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Protocols

psiDR specifications

Information


Unique identifier OMICS_20760
Name psiDR
Alternative name Pseudogene Decoration resource
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Mark Gerstein

Publication for Pseudogene Decoration resource

psiDR citations

 (4)
library_books

Global Intersection of Long Non Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome

2016
Front Genet
PMCID: 4805607
PMID: 27047535
DOI: 10.3389/fgene.2016.00026

[…] rlaps, we realized that a genome-wide, positionally non-redundant overlap of the several currently available public pseudogene collections had not yet been performed. The GENCODE pseudogene resource (psiDR) is itself an integration of pseudogene annotation data from Pseudopipe, retroFinder, HaVANA, ENCODE, and the 1000 Genomes Project (Pei et al., ). This resource provides a high confidence but fa […]

library_books

Dissecting the genetics of the human transcriptome identifies novel trait related trans eQTLs and corroborates the regulatory relevance of non protein coding loci†

2015
Hum Mol Genet
PMCID: 4512630
PMID: 26019233
DOI: 10.1093/hmg/ddv194

[…] ue < 0.05. A detailed listing and description of all included annotation sets is provided in Supplementary Material, Table S12. To characterize pseudogenes in detail, we used information described in psiDR version 1.0.0 (). […]

library_books

Pseudogenes transcribed in breast invasive carcinoma show subtype specific expression and ceRNA potential

2015
BMC Genomics
PMCID: 4344757
PMID: 25765044
DOI: 10.1186/s12864-015-1227-8

[…] We computed Pearson correlation coefficients on log-transformed gene and pseudogene expression levels using the parent gene annotations from the ENCODE pseudogene decoration resource (psiDR v. 0). To avoid detecting spurious correlations due to predominantly low expression, we required at least 20 samples in which gene and pseudogene are present at 1 […]

call_split

Selection on a Variant Associated with Improved Viral Clearance Drives Local, Adaptive Pseudogenization of Interferon Lambda 4 (IFNL4)

2014
PLoS Genet
PMCID: 4199494
PMID: 25329461
DOI: 10.1371/journal.pgen.1004681
call_split See protocol

[…] 1000 Genomes, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/; GENCODE, http://pseudogene.org/psidr/; HapMap, http://hapmap.ncbi.nlm.nih.gov; XP-EHH and iHS executables, http://hgdp.uchicago.edu/Software/; VCFtools, http://vcftools.sourceforge.net; ABCtoolbox: http://www.cmpg.iee.unibe.ch/cont […]

Citations

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psiDR institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Wellcome Trust Sanger Institute, Welcome Trust Campus, Hinxton, Cambridge, UK; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Center for Biomolecular Science and Engineering University of California, Santa Cruz, CA, USA; Centre for Genomic Regulation (CRG) and UPF, Barcelona, Catalonia, Spain; Department of Computer Science, Yale University, New Haven, CT, USA
psiDR funding source(s)
Supported by National Human Genome Research Institute (NHGRI)/National Institutes of Health (NIH) grants to the GENCODE (U54 HG004555) subgroup of the ENCODE project; the Swiss National Science Foundation, and the Wellcome Trust (WT077198/Z/05/Z).

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