HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases

TY - JOUR

T1 - HOODS

T2 - finding context-specific neighborhoods of proteins, chemicals and diseases

AU - Palleja, Albert

AU - Jensen, Lars J

PY - 2015

Y1 - 2015

N2 - Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.

AB - Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded.

U2 - 10.7717/peerj.1057

DO - 10.7717/peerj.1057

M3 - Journal article

C2 - 26157625

SN - 2167-8359

VL - 3

SP - 1

EP - 10

JO - PeerJ

JF - PeerJ

M1 - e1057

ER -