2021
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
Chen S, Liu Q, Cui X, Feng Z, Li C, Wang X, Zhang X, Wang Y, Jiang R. OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic Acids Research 2021, 49: w483-w490. PMID: 33999180, PMCID: PMC8262705, DOI: 10.1093/nar/gkab337.Peer-Reviewed Original ResearchConceptsGenomic regionsChromatin accessibilityRegulatory elementsAnnotation of genomic regionsActive DNA regulatory elementsFunction of transcription factorsRegulatory mechanismsGene functional relationshipsDNA regulatory elementsSingle-cell data analysisChromatin accessibility profilesCell type-specificHigh-throughput methodChromatin contactsTranscription factorsAccessibility profilesType-specificBiosample typesAnnotation resourcesPublic repositoriesChromatinUser-friendly functionsReal-time browsingWeb serverComprehensive profile
2019
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information
Song S, Cui H, Chen S, Liu Q, Jiang R. EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information. Quantitative Biology 2019, 7: 233-243. DOI: 10.1007/s40484-019-0175-8.Peer-Reviewed Original ResearchTranscription factor functionTranscription factorsEpigenetic informationRegulatory regionsRegulatory elementsFunctional interpretationTF functionFunction of transcription factorsRegulatory mechanismsChIP-seq dataTF binding sitesFactor functionExpression levels of target genesLevels of target genesCombination of sequenceChIP-seqNearby genesChromatin accessibilityTranscriptional regulationGO termsFunction of TFEpigenetic dataGene associationsGO enrichmentTranscription process
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