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Genomics Portals: integrative web-platform for mining genomics data

Kaustubh Shinde1, Mukta Phatak1, Freudenberg M Johannes1, Jing Chen1, Qian Li1, Joshi K Vineet1, Zhen Hu1, Krishnendu Ghosh1, Jaroslaw Meller2 and Mario Medvedovic1*

Author affiliations

1 Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av. ML 56, Cincinnati OH 45267-0056, USA

2 Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av. ML 56, Cincinnati OH 45267-0056, USA

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Citation and License

BMC Genomics 2010, 11:27  doi:10.1186/1471-2164-11-27

Published: 13 January 2010

Abstract

Background

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems.

Results

Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis.

Conclusion

The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org webcite.