A Computational Procedure To Identify Significant Overlap Of Differentially Expressed And Genomic…

…Imbalanced Regions In Cancer
Datasets

Silvio Bicciato
Morning Session, 2 September (11th MGED Meeting, 1-4 September, 2008)

Integrative genomics in the sense they're using it is bridging the gap between DNA copy number and RNA transcription through microarray technology. (There are many other definitions and types of "integrative"  genomics.) They are integrating genotyping, transcriptional and structural information before the analysis. The SODEGIR method is the acronym that is the same as the title of the talk. Step 1 is to transform SNP copy number and expression data into CN and GE scores. It estimates of CN and GE scores at the chromosomal locations of Entrez Gene IDs from the probe set data of the microarrays using a kernel regression estimator. Step 2 defines regions with concomitant alterations of gene CN and GE in single samples. Step 3 detects the presence of common SODEGIR signatures across all samples of an entire dataset using the binomial distribution.

These are just my notes and are not guaranteed to be correct.
Please feel free to let me know about any errors, which are all my
fault and not the fault of the speaker. 🙂

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