NetGrep: Fast network schema searches in interactomes

Eric Banks; Elena Nabieva; Ryan Peterson; Mona Singh

doi:10.1186/gb-2008-9-9-r138

NetGrep: Fast network schema searches in interactomes

Eric Banks, Elena Nabieva, Ryan Peterson, Mona Singh

Research output: Contribution to journal › Article › peer-review

28 Scopus citations

Abstract

NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.

Original language	English (US)
Article number	R138
Journal	Genome biology
Volume	9
Issue number	9
DOIs	https://doi.org/10.1186/gb-2008-9-9-r138
State	Published - Sep 18 2008

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2008-9-9-r138

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title = "NetGrep: Fast network schema searches in interactomes",

abstract = "NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.",

author = "Eric Banks and Elena Nabieva and Ryan Peterson and Mona Singh",

note = "Funding Information: MS thanks the NSF for grants MCB-0093399 and CCF-0542187, and the NIH for grants CA041086 and GM076275. EB is supported by the Quantitative and Computational Biology Program NIH grant T32 HG003284. This research has also been supported by the NIH Center of Excellence grant P50 GM071508. The authors thank the members of the Singh group for many helpful discussions.",

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doi = "10.1186/gb-2008-9-9-r138",

language = "English (US)",

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T2 - Fast network schema searches in interactomes

AU - Banks, Eric

AU - Nabieva, Elena

AU - Peterson, Ryan

AU - Singh, Mona

N1 - Funding Information: MS thanks the NSF for grants MCB-0093399 and CCF-0542187, and the NIH for grants CA041086 and GM076275. EB is supported by the Quantitative and Computational Biology Program NIH grant T32 HG003284. This research has also been supported by the NIH Center of Excellence grant P50 GM071508. The authors thank the members of the Singh group for many helpful discussions.

PY - 2008/9/18

Y1 - 2008/9/18

N2 - NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.

AB - NetGrep (http://genomics.princeton.edu/singhlab/netgrep/) is a system for searching protein interaction networks for matches to user-supplied 'network schemas'. Each schema consists of descriptions of proteins (for example, their molecular functions or putative domains) along with the desired topology and types of interactions among them. Schemas can thus describe domain-domain interactions, signaling and regulatory pathways, or more complex network patterns. NetGrep provides an advanced graphical interface for specifying schemas and fast algorithms for extracting their matches.

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NetGrep: Fast network schema searches in interactomes

Abstract

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