Proteomics and regulomics: The yin and yang of functional genomics

I. Introduction 25 A. A Brief History of Computer Application in Protein Sequence Analysis 25 B. Requirements of Current Proteomics Research 26 C. Mass Spectrometry Applications in Proteomics 26 II. Basics of Transcriptional Regulation 26 A. How Is Transcriptional Coregulation Achieved? 26 B. Promoters and Transcription Complexes 27 III. Synergisms Between Gene Regulation and Mass Spectrometry‐Based Proteomics 29 A. Expression Array‐Based Gene Selection 29 B. Protein Data‐Driven Coregulation Analysis 30 C. A Practical Application Example 30 IV. Conclusions 30 Acknowledgments 32 References 32 Protein analysis is a field of research with a long history. Recently, the development of a series of proteomics approaches, i.e., simultaneous analyses on all or a majority of proteins in a cell at a given state, has reinvigorated protein analyses. Mass Spectrometry also developed into one of the most versatile technical tools supporting or even enabling many proteomics‐oriented approaches, providing a convenient link between experimental protein analysis and the corresponding amino acid sequences. Thus direct links to the genomic sequence can be established, which opens the door for a synergistic combination with genomic sequence analysis. This review focuses especially on aspects of genome‐wide transcription control, regulomics in analogy to all the other ‐omics, and how a combination of MS‐based proteomics with in silico regulomics analyses can produce synergistic effects in the quest to understand how cells function. This is illustrated on a real life example showing how the MS‐analysis and in silico promoter analysis can extend the list of candidates for signaling pathways, here the MAP kinase pathway.