Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs (Q34066561)

30 July 2017

title

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs (English)

1 reference

30 July 2017

Andrew Hufton

2

0 references

Thomas Manke

Thomas Manke

7

0 references

Matthias Heinig

Matthias Heinig

3

0 references

Morgane Thomas-Chollier

Morgane Thomas-Chollier

1

0 references

Martin Vingron

8

Martin Vingron

1 reference

30 July 2017

Sean O'Keeffe

4

1 reference

30 July 2017

Nassim El Masri

5

1 reference

30 July 2017

Helge G Roider

6

1 reference

30 July 2017

publication date

3 November 2011

1 reference

30 July 2017

1 reference

30 July 2017

volume

6

1 reference

30 July 2017

issue

12

1 reference

30 July 2017

page(s)

1860-1869

1 reference

Applied bioinformatics for the identification of regulatory elements

30 July 2017

cites work

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Theoretical and empirical quality assessment of transcription factor-binding motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Predicting transcription factor affinities to DNA from a biophysical model

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Statistical modeling of transcription factor binding affinities predicts regulatory interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Quantifying the effect of sequence variation on regulatory interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

TRANSFAC: a database on transcription factors and their DNA binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Selective Glucocorticoid Receptor modulators

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

The UCSC Genome Browser database: update 2011

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Regulatory sequence analysis tools

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

RSAT 2011: regulatory sequence analysis tools.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Galaxy: a platform for interactive large-scale genome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

Glucocorticoid receptor, C/EBP, HNF3, and protein kinase A coordinately activate the glucocorticoid response unit of the carbamoylphosphate synthetase I gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

On the power of profiles for transcription factor binding site detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1038/NPROT.2011.409

31 March 2020

Identifiers

DOI

10.1038/NPROT.2011.409

1 reference

Dimensions Publication ID

30 July 2017

1008025323

0 references

1 reference