Data integration is a hot topic in bioinformatics, but the term means different things to different people. What do we think it means? Talk given at CSIRO Bioinformatics & Biostatistics group meeting, November 21 2012.

1. Data Integration: what I haven’t yet achieved
Neil Saunders
MATHEMATICS, INFORMATICS AND STATISTICS
www.csiro.au

2. My main project
Ludwig colorectal cancer study
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3. Multiple “omics” platforms
exon expression
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methylation
copy number

4. We want to “integrate” these data
but what does that mean?
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5. Integration can mean “portals”
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6. Integration can mean “visualization”
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7. Integration can mean “correlation”
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8. What do we think integration means?
A
+
B
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C
More information when combined than when separate
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9. What’s already “out there”? PubMed
PubMed Search: "data integration"
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articles / 100 000
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2008
2010

10. What’s already “out there”? CiteULike
http://www.citeulike.org/user/neils/tag/integration
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11. Buzz-word compliant
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12. Quote from integIRTy paper
These methods can be roughly grouped into four categories:
stepwise, regression-based, correlation-based and
latent variable models
integIRTy: a method to identify genes altered in cancer by accounting for
multiple mechanisms of regulation using item response theory
Bioinformatics, Vol. 28, No. 22. (15 November 2012), pp. 2861-2869
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13. Regression: SIM
Integrated analysis of DNA copy number and gene expression microarray data using gene sets
BMC Bioinformatics 2009, 10:203
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Chr
Correlation: DR-Integrator

15. Latent variable: iCluster
(file under impractical)
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16. Basics that are never explained 1/2
Integration across groups or description of samples?
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17. Basics that are never explained 2/2
Genes x Samples
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18. Conclusions 1/3
We’re not the first people doing this...
...but it’s becoming a “hot topic”
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19. Conclusions 2/3
Room for improvement in software, much of which is:
• Poorly-written
• Poorly-documented
• Difficult to implement
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20. Conclusions 3/3
Too much for one individual!
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21. CSIRO Mathematics, Informatics and Statistics
Neil Saunders
t
+61 2 9325 3144
e Neil.Saunders@csiro.au
w Mathematics, Informatics and Statistics web
MATHEMATICS, INFORMATICS AND STATISTICS
www.csiro.au