ENC ProtGeno Tracks
ENCODE Proteogenomics tracks   (All Expression tracks)

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UNC/BSU ProtGenc  Proteogenomics Hg19 and GENCODE Mapping from ENCODE/Univ. North Carolina/Boise State Univ.  
UNC/BSU ProtGeno  Proteogenomics Hg19 Mapping from ENCODE/Univ. North Carolina/Boise State Univ.  



This super track shows proteogenomic mappings of peptides from ENCODE cell types mapped to the human genome which represent fragments of translated proteins from the respective cell lines. Proteogenomic methods differ from conventional mass-spec proteomic methods. Conventional mass-spec proteomic methods identify peptides by comparing them to peptides produced from known proteins. In contrast, proteogenomic methods compare the peptides to all peptides that might theoretically be produced by the six possible translation frames of the genome (three on the forward strand plus three on the reverse strand) to identify the genomic region from which the peptides were produced. Study of proteogenomic data offers insights on numerous regulatory mechanisms, including: translation, pre-mRNA splicing and transcript diversity, nonsense-mediated decay, and transcription of novel protein-coding genes. Two tracks UNC/BSU ProtGenc and UNC/BSU ProtGeno that differ in database search scheme are presented here. UNC/BSU ProtGenc are the combined results from searching against Hg19 and GENCODE of peptides of both regular and post-translational modifications. UNC/BSU ProtGeno only contains the database search results of Hg19 of regular peptides.

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These data were generated and analyzed as part of the ENCODE project, a genome-wide consortium project with the aim of cataloging all functional elements in the human genome. This effort includes collecting a variety of data across related experimental conditions to facilitate integrative analysis. Consequently, additional ENCODE tracks may contain data that is relevant to the data in these tracks.


Giddings MC, Shah AA, Gesteland R, Moore B. Genome-based peptide fingerprint scanning. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):20-5.

Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77.

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