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Citations per year

Number of citations per year for the bioinformatics software tool ESPERR
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Tool usage distribution map

This map represents all the scientific publications referring to ESPERR per scientific context
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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

 (15)
library_books

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

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

[…] nexus (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 re […]

library_books

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

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

[…] tructs 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 to −32 […]

library_books

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

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

[…] repeats. 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 on the tran […]

library_books

Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease

2011
Nat Genet
PMCID: 3242065
PMID: 22057235
DOI: 10.1038/ng.998

[…] oform NM_001162422.1, and one of the variants (imm_11_127897147/rs61907765) has predicted regulatory potential and overlaps multiple transcription factor binding sites (UCSC GenomeBrowser ChipSeq and ESPERR tracks, ). Similarly interesting variants are observed in regulatory regions of RUNX3 (imm_1_25165788/rs11249212), and RGS1 (imm_1_190807644/rs1313292, imm_1_190811418/rs2984920) (). Such an ap […]

library_books

Computational Identification of Transcriptional Regulators in Human Endotoxemia

2011
PLoS One
PMCID: 3103499
PMID: 21637747
DOI: 10.1371/journal.pone.0018889

[…] include the structural constraints (FrameWorker , CMA ) or without the structural constraints (CREME , ModuleMiner , Stubb ). Some methods attempt to incorporate a priori knowledge of CRMs (HexDiff , ESPERR , ) to increase the specificity of the prediction while some others are purely computationally discovery of CRMs (CisModule , CSam and D2Z-set ).However, given a methodology to search for CRMs, […]

call_split

A genome wide view of mutation rate co variation using multivariate analyses

2011
Genome Biol
PMCID: 3129677
PMID: 21426544
DOI: 10.1186/gb-2011-12-3-r27
call_split See protocol

[…] tor binding sites, RNA polymerase II binding sites), and computationally predicted ones (most conserved elements produced by phastCons, vista enhancers, predicted CTCF binding sites, and regions with ESPERR (evolutionary and sequence pattern extraction through reduced representations) regulatory potential scores above 0.05), all as annotated in the UCSC Genome Browser [,], to remove the coding and […]


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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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