MotifDb statistics

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Protocols

MotifDb specifications

Information


Unique identifier OMICS_28174
Name MotifDb
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download
User data submission Not allowed
Version 1.22.0
Requirements
methods, BiocGenerics, IRanges, R(>=2.15.0), S4Vectors, Biostrings, rtracklayer, seqLogo, RUnit, MotIV, splitstackshape
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Documentation


Maintainer


  • person_outline Paul Shannon

MotifDb citations

 (6)
library_books

β1 Integrin Deletion From the Lens Activates Cellular Stress Responses Leading to Apoptosis and Fibrosis

2017
PMCID: 5539801
PMID: 28763805
DOI: 10.1167/iovs.17-21721

[…] ding sites similar to the position weight matrix for the Egr1 motif were identified in the region 2.5 kb upstream of the TSS of β1MLR10 lens DRGs (n = 120) using an in-house script implemented in the MotifDb R-package (www.bioconductor.org). This Egr1 motif matching was performed with a minimum score match percentage (80%) using the matchPMW function in the “Biostring” package (www.bioconductor.or […]

call_split

Detection of statistically significant network changes in complex biological networks

2017
BMC Syst Biol
PMCID: 5336651
PMID: 28259158
DOI: 10.1186/s12918-017-0412-6
call_split See protocol

[…] od. In this last case we also used intersection with transcription factor (TF) binding sites to keep only relationships due to promoter binding. We used a set of 457 TF binding sites available in the MotifDB Bioconductor package.Master Regulator Analysis (MRA) algorithm [] was applied to the global glioma network in order to compute the statistical significance of the overlap between the regulon o […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] ocLite.R" ) 2 packages <– c ( "TCGAbiolinks" , "ELMER" , "gaia" , "ChIPseeker" , 3 "AnnotationHub" , "ComplexHeatmap" , 4 "clusterProfiler" , "RTCGAToolbox" , 5 "minet" , "biomaRt" , "pathview" , "MotifDb" , 6 "MotIV" , "motifStack" , "rGADEM" ) 7 new.packages <– packages [ ! ( packages %in% installed . packages () [, "Package" ])] 8 if ( length ( new . packages )) biocLite( new . packages ) 9 […]

library_books

Genome wide identification of Drosophila dorso ventral enhancers by differential histone acetylation analysis

2016
Genome Biol
PMCID: 5037609
PMID: 27678375
DOI: 10.1186/s13059-016-1057-2

[…] Drosophila melanogaster motifs in the Bioconductor MotifDb package v1.10 [] were first filtered to include only those where the corresponding transcription factor is expressed in either gd7 or Tl10b (mRNA-seq FPKM greater than 3). Motifs derived from […]

library_books

Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells

2015
PLoS One
PMCID: 4658012
PMID: 26599758
DOI: 10.1371/journal.pone.0143627

[…] e. We obtained 690 files of ChIP-seq peaks performed with 91 human cell lines and representing 161 unique regulatory factors.To define a wide collection of human PWMs we used the Bioconductor Package MotifDB ([]), that collects TF binding preference information from several sources (among which Jaspar [], UniPROBE [], hPDI [] and Ref. []). We were able to retrieve 1298 matrices associated with a h […]

library_books

Lipid mediated regulation of SKN 1/Nrf in response to germ cell absence

2015
eLife
PMCID: 4541496
PMID: 26196144
DOI: 10.7554/eLife.07836.042

[…] package ().Functional annotations and phenotypes were obtained from WormBase build WS246. SKN-1 transcription factor binding site analysis of hits was conducted with biomaRt, GenomicFeatures, JASPAR, MotifDb, motifStack, MotIV, and Rsamtools (; , ; ; ; ; ). JASPAR analysis was performed with the SKN-1 matrix MA0547.1 using 2 kb upstream sequences obtained from Ensembl WBcel235 (). modENCODE SKN-1: […]

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