Version History

July 2014
Initial import

November 2014
Update TCGA data sets. Release for PSB paper.

April 2015
Update TCGA data sets.

Added Astrazenica cell line collection. (U133P2 gene expression microarrays)
GSE10846
GSE19069
GSE4475
GSE53482
GSE6338
Meta data annotations for TCGA from PMID:25765070

Removed redundant TCGA mutations.

Functionality:
Survival plots based on expression or miRNA levels.
Find CNV with differential expression levels.
Find mutations with differential expression levels.
Added pan TCGA dataset option (TCGA-TOTAL)
Added lm fit option to expression plot.
Added box plots of expression vs. CNV or mutation status to expression_plot.
Beta 3D expression plot.

Use mutation count per sample as a "gene" expression value.
eg. tests for mutation burden vs. cnv, mutation, metadata, expression.

Search criteria for CNV modified from >= 10 SNPs to >= 5 SNPs. Minimum length modified from 10kb to 90bp. Applies to genome wide CNV tests. For expression plot, the default is still 10 SNPs, 10kb. Can be configured by changing the values in the minsnp, minbp boxes.

Bug fixes:
Fixed merge CNV bug, excluded first line of the table.

November 2015
Update TCGA data.
Addition of new datasets.
Modified UI.
Additional analysis functions.

Development

Import of TCGA-LAML meta data from NEJM publication.
Multiple gene expression vs. meta data plot.

venn_summary, addition of option to remove from consideration samples without both CNV and mutation data.

fix the summary table for matrix ( was not median centering data before calculation )