Proteomics and regulomics: the yin and yang of functional genomics.
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.
Werner
Thomas
T
Genomatix Software GmbH, Landsbergerstr 6, D-80339 München, Germany. Werner@genomatix.de
D004734:Energy Metabolism / Q000502:physiology*; D005786:Gene Expression Regulation / Q000502:physiology*; D023281:Genomics / Q000379:methods; D013058:Mass Spectrometry / Q000379:methods*; D011506:Proteins / Q000032:analysis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000032:analysis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
D011506:Proteins; D020543:Proteome