2024
Less-is-more: selecting transcription factor binding regions informative for motif inference
Xu J, Gao J, Ni P, Gerstein M. Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic Acids Research 2024, 52: e20-e20. PMID: 38214231, PMCID: PMC10899791, DOI: 10.1093/nar/gkad1240.Peer-Reviewed Original ResearchConceptsChIP-seq signalsChIP-seqGenomic regionsMotif inferenceTranscription factorsTargeting motifTranscription factor binding regionsChIP-seq datasetsNon-specific interactionsC-scoreDNA motifsBinding regionMotifTranscriptionTF signalingAccurate inferenceStronger signalSignalDNARegionTargetInteraction
2006
Genomic analysis of the hierarchical structure of regulatory networks
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 14724-14731. PMID: 17003135, PMCID: PMC1595419, DOI: 10.1073/pnas.0508637103.Peer-Reviewed Original ResearchConceptsTranscription factorsMaster transcription factorRegulatory networksRegulatory hierarchyProtein-protein interaction networkMost transcription factorsExpression of thousandsExpression level changesGenomic analysisProtein interactionsInteraction networksTarget genesDirect targetGenesEukaryotesProkaryotesCellsFundamental questionsBiologyTargetExpression