psiDR: The Pseudogene Decoration Resource
www.gencodegenes.org is mirroring the data from the The Pseudogene Decoration Resource psiDR.
This resource is developed and maintained by Yale Gerstein Group. It contains a comprehensive knowledgebase of identified pseudogenes, various publication data sets and the pseudogene decoration resource file (psiDR).
The pseudogene decoration resource file is collected and organized in a consistent manner the large variety of genomic information related to each pseudogene, such as transcriptional activity, chromatin features, functional genomics and evolutionary constraint. Illumina Human BodyMap 2.0 project data, functional genomics data for ENCODE tier 1 and tier 2 cell lines (GM12878, K562, H1-hesc, HeLa-S3 and HepG2) and experimental data were used to create (psiDR). Various models and filters were applied to the corresponding data to predict biological features of pseudogenes. At the end, a list of quantifiers was assigned to each pseudogene according to the model output, such as whether a pseudogene is transcribed, has an active chromatin state or associates with active promoter regions. Tissue/cell line specific information is recorded wherever applicable.
Contact
Principle Investigator: Dr. Mark Gerstein
Resources
- New! Pseudogene Resource psiDR
- Current PseudoPipe Human Pseudogene Set
- Gencode v7 Annotation File
- 2-way Consensus Annotation File
- Gencode v7 Pseudogenes Annotation File
- Gencode v7 Pseudogenes Levels 1&2
- Gencode v7 Pseudogenes Levels 3
- Gencode v7 Polymorphic Pseudogenes Levels 1,2&3
- Gencode v7 Pseudogenes Delta 2-way Consensus