NDLI: HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Content Provider	PubMed Central
Author	Kulakovskiy, Ivan V. Vorontsov, Ilya E. Yevshin, Ivan S. Soboleva, Anastasiia V. Kasianov, Artem S. Haitham, Ashoor Wail, Ba-alawi Bajic, Vladimir B. Medvedeva, Yulia A. Kolpakov, Fedor A. Makeev, Vsevolod J.
Copyright Year	2016
Abstract	Models of transcription factor (TF) binding sites provide a basis for a wide spectrum of studies in regulatory genomics, from reconstruction of regulatory networks to functional annotation of transcripts and sequence variants. While TFs may recognize different sequence patterns in different conditions, it is pragmatic to have a single generic model for each particular TF as a baseline for practical applications. Here we present the expanded and enhanced version of HOCOMOCO (http://hocomoco.autosome.ru and http://www.cbrc.kaust.edu.sa/hocomoco10), the collection of models of DNA patterns, recognized by transcription factors. HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs. Furthermore, we introduce the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs. The update is based on the analysis of massive ChIP-Seq and HT-SELEX datasets, with the validation of the resulting models on in vivo data. To facilitate a practical application, all HOCOMOCO models are linked to gene and protein databases (Entrez Gene, HGNC, UniProt) and accompanied by precomputed score thresholds. Finally, we provide command-line tools for PWM and diPWM threshold estimation and motif finding in nucleotide sequences.
Related Links	http://dx.doi.org/10.1093/nar/gkv1249
Starting Page	116
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Database issue
Volume Number	44
Language	English
Publisher	Oxford University Press
Publisher Date	2016-01-04
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites

Pseudocounts for transcription factor binding sites

Positional distribution of human transcription factor binding sites

Lineage-specific expansion of DNA-binding transcription factor families

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

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