files with their sources and access dates."],"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":"2026-06-18T00:41:08.234753Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}