Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data

14 years 11 months ago

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: A series of genome-scale algorithms and high-performance implementations is described and shown to be useful in the genetic analysis of gene transcription. With them it is possible to address common questions such as: "are the sets of genes coexpressed under one type of conditions the same as those sets co-expressed under another?" A new noise-adaptive graph algorithm, dubbed "paraclique," is introduced and analyzed for use in biological hypotheses testing. A notion of vertex coverage is also devised, based on vertex-disjoint paths within correlation graphs, and used to determine the identity, proportion and number of transcripts connected to individual phenotypes and quantitative trait loci (QTL) regulatory models. A major goal is to identify which, among a set of candidate genes, are the most likely regulators of trait variation. These methods are applied in an effort to identify multiple-QTL regulatory models for large groups of genetically co-expressed genes, ...

Elissa J. Chesler, Michael A. Langston

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