PathCards: multi-source consolidation of human biological pathways.
The study of biological pathways is key to a large number of systems analyses. However, many relevant tools consider a limited number of pathway sources, missing out on many genes and gene-to-gene connections. Simply pooling several pathways sources would result in redundancy and the lack of systematic pathway interrelations. To address this, we exercised a combination of hierarchical clustering and nearest neighbor graph representation, with judiciously selected cutoff values, thereby consolidating 3215 human pathways from 12 sources into a set of 1073 SuperPaths. Our unification algorithm finds a balance between reducing redundancy and optimizing the level of pathway-related informativeness for individual genes. We show a substantial enhancement of the SuperPaths' capacity to infer gene-to-gene relationships when compared with individual pathway sources, separately or taken together. Further, we demonstrate that the chosen 12 sources entail nearly exhaustive gene coverage. The computed SuperPaths are presented in a new online database, PathCards, showing each SuperPath, its constituent network of pathways, and its contained genes. This provides researchers with a rich, searchable systems analysis resource. Database URL: http://pathcards.genecards.org/
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel Frida.Belinky@weizmann.ac.il.
Frida
F
Belinky
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Noam
N
Nativ
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Gil
G
Stelzer
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Shahar
S
Zimmerman
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Tsippi
T
Iny Stein
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Marilyn
M
Safran
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
Doron
D
Lancet
D053898:Biosynthetic Pathways / Q000502:physiology*; D030541:Databases, Genetic; D004843:Epistasis, Genetic / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000502:physiology*; D006801:Humans