iDEA Challenge 2011: Illumina’s Data Excellence Award

Illumina is holding a data visualization contest to promote the development of new ideas for visualizing high throughput sequencing data. I think ExpressionPlot fits the bill well since it makes it easy for all biologists to create the types of plots necessary for interpreting their RNA-Seq data and comparing it with other data sets.

Key links:

The iDEA contest began with 8 breast cancer cell lines analyzed by a variety of *-Seq technologies. Two types of RNA-Seq were included: (non-stranded) paired-end RNA-Seq and Directional (single-end) RNA-Seq. I’ve processed both of these through the default ExpressionPlot back ends. They are accessible on the prototype server, with the names “iDEA Breast Cancer Cell Lines Paired-End RNA-Seq” and “iDEA Breast Cancer Cell Lines Directional RNA-Seq”.

I prepared a PDF document describing ExpressionPlot with examples from the iDEA dataset for my entry into the competition. Here are some of the plots from the submission (the PDF contains additional explanatory material):

Pair-dist Plot

iDEA Pair-Dist Plot

Correlation Plot

iDEA Correlation Plot

Clustering Plot

iDEA Clustering Plot

2way Plot

iDEA 2way Plot

SeqView Plot (Sec31a)

iDEA SeqView Plot

4way Plot

iDEA 4way Plot

Heatmap Plot

iDEA Heatmap Plot

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A web-based framework for analysis of RNA-Seq and microarray gene expression data