Title
Bioinformatics approaches for the functional interpretation of protein lists : from ontology term enrichment to network analysis
Author
Faculty/Department
Faculty of Sciences. Mathematics and Computer Science
Faculty of Pharmaceutical, Biomedical and Veterinary Sciences . Biomedical Sciences
Publication type
article
Publication
Weinheim ,
Subject
Chemistry
Biology
Computer. Automation
Source (journal)
Proteomics. - Weinheim
Volume/pages
15(2015) :5-6 , p. 981-996
ISSN
1615-9853
ISI
000352510500011
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
The main result of a great deal of the published proteomics studies is a list of identified proteins, which then needs to be interpreted in relation to the research question and existing knowledge. In the early days of proteomics this interpretation was only based on expert insights, acquired by digesting a large amount of relevant literature. With the growing size and complexity of the experimental datasets, many computational techniques, databases and tools have claimed a central role in this task. In this review we discuss commonly and less commonly used methods to functionally interpret experimental proteome lists and compare them with available knowledge. We first address several functional analysis and enrichment techniques based on ontologies and literature. Then we outline how various types of network and pathway information can be used. While the problem of functional interpretation of proteome data is to an extent equivalent to the interpretation of transcriptome or other omics data, this paper addresses some of the specific challenges and solutions of the proteomics field.
E-info
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