Computational Methods for Analysis of the DNA-Binding Preferences of Cys2His2 Zinc-Finger Proteins

Basit Öğe Kaydı
dc.authoridDogan, Berat/0000-0003-4810-1970
dc.authoridNajafabadi, Hamed/0000-0003-2735-4231
dc.authorwosidDogan, Berat/AAJ-7288-2020
dc.contributor.authorDogan, Berat
dc.contributor.authorNajafabadi, Hamed S.
dc.coverage.doi10.1007/978-1-4939-8799-3
dc.date.accessioned2024-08-04T20:45:23Z
dc.date.available2024-08-04T20:45:23Z
dc.date.issued2018
dc.departmentİnönü Üniversitesien_US
dc.description.abstractCys(2)His(2) zinc-finger proteins (C2H2-ZFPs) constitute the largest class of human transcription factors (TFs) and also the least characterized one. Determining the DNA sequence preferences of C2H2-ZFPs is an important first step toward elucidating their roles in transcriptional regulation. Among the most promising approaches for obtaining the sequence preferences of C2H2-ZFPs are those that combine machine--learning predictions with in vivo binding maps of these proteins. Here, we provide a protocol and guidelines for predicting the DNA-binding preferences of C2H2-ZFPs from their amino acid sequences using a machine learning-based recognition code. This protocol also describes the tools and steps to combine these predictions with ChIP-seq data to remove inaccuracies, identify the zinc-finger domains within each C2H2-ZFP that engage with DNA in vivo, and pinpoint the genomic binding sites of the C2H2-ZFPs.en_US
dc.identifier.doi10.1007/978-1-4939-8799-3_2
dc.identifier.endpage28en_US
dc.identifier.isbn978-1-4939-8799-3
dc.identifier.isbn978-1-4939-8798-6
dc.identifier.issn1064-3745
dc.identifier.issn1940-6029
dc.identifier.pmid30155812en_US
dc.identifier.scopus2-s2.0-85052703065en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.startpage15en_US
dc.identifier.urihttps://doi.org/10.1007/978-1-4939-8799-3_2
dc.identifier.urihttps://hdl.handle.net/11616/98453
dc.identifier.volume1867en_US
dc.identifier.wosWOS:000458610500003en_US
dc.identifier.wosqualityN/Aen_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherHumana Press Incen_US
dc.relation.ispartofZinc Finger Proteins: Methods and Protocolsen_US
dc.relation.publicationcategoryKitap Bölümü - Uluslararasıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectCys(2)His(2) zinc-finger proteinsen_US
dc.subjectTranscription factorsen_US
dc.subjectDNA motifsen_US
dc.subjectChIP-seqen_US
dc.subjectMachine learningen_US
dc.subjectRecognition codeen_US
dc.titleComputational Methods for Analysis of the DNA-Binding Preferences of Cys2His2 Zinc-Finger Proteinsen_US
dc.typeBook Chapteren_US

Dosyalar

Koleksiyon

WoS İndeksli Yayınlar Koleksiyonu
PubMed İndeksli Yayın Koleksiyonu
Scopus İndeksli Yayınlar Koleksiyonu