Portals is a web-based integrative computational platform for
the analysis and mining of genomics data.
Portals Reference: Shinde K, Phatak M, Freudenberg JM, Chen J,
Li Q, Joshi VK, Hu Z, Ghosh K, Meller J, Medvedovic M. Genomics
Portals: Integrative Web-Platform for Mining Genomics Data.
BMC Genomics. Jan 13;11(1):27. 2010.
(Generalized Random Sets) Analysis Reference: Johannes M.
Freudenberg, Siva Sivaganesan, Mukta Phatak, Kaustubh Shinde,
Mario Medvedovic. Generalized random set framework for
functional enrichment analysis using primary genomics datasets.
Bioinformatics. 2011 Jan 1;27(1):70-7.
(True REGulation) Analysis Reference: Jing Chen, Zhen Hu, Mukta Phatak, Johannes M Freudenberg, John Reichard, Siva Sivaganesan and Mario Medvedovic. Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PLoS Comp Biol, In Press. Preprint.
Portals integrates the primary
genomics data, functional
knowledge base and analytical
tools within a single framework.
genomics data stored in the back-end
databases consists of >82,000 genome-scale vectors of
measurements (more than 1.8 billion data points) produced by
various experimental assays (expression microarrays, CGH
microarrays, ChIP-chip and ChIP-seq) or computationally
constructed scores (eg transcription factor binding scores and
microRNA target scores). For example, the complete set of human, mouse and rat GEO DataSets.
knowledge base is encoded in >20,000
functionally coherent gene lists derived from numerous sources.
Additionally, one can construct new gene lists by searching gene RIF's and querying the database of all known
datasets are organized thematically into
Different portals can contain datasets related to different diseases (eg Breast Cancer and Prostate Cancer),
specific types of
genomics data (eg Epigenomics and Transcription Factors), or
different biological processes (eg Development). The
same dataset can be assigned to different portals.
analysis starts by constructing
a list of genes by either using the predefined lists of pasting
a gene list of interest, querying
one of the databases with genome-scale data and producing analysis summaries.