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GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus

Djordje Djordjevic, Yun Xin Chen, Shu Lun Shannon Kwan, Raymond W. K. Ling, Gordon Qian, Chelsea Y. Y. Woo, Samuel J. Ellis, Joshua W. K. Ho
doi: https://doi.org/10.1101/150896
Djordje Djordjevic
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
2 St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
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Yun Xin Chen
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Shu Lun Shannon Kwan
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Raymond W. K. Ling
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Gordon Qian
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Chelsea Y. Y. Woo
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Samuel J. Ellis
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
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Joshua W. K. Ho
1 Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
2 St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
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Abstract

Summary There exists over 1.6 million publicly available gene expression samples across 79,000 data series in NCBI’s Gene Expression Omnibus database. Due to the lack of the use of standardised ontology terms to annotate the experimental type and sample type, this database remains difficult to harness computationally without significant manual intervention. In this work, we present an interactive R/Shiny tool called GEOracle that utilises text mining and machine learning techniques to automatically identify perturbation experiments, group treatment and control samples and perform differential expression. We present applications of GEOracle to discover conserved signalling pathway target genes and identify an organ specific gene regulatory network.

Availability GEOracle is available at http://georacle.victorchang.edu.au/

Contact jho{at}victorchang.edu.au

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 16, 2017.
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GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus
Djordje Djordjevic, Yun Xin Chen, Shu Lun Shannon Kwan, Raymond W. K. Ling, Gordon Qian, Chelsea Y. Y. Woo, Samuel J. Ellis, Joshua W. K. Ho
bioRxiv 150896; doi: https://doi.org/10.1101/150896
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GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus
Djordje Djordjevic, Yun Xin Chen, Shu Lun Shannon Kwan, Raymond W. K. Ling, Gordon Qian, Chelsea Y. Y. Woo, Samuel J. Ellis, Joshua W. K. Ho
bioRxiv 150896; doi: https://doi.org/10.1101/150896

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