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Interprets omics lists in the context of metabolic pathway and regulatory networks using a statistical model for flow within the networks. Pathway Flow allows to visualized statistical results for all response groups in plots. The statistical tests are based on the Erlang distribution model under the assumption of independent and identically Exponential-distributed random walk flows through pathways. As a proof of concept, this method was applied to an Escherichia coli transcriptomics dataset where it was confirmed common knowledge of the E.coli transcriptional response to Lipid A deprivation. The main response is related to osmotic stress, and it detects novel responses that are supported by the literature. This method was also applied to an Arabidopsis thaliana expression dataset from an abscisic acid study. In both cases, conventional pathway enrichment tests detected nothing, while this approach discovered biological processes beyond the original studies.

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Pathway Flow classification

Pathway Flow specifications

Software type:
Package
Restrictions to use:
None
Computer skills:
Basic
Interface:
Web user interface
Input data:
A list of BioCyc IDs, the pathway network, the response groups to consider.
Stability:
Stable

Pathway Flow support

Maintainer

Credits

Publications

Institution(s)

Bioinformatics and Computational Biology, Electrical and Computer Engineering Department, Iowa State University, Ames, IA, USA

Funding source(s)

This work was supported by the National Science Foundation programs DBI (grant number 0604755) and EEC (grant number 0813570).

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