Transcriptome and Proteome Analysis: A Perspective on Correlation

Database, MOPED,21 the Human Protein Reference Database, HPRD 22,23 and the recently described Human Proteome Map 24 and proteomics Db.The last two mentioned studies together account for approximately 84% of the total annotated protein-coding genes in humans.Together, these two studies identified >18,000 proteins encoded by both known genes and uncharacterized Open Reading Frames.Over 20,000 protein isoforms expressions were also characterized. 25,26merous normal tissues, body fluids and cell lines were used in these two studies.These recently described protein expression databases greatly expand our ability to establish correlative evidence for mRNA and protein expression for most of the human proteome.Based on mRNA expression using a high throughput transcriptome analysis, interpretations are often made about the functional relevance, pathways, interacting proteins and the possibility of drug therapy use.Protein expression is often inferred, but frequently a correlation of mRNA versus protein is missing in studies.The complex regulation of protein expression at the level of noncoding RNAs, DNA methylation, epigenetic changes, gene amplifications, copy number variations, mutations, post translational modifications such as acetylation, amidation, myristylation, phosphorylation, sumoylation, Ubiquitination etc., stability and degradation as well as the interacting proteins adds to the complexity of transcriptome-based interpretations. 27,