Identifier mapping performance for integrating transcriptomics and proteomics experimental results

被引:67
作者
Day, Roger S. [1 ,2 ]
McDade, Kevin K. [1 ]
Chandran, Uma R. [1 ]
Lisovich, Alex [1 ]
Conrads, Thomas P. [3 ]
Hood, Brian L. [3 ]
Kolli, V. S. Kumar [4 ]
Kirchner, David [4 ]
Litzi, Traci [5 ]
Maxwell, G. Larry [3 ,5 ]
机构
[1] Univ Pittsburgh, Sch Med, Dept Biomed Informat, Pittsburgh, PA 15261 USA
[2] Univ Pittsburgh, Dept Biostat, Pittsburgh, PA 15260 USA
[3] Inova Hlth Syst, Womens Hlth Integrated Res Ctr, Falls Church, VA 22042 USA
[4] Windber Res Inst, Windber, PA 15963 USA
[5] Walter Reed Army Med Ctr, Div Gynecol Oncol, Washington, DC 20307 USA
关键词
MESSENGER-RNA EXPRESSION; COMPARING PROTEIN ABUNDANCE; ANNOTATION DATABASE; GENE; RESOURCES; CANCER; TOOL;
D O I
10.1186/1471-2105-12-213
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: Studies integrating transcriptomic data with proteomic data can illuminate the proteome more clearly than either separately. Integromic studies can deepen understanding of the dynamic complex regulatory relationship between the transcriptome and the proteome. Integrating these data dictates a reliable mapping between the identifier nomenclature resultant from the two high-throughput platforms. However, this kind of analysis is well known to be hampered by lack of standardization of identifier nomenclature among proteins, genes, and microarray probe sets. Therefore data integration may also play a role in critiquing the fallible gene identifications that both platforms emit. Results: We compared three freely available internet-based identifier mapping resources for mapping UniProt accessions (ACCs) to Affymetrix probesets identifications (IDs): DAVID, EnVision, and NetAffx. Liquid chromatography-tandem mass spectrometry analyses of 91 endometrial cancer and 7 noncancer samples generated 11,879 distinct ACCs. For each ACC, we compared the retrieval sets of probeset IDs from each mapping resource. We confirmed a high level of discrepancy among the mapping resources. On the same samples, mRNA expression was available. Therefore, to evaluate the quality of each ACC-to-probeset match, we calculated proteome-transcriptome correlations, and compared the resources presuming that better mapping of identifiers should generate a higher proportion of mapped pairs with strong inter-platform correlations. A mixture model for the correlations fitted well and supported regression analysis, providing a window into the performance of the mapping resources. The resources have added and dropped matches over two years, but their overall performance has not changed. Conclusions: The methods presented here serve to achieve concrete context-specific insight, to support well-informed decisions in choosing an ID mapping strategy for "omic" data merging.
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页数:13
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