Network-based characterization of drug-regulated genes, drug targets, and toxicity

Attempt to replicate:

Network-based characterization of drug-regulated genes, drug targets, and toxicity

Status: Failed

Drug targets. Drugs and their targets were downloaded from the DrugBank database.

I signed up on DrugBank to gain access to this database. They waitlisted me before approving my request for access.

We obtained drug response data from the Connectivity Map (CMap) database [41] (build 02). In particular, we downloaded rankMatrix.txt

Signed up at clue.io to gain access to Connectivity Map. There were 2 open-source options to download under CMap. None were rankMatrix.txt. I skimmed Google for more modern references to rankMatrix.txt, since the paper is from 2012. I found at least two more modern references to what seems to be the same data successfully accessed for research purposes: “RNA sequencing-based cell proliferation analysis across 19 cancers identifies a subset of proliferation-informative cancers with a common survival signature”  claims to have accessed it in 2016; “Gene Expression-Based Drug Repurposing to Target Ageing” is a 2018 paper which claims to have used “the ‘rankMatrix.txt’ data provided on the CMap website.

Seeing no path forward, I will no longer seek to replicate this beautiful paper.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s