| Network-based inference from complex proteomic mixtures using SNIPE. | |
| | |
MedLine Citation:
|
PMID: 23060611 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
|
MOTIVATION: Proteomics presents the opportunity to provide novel insights about the global biochemical state of a tissue. However, a significant problem with current methods is that shotgun proteomics has limited success at detecting many low abundance proteins such as transcription factors from complex mixtures of cells and tissues. The ability to assay for these proteins in the context of the entire proteome would be useful in many areas of experimental biology. RESULTS: We utilized network-based inference in an approach named SNIPE (Software for Network Inference of Proteomics Experiments) that selectively highlights proteins that are more likely to be active but are otherwise undetectable in a shotgun proteomic sample. SNIPE integrates spectral counts from paired case-control samples over a network neighborhood and assesses the statistical likelihood of enrichment by a permutation test. As an initial application SNIPE was able to select several proteins required for early murine tooth development. Multiple lines of additional experimental evidence confirm that SNIPE can uncover previously unreported transcription factors in this system.We conclude that SNIPE can enhance the utility of shotgun proteomics data to facilitate the study of poorly detected proteins in complex mixtures.Availability and Implementation: An implementation for the R statistical computing environment named snipeR has been made freely available at http://genetics.bwh.harvard.edu/snipe/. CONTACT: ssunyaev@rics.bwh.harvard.edu. |
| | |
Authors:
|
David P Nusinow; Adam Kiezun; Daniel J O'Connell; Joel M Chick; Yingzi Yue; Richard L Maas; Steven P Gygi; Shamil R Sunyaev |
Publication Detail:
|
Type: JOURNAL ARTICLE Date: 2012-10-11 |
Journal Detail:
|
Title: Bioinformatics (Oxford, England) Volume: - ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2012 Oct |
Date Detail:
|
Created Date: 2012-10-12 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: - |
Other Details:
|
Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
|
Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, 77 Ave. Louis Pasteur, Boston MA 02115, USA. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: CD-HIT: accelerated for clustering the next generation sequencing data.
Next Document: Towards the development of standardized methods for comparison, ranking and evaluation of structure ...