Home
Random
Nearby
Log in
Settings
Donate
About Wikidata
Disclaimers
Search
(Q30830996)
Watch
English
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
scientific article
In more languages
edit
Statements
instance of
scholarly article
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
title
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
(English)
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
author
Wyeth Wasserman
series ordinal
4
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
Anthony Mathelier
series ordinal
2
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
Luis del Peso
series ordinal
3
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
author name string
Rebecca Worsley Hunt
series ordinal
1
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
language of work or name
English
0 references
publication date
13 June 2014
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
published in
BMC Genomics
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
volume
15
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
page(s)
472
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
exact match
https://scigraph.springernature.com/pub.10.1186/1471-2164-15-472
0 references
cites work
Widespread misinterpretable ChIP-seq bias in yeast
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
DNA-binding specificities of human transcription factors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
ENCODE data in the UCSC Genome Browser: year 5 update
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
An integrated encyclopedia of DNA elements in the human genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
The UCSC genome browser and associated tools
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Inferring direct DNA binding from ChIP-seq
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Improved models for transcription factor binding site identification using nonindependent interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Inferring transcription factor complexes from ChIP-seq data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
MEME-ChIP: motif analysis of large DNA datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Theoretical and empirical quality assessment of transcription factor-binding motifs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Nrf2-ARE stress response mechanism: a control point in oxidative stress-mediated dysfunctions and chronic inflammatory diseases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Deep and wide digging for binding motifs in ChIP-Seq data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Evaluation of algorithm performance in ChIP-seq peak detection
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
MER41 repeat sequences contain inducible STAT1 binding sites
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
GREAT improves functional interpretation of cis-regulatory regions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Evidence-ranked motif identification
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Human DNA methylomes at base resolution show widespread epigenomic differences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Mapping accessible chromatin regions using Sono-Seq
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Distinguishing direct versus indirect transcription factor-DNA interactions
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Biopython: freely available Python tools for computational molecular biology and bioinformatics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Asap: a framework for over-representation statistics for transcription factor binding sites
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
The long terminal repeat (LTR) of ERV-9 human endogenous retrovirus binds to NF-Y in the assembly of an active LTR enhancer complex NF-Y/MZF1/GATA-2.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Estrogen receptor-related receptor gamma has an exceptionally broad specificity of DNA sequence recognition.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
The UCSC Table Browser data retrieval tool
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
TFBS: Computational framework for transcription factor binding site analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
FLI1 and EWS-FLI1 function as ternary complex factors and ELK1 and SAP1a function as ternary and quaternary complex factors on the Egr1 promoter serum response elements
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
14 July 2018
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
25 November 2018
RSAT 2011: regulatory sequence analysis tools.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
25 November 2018
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4082612
retrieved
25 November 2018
Transposable B2 SINE elements can provide mobile RNA polymerase II promoters
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24927817
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
A chromatin-modifying function of JNK during stem cell differentiation
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24927817
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1186/1471-2164-15-472
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
Dimensions Publication ID
1051872966
1 reference
stated in
SciGraph
retrieved
9 September 2019
reference URL
https://scigraph.springernature.com/pub.10.1186/1471-2164-15-472
PMC publication ID
4082612
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
PubMed publication ID
24927817
1 reference
stated in
Europe PubMed Central
PMC publication ID
4082612
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24927817%20AND%20SRC:MED&resulttype=core&format=json
retrieved
20 March 2020
ResearchGate publication ID
263098942
0 references
Sitelinks
Wikipedia
(0 entries)
edit
Wikibooks
(0 entries)
edit
Wikinews
(0 entries)
edit
Wikiquote
(0 entries)
edit
Wikisource
(0 entries)
edit
Wikiversity
(0 entries)
edit
Wikivoyage
(0 entries)
edit
Wiktionary
(0 entries)
edit
Multilingual sites
(0 entries)
edit