title: INsPeCT: INtegrative Platform for Cancer Transcriptomics.
abstract: The emergence of transcriptomics, fuelled by high-throughput sequencing technologies, has changed the nature of cancer research and resulted in a massive accumulation of data. Computational analysis, integration, and data visualization are now major bottlenecks in cancer biology and translational research. Although many tools have been brought to bear on these problems, their use remains unnecessarily restricted to computational biologists, as many tools require scripting skills, data infrastructure, and powerful computational facilities. New user-friendly, integrative, and automated analytical approaches are required to make computational methods more generally useful to the research community. Here we present INsPeCT (INtegrative Platform for Cancer Transcriptomics), which allows users with basic computer skills to perform comprehensive in-silico analyses of microarray, ChIP-seq, and RNA-seq data. INsPeCT supports the selection of interesting genes for advanced functional analysis. Included in its automated workflows are (i) a novel analytical framework, RMaNI (regulatory module network inference), which supports the inference of cancer subtype-specific transcriptional module networks and the analysis of modules; and (ii) WGCNA (weighted gene co-expression network analysis), which infers modules of highly correlated genes across microarray samples, associated with sample traits, eg survival time. INsPeCT is available free of cost from Bioinformatics Resource Australia-EMBL and can be accessed at http://inspect.braembl.org.au.
authors.affiliation: The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Brisbane, Queensland, Australia. ; Australian Research Council Centre of Excellence in Bioinformatics, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: Piyush B
authors.initials: PB
authors.lastname: Madhamshettiwar
authors.affiliation: The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Brisbane, Queensland, Australia. ; Australian Research Council Centre of Excellence in Bioinformatics, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: Stefan R
authors.initials: SR
authors.lastname: Maetschke
authors.affiliation: The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Brisbane, Queensland, Australia. ; Australian Research Council Centre of Excellence in Bioinformatics, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Davis
authors.affiliation: CSIRO Animal, Food and Health Sciences, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: Antonio
authors.initials: A
authors.lastname: Reverter
authors.affiliation: The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Brisbane, Queensland, Australia. ; Australian Research Council Centre of Excellence in Bioinformatics, St. Lucia, Brisbane, Queensland, Australia.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Ragan
keywords: ChIP-seq; RNA-seq; cancer; microarray; systems biology; transcriptional module networks; transcriptomics