e-journal

Biological process annotation of proteins across the plant kingdom

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tAccurate annotation of protein function is key to understanding life at the molecular level, but auto-mated annotation of functions is challenging. We here demonstrate the combination of a method forprotein function annotation that uses network information to predict the biological processes a proteinis involved in, with a sequence-based prediction method. The combined function prediction is based onco-expression networks and combines the network-based prediction method BMRF with the sequence-based prediction method Argot2. The combination shows significantly improved performance comparedto each of the methods separately, as well as compared to Blast2GO. The approach was applied to redictbiological processes for the proteomes of rice, barrel clover, poplar, soybean and tomato. The novel func-tion predictions are available at www.ab.wur.nl/bmrf. Analysis of the relationships between sequencesimilarity and predicted function similarity identifies numerous cases of divergence of biological pro-cesses in which proteins are involved, in spite of sequence similarity. This indicates that the integrationof network-based and sequence-based function prediction is helpful towards the analysis of evolutionaryrelationships. Examples of potential divergence are identified for various biological processes, notably forprocesses related to cell development, regulation, and response to chemical stimulus. Such divergencein biological process annotation for proteins with similar sequences should be taken into account whenanalyzing plant gene and genome evolution.DATA: All gene functions predictions are available online (http://www.ab.wur.nl/bmrf/). The onlineresource can be queried for predictions of proteins or for Gene Ontology terms of interest, and the resultscan be downloaded in bulk. Queries can be based on protein identifiers, biological process Gene Ontologyidentifiers, or text descriptors of biological procesess.

Keywords:Gene function predictionGene function divergencea

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Informasi Detail

Judul Seri

Current Plant Biology

No. Panggil

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Penerbit

: Elsevier., 2014

Deskripsi Fisik

Current Plant Biology 1 (2014) 73–82

Bahasa

English

ISBN/ISSN

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Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

KIMIA

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

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