Description

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.

Display Conventions and Configuration

Most ENCODE tracks contain multiple subtracks corresponding to multiple experimental conditions. If a track contains a large number of subtracks, only some subtracks will be displayed by default. The user can select which subtracks are displayed via the display controls on the track details pages.

Credits

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.

References

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.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.