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Protocols

ESPERR specifications

Information


Unique identifier OMICS_23743
Name ESPERR
Alternative name Evolutionary and Sequence Pattern Extraction through Reduced Representations
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Requirements
Numeric python, Scipy, Pyrex, Pypar, the bx-python librairies
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline James Taylor <>
  • person_outline Francesca Chiaromonte <>

Publication for Evolutionary and Sequence Pattern Extraction through Reduced Representations

ESPERR citations

 (20)
library_books

Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

2016
PMCID: 4853421
PMID: 27117709
DOI: 10.1038/ncomms11375

[…] (http://snp-nexus.org/test/snpnexus). the presence of snps in transcription factor binding sites using transfac and mirna binding sites using targetscan were noted. regulatory potential scores (esperr regulatory potential) were obtained from the ucsc genome bioinformatics browser (http://genome.ucsc.edu/). regulomedb (http://regulomedb.org) was used to assess snps for transcription factor […]

library_books

Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE like Disease

2015
PMCID: 4461293
PMID: 26057447
DOI: 10.1371/journal.pgen.1005248

[…] thus limiting the power of statistical analysis of the vrk1 expression., among the three top variants, only snp chr8:68,708,503 lies in a region with high regulatory potential as predicted by esperr [] (). this region also contains enhancer-associated h3k4me1 histone-modification marks in lymphablastoid cells, encode chip-seq and dnase i hypersensitive sites. the snp is located only 5 bp […]

library_books

Transcriptional regulation of tenascin‐W by TGF‐beta signaling in the bone metastatic niche of breast cancer cells

2015
PMCID: 5029769
PMID: 25868708
DOI: 10.1002/ijc.29565

[…] revealed that the main control region was contained within −512 bp of the tss as longer constructs gave similar results. thus, the promoter region coincides with the ucsc genome browser tracks esperr regulatory potential (fig. b light blue) and the vertebrate multiple sequence alignment & conservation tracks (fig. b dark blue). however, further shortening of the promoter constructs […]

library_books

Multi species, multi transcription factor binding highlights conserved control of tissue specific biological pathways

2014
PMCID: 4359374
PMID: 25279814
DOI: 10.7554/eLife.02626.031

[…] appeared to be the most promising and accessible regulatory prediction dataset we could compare to our data. using the gat tool , we asked which of our phylogenetic categories were captured by the “esperr regulatory potential (7 species) described by taylor et al. 2006 and kolbe et al. 2004. as expected, of all of the phylogenetic categories significantly overlapped esperr regions, […]

library_books

Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population

2013
PMCID: 3652798
PMID: 23617307
DOI: 10.1186/1471-2350-14-47

[…] the alternative splice site predictor (assp) tool (http://wangcomputing.com/assp/index.html) []. alignments of intron 1 and regions of high homology between multiple species were determined using esperr (evolutionary and sequence pattern extraction through reduced representations) []. to investigate whether there might be conserved transcriptional elements in intron 1 of the gene encoding […]

library_books

CD6 and Syntaxin Binding Protein 6 Variants and Response to Tumor Necrosis Factor Alpha Inhibitors in Danish Patients with Rheumatoid Arthritis

2012
PMCID: 3369852
PMID: 22685579
DOI: 10.1371/journal.pone.0038539

[…] adjacent to the variation is a possible transcription binding site for peroxisome proliferator-activated receptor gamma (pparg), and a highly conserved 250 bp long genomic region with a high evolutionary and sequence pattern extraction through reduced representations (esperr) score suggesting a potential functional element in the genome . the variation may have a direct effect […]


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ESPERR institution(s)
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, USA
ESPERR funding source(s)
Supported by NIH grants HG02238 and DK65806.

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