Pattern search in BioPAX models

被引：18

作者：

Babur, Ozgun ^{[1
]}

Aksoy, Bulent Arman ^{[1
,2
]}

Rodchenkov, Igor ^{[3
]}

Sumer, Selcuk Onur ^{[1
]}

Sander, Chris ^{[1
]}

Demir, Emek ^{[1
]}

机构：

[1] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10065 USA

[2] Triinst Training Program Computat Biol & Med, New York, NY 10065 USA

[3] Univ Toronto, Banting & Best Dept Med Res, Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 3E1, Canada

来源：

BIOINFORMATICS | 2014年 / 30卷 / 01期

关键词：

BIOLOGICAL NETWORKS; PATHWAY RESOURCE;

D O I：

10.1093/bioinformatics/btt539

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the inherent complexity of a BioPAX model, searching for a specific type of subnetwork can be non-trivial and difficult. Results: We developed an open source and extensible framework for defining and searching graph patterns in BioPAX models. We demonstrate its use with a sample pattern that captures directed signaling relations between proteins. We provide search results for the pattern obtained from the Pathway Commons database and compare these results with the current data in signaling databases SPIKE and SignaLink. Results show that a pattern search in public pathway data can identify a substantial amount of signaling relations that do not exist in signaling databases.

引用

页码：139 / 140

页数：2

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