NDLI: Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views

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Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views

Content Provider	Royal Society of Chemistry (RSC)
Author	Nikoloski, Zoran Mutwil, Marek Klie, Sebastian Persson, Staffan
Copyright Year	2012
Abstract	Inference of accurate gene annotations requires integration of existing biological knowledge, structured in a form of ontology, with data from transcriptomics high-throughput technologies. This undertaking requires developing algorithms that integrate genome-scale data, even for model organisms. Gene relevance networks have emerged as a powerful representative of the structure of the data. Such networks can be used for intra-species transfer of gene annotations following the guilt-by-association principle. An analogous principle can serve as a basis for inter-species transfer of gene annotations by comparing well-defined subnetworks. In this review, we compare and contrast the concepts of relevance and proximity networks and briefly review the concept of semantic similarity. We then provide a detailed account of quantitative guilt-by-association inference in the setting of genome-scale relevance networks. Moreover, we systematically survey the existing network-based approaches for automated gene function annotation and categorize them under one umbrella in terms of employed methodology. Furthermore, we discuss suitable data selection strategies required for deriving meaningful and unbiased genome-scale networks from large transcriptomics compendia. Lastly, by simulating gene function prediction with a classical network-based algorithm, we show how the number of genes of unknown function influences prediction within a species and pinpoint the need and the requirements for inter-species knowledge transfer.
Starting Page	2233
Ending Page	2241
Page Count	9
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	8
Issue Number	9
Journal	Molecular BioSystems
DOI	10.1039/c2mb25089f
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Ontology Transcriptome Semantic similarity Algorithm DNA sequencing
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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