Pathway databases gene ontology

Modular analysis integrates the primary microarray analysis results and their functional annotations based on precompiled databases of pathways derived from large-scale literature analysis or computer-assisted annotation, such as Gene Ontology [39], KEGG [40], Biocarta (http //www.biocarta.com/), and GenMAPP [41]. 

A new subdiscipline of bioinformatics, comparative proteogenomics, is based on the possibility of mapping sets of sequenced peptides onto the positions in the genome that code for them, i.e., integration of data from MS-based proteomics with DNA sequence data sets. Databases and software to determine if the available data are over- or underrepresented include Gene Ontology, protein domains, and pathway databases. Another application (of many) is the combination of MS-based proteomic data with information from transcriptomics to study the processes and regulation of cellular functions. 

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