Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins

Journal Article · Thu May 04 04:00:00 EDT 2006 · Bioinformatics, 22(13):1641-1647

DOI:https://doi.org/10.1093/bioinformatics/btl134· OSTI ID:889037

Nie, Lei; Wu, Gang; Brockman, Fred J; Zhang, Weiwen

Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 889037
• Report Number(s): PNNL-SA-45108; 15891
• Journal Information: Bioinformatics, 22(13):1641-1647, Journal Name: Bioinformatics, 22(13):1641-1647 Journal Issue: 13 Vol. 22
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ABUNDANCE
ALCOHOL DEHYDROGENASE
DESULFOVIBRIO
DISTRIBUTION
DNA
Environmental Molecular Sciences Laboratory
GENES
HYDROGENASES
Integration
Microarray
Proteomics
PROBABILITY
PROTEINS
STATISTICAL MODELS
SYNTHESIS