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ENCODE-motifs specifications


Unique identifier OMICS_07644
Name ENCODE-motifs
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Pouya Kheradpour

Publication for ENCODE-motifs

ENCODE-motifs citations


Mocap: large scale inference of transcription factor binding sites from chromatin accessibility

Nucleic Acids Res
PMCID: 5416775
PMID: 28334916
DOI: 10.1093/nar/gkx174

[…] Human TF motifs (PWMs) were downloaded from the ENCODE motif collection (http://compbio.mit.edu/encode-motifs) and the CisBP motif database (http://cisbp.ccbr.utoronto.ca) (,). We combined information from the two motif collections and filtered PWMs representing the same TF using pairwise compar […]


The systematic analysis of coding and long non coding RNAs in the sub chronic and chronic stages of spinal cord injury

Sci Rep
PMCID: 5247719
PMID: 28106101
DOI: 10.1038/srep41008

[…] To identify TFs potentially involved in the regulation of DE lncRNAs, motif analysis was performed. The motif data set at ENCODE (http://compbio.mit.edu/encode-motifs) was downloaded. Motifs were used to scan the regulatory regions of DE lncRNAs using FIMO with an FDR < 0.05.The regulatory regions of lncRNAs were defined as 5 kb upstream and 1 kb down […]


Most brain disease associated and eQTL haplotypes are not located within transcription factor DNase seq footprints in brain

Hum Mol Genet
PMCID: 5351933
PMID: 27798116
DOI: 10.1093/hmg/ddw369

[…] rected for using 1Mb quintile isochores. Empirically determined standard deviations were plotted for all shown fold enrichment values. Nucleotide conservation scores (Phylo46way) were downloaded from ENCODE (). Motifs were identified using FIMO to search for JASPAR vertebrate motifs with a P-value threshold of 10 − 4, repeats masked and a 1st order markov background on both the reference genome an […]


Longevity and Plasticity of CFTR Provide an Argument for Noncanonical SNP Organization in Hominid DNA

PLoS One
PMCID: 4211684
PMID: 25350658
DOI: 10.1371/journal.pone.0109186

[…] Assumptions such as these have been challenged to some degree by recent studies indicating up to 80% of the non-coding genome subserves important regulatory function, and that point mutations within ENCODE motifs might often give rise to significant effects on fitness –.Data from dbSNP and HapMap are not optimal for addressing SNP frequency or distribution, since ascertainment bias skews these co […]


Comprehensive characterization of erythroid specific enhancers in the genomic regions of human Krüppel like factors

BMC Genomics
PMCID: 3846580
PMID: 23985037
DOI: 10.1186/1471-2164-14-587

[…] motifs embedded in erythroid-specific KLF enhancers were analyzed using the MEME software (http://meme.ebi.edu.au/meme/cgi-bin/meme.cgi), and these de novo discovered motifs were searched against the ENCODE-motifs database (http://www.broadinstitute.org/~pouyak/motif-disc/human/) using TOMTOM algorithm (http://meme.ebi.edu.au/meme/cgi-bin/tomtom.cgi) []. […]


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ENCODE-motifs institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA

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