MotifMap protocols

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MotifMap specifications

Information


Unique identifier OMICS_17640
Name MotifMap
Interface Web user interface
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Pierre Baldi <>

Publication for MotifMap

MotifMap in pipelines

 (2)
2016
PMCID: 4902921
PMID: 27287690
DOI: 10.1186/s12863-016-0381-6

[…] upstream sequence of the tst gene (15:78405000 - 78406400) was analysed for predicted transcription factor binding sites using alibaba2.1 program []. default parameters settings were employed., the motifmap [] system was used to obtain additional predictions of candidate regulatory elements. in the “gene search” window, tst gene was selected and searched for transcription factor binding sites […]

2012
PMCID: 3334587
PMID: 22293038
DOI: 10.1186/gb-2012-13-1-r7

[…] provide valuable information on the location of regulatory elements [,]. we obtained phastcons conserved elements [], phylop negatively selected sites [], conserved tf binding sites ('tfbscons' and 'motifmap') [,] and regions of high 'regulatory potential' []. in general, we find that conservation provides surprisingly little information for predicting eqtn location. only the 'regulatory […]


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MotifMap in publications

 (33)
PMCID: 5720494
PMID: 29216180
DOI: 10.1371/journal.pbio.2002940

[…] genes. the cell cycle/core-clock loop in module 1 is completed by a predicted transcriptional activation of bmal by e2f because e2f potentially binds to the promoter region of bmal1 (as reported by motifmap, the genome-wide map of candidate regulatory motif sites for humans []). the prediction of e2f as an important binding element between the clock and the cell cycle is further supported […]

PMCID: 5626401
PMID: 28904110
DOI: 10.1084/jem.20170416

[…] selected footprints. finally, in addition to footprint and motif enrichment analyses, known tf motifs were retrieved for the region around il7r tss (−10 kb upstream, +1 kb downstream) using the motifmap tool () at a 20% fdr., all sequence data (rna-seq and atac-seq) have been deposited in the european genome-phenome archive (ega), which is hosted by the ebi and the crg, under accession […]

PMCID: 5493129
PMID: 28680507
DOI: 10.1186/s13148-017-0367-x

[…] for purposes of this study via in silico modeling or molecular assay not specific to tissue source cregres coeff refers to the regression coefficient from beta regressions dtfb identified via motifmap etfb identified via encode ftfb identified via physbinder (avg precision) gtfb identified via hmr conservation 1smith et al. [] 2thaler et al. []; fuchikami et al. []; martinowich et al. []; […]

PMCID: 5462476
PMID: 28542178
DOI: 10.1371/journal.pcbi.1005538

[…] of b lineage differentially expressed enhancers identified from the fantom5 project []., for both drosophila and human analyses, we used transcription factor binding site (tfbs) motifs from the motifmap database (http://motifmap.ics.uci.edu/)., the proposed glmi assumed a linear relation between logarithm of hi-c counts and the logarithm of distance between bins as previously shown in []. […]

PMCID: 5441030
PMID: 28532435
DOI: 10.1186/s12867-017-0092-1

[…] [, ]. the santa cruz egr1 control probe was purchased from santa cruz biotechnology (sc-2529). all other probes were developed using binding site predictions and consensus information from motifmap, matinspector and tfbind. biotin labeled probes were purchased from integrated dna technologies (table ). emsas were performed using the lightshift™ chemiluminescent emsa protocol […]


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MotifMap institution(s)
Department of Computer Science, University of California Irvine, Irvine, CA, USA; Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA, USA; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
MotifMap funding source(s)
Supported in part by National Institutes of Health grants LM010235-01A1 and 5T15LM007743, National Science Foundation grant MRI EIA-0321390 and the UCI Institute for Genomics and Bioinformatics.

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