(Q36280574)

13 August 2017

Inferring direct DNA binding from ChIP-seq (English)

1 reference

13 August 2017

Philip Machanick

2

1 reference

15 November 2018

1

1 reference

PMCID

3458523

15 November 2018

language of work or name

English

0 references

publication date

18 May 2012

1 reference

13 August 2017

Nucleic Acids Research

1 reference

13 August 2017

40

1 reference

13 August 2017

17

1 reference

13 August 2017

e128

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

13 August 2017

start time

8 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Inferring transcription factor complexes from ChIP-seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

DREME: motif discovery in transcription factor ChIP-seq data

30 September 2017

1 reference

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A user's guide to the encyclopedia of DNA elements (ENCODE)

30 September 2017

1 reference

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Nuclear factor I revealed as family of promoter binding transcription activators

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Evaluation of algorithm performance in ChIP-seq peak detection

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

30 September 2017

1 reference

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A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

PASTAA: identifying transcription factors associated with sets of co-regulated genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Design and analysis of ChIP-seq experiments for DNA-binding proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Model-based analysis of ChIP-Seq (MACS)

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

RSAT: regulatory sequence analysis tools

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Detection of functional DNA motifs via statistical over-representation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Interaction of YY1 with E2Fs, mediated by RYBP, provides a mechanism for specificity of E2F function

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

DNA binding sites: representation and discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Identification of DNA binding-site preferences for nuclear factor I-A.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3458523

Information content and free energy in DNA--protein interactions

22 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22610855

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKS433

1 reference

13 August 2017

1 reference

13 August 2017

1 reference

PMCID

3458523