Does anyone know of any free online pipelines that I can enter a list of genes from mRNA seq data and can get information about disease groups the genes are generally found in?
2 online databases that you can just copy and paste gene lists into:
http://www.pantherdb.org
https://david.ncifcrf.gov
An R implementation for gene ontology analysis that again involves just a list of genes that are differentially expressed vs those that are not:
https://bioconductor.org/packages/release/bioc/html/goseq.html
A gene set analysis pipeline that requires some more data prep than just having a list of differential genes:
https://www.gsea-msigdb.org/gsea/index.jsp
And a few R implementations of gene set analyses that require more data prepping:
https://bioconductor.org/packages/release/bioc/html/fgsea.html
https://bioconductor.org/packages/release/bioc/html/gage.html
https://academic.oup.com/nar/article/40/17/e133/2411151
I hope this helps. Happy analyzing!
2 online databases that you can just copy and paste gene lists into:
http://www.pantherdb.org
https://david.ncifcrf.gov
An R implementation for gene ontology analysis that again involves just a list of genes that are differentially expressed vs those that are not:
https://bioconductor.org/packages/release/bioc/html/goseq.html
A gene set analysis pipeline that requires some more data prep than just having a list of differential genes:
https://www.gsea-msigdb.org/gsea/index.jsp
And a few R implementations of gene set analyses that require more data prepping:
https://bioconductor.org/packages/release/bioc/html/fgsea.html
https://bioconductor.org/packages/release/bioc/html/gage.html
https://academic.oup.com/nar/article/40/17/e133/2411151
I hope this helps. Happy analyzing!
If you go to https://david.ncifcrf.gov/summary.jsp , you simply copy and paste in the little white box on the left your genes list.
In the step 2, below the white box where you pasted your genes list, select the appropriate gene identifier. However, if you are uncertain about it, at the end of the list you find the option "not sure" and DAVIS will try to guess what kind of input data you have.
In the step 3 select "Gene list" and go ahead.
Among all the results got, as first one you get "disease". Clicking on the + symbol, you can choose the database that shows the highest coverage according to your input data.
Good luck!
Generally speaking, you can collect a bunch of expression data of your genes of interest from both the ENSEMBL and the UCSC browsers. You can also check on GEPIA2 (http://gepia2.cancer-pku.cn/#index) since they have cancer data that might be interesting for you (expression, survival, etc).
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