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RTFBSDB specifications

Information


Unique identifier OMICS_11801
Name RTFBSDB
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL https://codeload.github.com/Danko-Lab/rtfbs_db/zip/master
Maintained Yes

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Maintainer


  • person_outline Zhong Wang <>

Publication for RTFBSDB

RTFBSDB in publications

 (3)
PMCID: 5925605
PMID: 29740534
DOI: 10.3389/fonc.2018.00100

[…] than one tumor sample were reported., we investigated the enrichment of tf-binding motifs in both the identified dmrs and their immediate surroundings (±5 kb) using the pipeline recommended by the rtfbsdb package (). first, the entire direct and inferred homo sapiens tf-binding motifs were downloaded from the cis-bp database (). every dmr sequence and its ±5 kb surroundings were scanned […]

PMCID: 5882141
PMID: 29614078
DOI: 10.1371/journal.pone.0194522

[…] covered by each dreg-hd site were counted. deseq2 [] was used for differential gene expression analysis (false discovery rate (fdr) < 0.01)., motif enrichment analyses were completed using our rtfbsdb as described previously []. we used the set of 1,964 human motifs in rtfbsdb clustered into 622 maximally distinct dna binding specificities, which represents the default settings […]

PMCID: 5880349
PMID: 29608602
DOI: 10.1371/journal.pone.0194023

[…] that coordinate changes between tams and tamr lines. we identified 12 clusters of motifs enriched in tres that are differentially active in the tams and tamr lines (bonferroni corrected p< 0.05; rtfbsdb []). the top scoring motif in this analysis corresponds to an estrogen response element (ere), the canonical dna binding sequence that recruits erα to estrogen responsive enhancers (). […]

RTFBSDB institution(s)
Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
RTFBSDB funding source(s)
This work was supported by National Heart, Lung, and Blood Institute UHL129958A.

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