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Protocols

GERP specifications

Information


Unique identifier OMICS_00174
Name GERP
Alternative names Genomic Evolutionary Rate Profiling, GERP++, GERP2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://mendel.stanford.edu/SidowLab/downloads/gerp/gerp++.tar.gz
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Arend Sidow

Publications for Genomic Evolutionary Rate Profiling

GERP citations

 (276)
call_split

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] e SeattleSeq annotation 147 (http://snp.gs.washington.edu/SeattleSeqAnnotation147/index.jsp). Pathogenicity was modeled using PolyPhen, CADD and FATHMM methods, and conservation was assessed based on GERP scores–. Transcription factor binding sites were analyzed using TRANSFAC 7.0. […]

library_books

Association of IL17RC and COL6A1 genetic polymorphisms with susceptibility to ossification of the thoracic posterior longitudinal ligament in Chinese patients

2018
PMCID: 5952594
PMID: 29764467
DOI: 10.1186/s13018-018-0817-y

[…] inese Han patients, four different algorithms [including SIFT(http://sift.jcvi.org/) [], PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) [], MutationTaster (http://www.mutationtaster.org/) [], and GERP++ (http://mendel.stanford.edu/SidowLab/downloads/gerp/) []] were used to predict deleterious variations at different SNP loci. We found that rs201153092 was predicted to be deleterious by four al […]

library_books

ICAM 1 related long non coding RNA: promoter analysis and expression in human retinal endothelial cells

2018
BMC Res Notes
PMCID: 5944171
PMID: 29743093
DOI: 10.1186/s13104-018-3384-8

[…] TSS) and, by extrapolation, the promoter region, differ between human and mouse genes, we conducted separate analyses to identify regions of constrained DNA sequence across multiple eutherians.Fig. 1 Genomic evolutionary rate profiling (GERP) was performed using the Ensembl genome browser (Ensembl release 89—May 2017) [] to identify evolutionarily constrained elements across annotated eutherian se […]

library_books

Cancer driver mutation prediction through Bayesian integration of multi omic data

2018
PLoS One
PMCID: 5940219
PMID: 29738578
DOI: 10.1371/journal.pone.0196939

[…] functionality []. Importantly, these methods do not integrate known evolutionary and structural properties of mutations characterized by functional impact scores (FISs) generated by programs such as GERP [] and SIFT [], which have been shown to be very informative at identifying functional variants. Increasingly more projects such as TCGA and ICGC now generate multi-omic data from the same tumor […]

library_books

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

2018
Nat Commun
PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] .75, where Ptfbs is the probability that the TFBS is bound by a TF for any given ENCODE cell line. Ptfbs for all TFBSs were obtained from the ENSEMBL regulatory build. Conserved elements generated by GERP from the alignment of hg19 to 36 mammals were downloaded from the UCSC genome browser.The expected fraction of hotspot (or non-hotspot) mutations in the functional region type (p2) is the fractio […]

call_split

Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early onset/familial prostate cancer

2018
PLoS Genet
PMCID: 5919682
PMID: 29659569
DOI: 10.1371/journal.pgen.1007355
call_split See protocol

[…] sistant, which includes the functional predictors SIFT, PolyPhen2, LRT, MutationTaster, PROVEAN, FATHMM, CADD, MutationAssessor, MetaLR, MetaSVM and VEST3, and the conservation analysis tools PhyloP, GERP++, PhastCons and SiPhy, as previously described []. […]

Citations

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GERP institution(s)
Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Biomedical Informatics Program, Stanford University, Stanford, CA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
GERP funding source(s)
Supported in part by an Encode subcontract (PI, Richard Myers), NIH/NHGRI, US National Library of Medicine (K22 LM008261 and T15 LM007033), andin part by NSF grant #0347952.

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