Step1: Select query dataset Step2: Select reference dataset Step3: Calculating GRS Step4: Results

We have developed a new statistical method called "Generalized Random Set" (GRS) to perform the concordance analysis between two genome-scale differential expression profiles (Query and Reference profiles). The method produces the statistical significance of the overall cocordance without requiring specification of significance cutoffs as well as the list of genes contributing to the overall concordance. The Query and Reference differential expression profiles can be constructed by the real-time analysis of the datasets in Genomics Portals or can be separately uploaded in the form of the gene list with p-values of differential expression. For details, see paper below:

Freudenberg JM, Sivaganesan S, Phatak M, Shinde K, Medvedovic M. Generalized Random Set Framework for Functional Enrichment Analysis Using Primary Genomics Datasets. Bioinfromatics 27(1):70-7. 2011.(Pre-print)(R package)(Server).


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Select a genomics dataset to query and analyze

Genomics datasets are organized thematically into different portals. Different portals can contain datasets related to different diseases (e.g., Breast Cancer and Prostate Cancer), specific types of genomics data (e.g., Epigenomics and Transcription Factors), or different biological processes (e.g., Development). The same dataset can be assigned to different portals.

Step1: Select query dataset Step2: Select reference dataset Step3: Calculating GRS Step4: Results

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Organism Sample type
Data type Portal
Keyword

Portal Description
Breast Cancer
 Genome-scale datasets related to breast cancer
AHR
 Gene expression and ChIP-chip datasets related to AHR-related gene expression regulation
BCERC
 Gene expression microarray datasets generated by the BCERC project (mostly private)
Prostate Cancer
 Genome-scale datasets related to prostate cancer
Multicancer
 Datasets assessing multiple types of cancer
Reference
 Uncategorized useful gene expression datasets
Toxicogenomics
 A collection of toxicogenomics datasets
Development
 Genomics datasets related to stem cells and development
CTSA
 Clinical and Translational Science Awards (CTSA) program
Transcription Factors
 Genomics datasets pertaining to transcription factor regulatory targets
Epigenomics
 Datasets assessing different epigenomics events on the whole-genome scale
CGH
 Comparative Genomics Hybridization datasets
GDS
 Gene Expression Omnibus Datasets (GDS)
Predicted TF Binding Sites
 Computationally predicted binding sites for human, mouse and rat promoters
Encode ChIP-Seq
 Production phase ENCODE data from Genome Browser
BPA Genomics
 Genomics datasets assessing health effects of Bisphenol A
JRA Genomics
 Juvenile Rheumatoid Arthritis (JRA)
MCF-7 Toxicogenomics
 Toxicogenomics data for MCF-7 cell line