Rephetio: Repurposing drugs on a hetnet [rephetio]

Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets

The ADEPTUS resource for expression signatures of disease

A recently published study [1], which calls itself ADEPTUS, calculated differential expression profiles for 14 diseases.

Their disease concepts are broad, so only 3 match a DO Slim disease (notebook, downloads). Those diseases along with the corresponding number of up and down-regulated genes are:

disease iddisease namegenes downgenes up
DOID:1324lung cancer101211
DOID:1612breast cancer6168
DOID:2531hematologic cancer512631

We're included these edges in our network as a placeholder until STARGEO is ready. STARGEO currently contains 463,824 sample annotations (tags) whereas ADEPTUS contains only 14,840.

  • Dexter Hadley: It would be useful to compare and contrast STARGEO with this ADEPTUS list. To be clear the 400+ annotations cover about 200+ distinct tags made on samples — i.e samples can be redundantly annotated to check for validity of the original annotations. This validation on demand allows us to weed out problematic studies that poorly describe their samples and individual sample annotations whose semantics are imprecise.

Permission to reuse ADEPTUS

Now that our STARGEO analysis is ready, we're no longer including ADEPTUS in our hetnet. From STARGEO, we extracted differential expression signatures for 49 diseases, so integrating the signatures for the 3 diseases from ADEPTUS no longer made sense.

However, on August 29, 2015 I emailed the authors requesting permission to reuse the ADEPTUS data as I did not see a license on their website. This was part of a broader effort to try to comply with the copyrights and licenses of our sources.

Today, David Amar responded stating that we have permission to use the datasets in question. Specifically, he noted that the publication itself [1] grants permission to use any of their results.

Status: Completed
Referenced by
Cite this as
Daniel Himmelstein (2015) The ADEPTUS resource for expression signatures of disease. Thinklab. doi:10.15363/thinklab.d101

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