Replication of the TCGA PARADIGM analysis

[Artem Lysenko]

Dear TCGA GDAC Team,

 

We are trying to reproduce the PARADIGM analysis according to what was reported in https://gdac.broadinstitute.org/runs/analyses__latest/reports/cancer/OV-TP/Pathway_Paradigm_RNASeq/nozzle.html however in all of our many attempts so far we are getting very different IPA values compare to those listed on this page (~0.3 correlation).  The report states that  OV-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt was used as input, but we were unable to find this file in any data available for download. Also, the pathway definition file likewise has not been made available. The website mentions that “NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities”, but this database is now defunct – and a snapshot in the Internet archives shows that none of the pathway sets listed around that date matched this summary.

 

Would it be possible to get some details about how we can reproduce this analysis – ideally we would like to see the script used to automate this analysis, the pathway file and configuration settings used to run PARADIGM and some clarification about how the OV-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt was generated from one of the files that were made available for download.

 

Thank you for your help,

 

Artem Lysenko.

 

 

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Artem Lysenko, Ph.D. Research Scientist, Laboratory for Medical Science Mathematics RIKEN

Center for Integrative Medical Sciences

1-7-22 Suehiro-cho, Tsurumi

Yokohama 230-0045, Japan

Tel: +81-45-503-9555

E-mail: artem....@riken.jp