Question: Search for Drugs related to results of differential expression analysis using RNA-seq
0
gravatar for bioinformatics
2.1 years ago by
bioinformatics10 wrote:

Hello World,

We have a list of differentially expressed genes from a RNA-seq experiment, including the fold changes p-values etc.

Our goal is to link these genes to drugs that have influences on these genes. This could lead to potential drugs that can help to induce or delay a diseased phenotype(maybe delete).

From our research we have found several interesting packages from bioconductor that may help to contribute to our goal, which are : gCMAP,gCMAPWeb and DrugVsDisease(DVD).

We do not have any experience with these packages and are unsure if we can use them. From the documentation the DrugVSDisease package may suite the best, and has a good manual. But this is meant for microarray data. The gCMAP(Web) mentions RNA-seq data in their manual but does seem to lack the ability to link to diseases.

Is it possible ( and reliable/easy ) to use a combination of the packages, so use the DVD package with RNA-seq result data?

What is the best approach for our research in finding drugs of interest and have some background information about which diseases are associated with these ?

We want to use R for our experiment, so for example  the cmap web tool would not be the right choice.

 

We are very grateful for any help in regards to this matter !

ADD COMMENTlink modified 2.1 years ago by saezrodriguez0 • written 2.1 years ago by bioinformatics10
Answer: Search for Drugs related to results of differential expression analysis using RN
0
gravatar for svlachavas
2.1 years ago by
svlachavas660
Greece/Athens/National Hellenic Research Foundation
svlachavas660 wrote:

Dear bioinformatics, 

actually i think this a rather off-topic post, as it is not "mandatory" to use any Bioconductor/R packages related to your question of interest. Actually, i would argue why you would like to use R for this kind of analysis ? considering only the gene expression list from the RNA-Seq data, an excellent choise (and rather easy from my personal experience) would be to use the L1000CDS2 drug repo tool :

http://amp.pharm.mssm.edu/L1000CDS2/#/index

It is very easy and with a detailed tutorial (http://amp.pharm.mssm.edu/L1000CDS2/help/). You could also check the relative publication for more details.

Hope that helps

Best,

Efstathios

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by svlachavas660
1

Dear Efstathios,

I would like to thank you for your previous reply, the website ( tool ) you mentioned seems to be working very well. There is also documentation available on how to use API's and drug candidates can also be searched using API. This really did help a lot !

 

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by bioinformatics10

Dear Efstathios,

Thank you for your quick and helpful reply. We will have a look at the L1000CDS2, which seems to be a

very interesting and easy way to get to a solution for our described problem.

The question we provided was specifically in regards to bioconductor packages, as when used we want to be able to be flexible. For example when results are found, the DVD package can deliver functionality in visualization of drug disease interactions. When however we would like to remove certain hits for different reasons we can specify this in our own complexity. Another example is to use an API in R to retrieve certain information, while true maybe available for online (gui) tools we do want to have the ability to change things manually( in an extended way ). We would like to know before diving into the programming if it is possible to use the DVD package or a similar package in R with RNA-seq result data.

ADD REPLYlink written 2.1 years ago by bioinformatics10
Answer: Search for Drugs related to results of differential expression analysis using RN
0
gravatar for saezrodriguez
2.1 years ago by
Germany
saezrodriguez0 wrote:

Dear bioinformatics,

Thanks for your post and we are glad that DvD can be useful for you. We have not applied it ourselves to RNAseq, but it should work, as long as you use the pre-computed rank list options.

Let us know if you have further questions.

Best wishes,

Julio

ADD COMMENTlink written 2.1 years ago by saezrodriguez0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 383 users visited in the last hour