Genomics Portals is a web-based integrative computational platform for the analysis and mining of genomics data.

Genomics 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.

GRS (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.

TREG (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.

Genomics Portals integrates the primary genomics data, functional knowledge base and analytical tools within a single framework.

Primary 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.

Functional 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 protein-protein interaction.

Genomics datasets are organized thematically into different portals. 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.

A typical 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.

One can also start by searching for dataset of interest, and then constructing the query gene lists. In this case, gene lists can also be constructed by browsing pre-computed clustering results.

The basic data manipulations and analysis options consist of sub-setting the data, selecting grouping variables for the samples in the datasets, identifying differentially expressed genes, cluster analysis, assessing enrichment of differentially expressed genes within the query list, etc. The results of such analyses are provided as static annotated heatmaps, or can be browsed using our FTreeView browser. Analyses of results can also be incorporated within the images of KEGG pathways. One can also retrieve data in the form of a spreadsheet or R expressionSet.

Click on the "Gene List" link on the side-bar to start using Genomics Portals by first constructing a gene list.

Click on the "Experiments"  link to start using Genomics Portals by browsing/searching genomics datasets.

For the complete documentation and to contact us follow the "Help" link. If you would like to have your experimental data uploaded to Genomics Portals please contact us.