Hi all,
Following a single cell RNAseq experiment, I found two cell populations of interest with starkly different transcriptomes. I would like to take the top 100 deferentially expressed genes between those populations, and do some kind of gene ontology analysis, however, no tool that I found seems able to do such a thing. Presumably the tool should be able to accept a file with three columns: a list of genes, and then a column of gene expression values for each population (so three columns, in my case). Would anybody be able to tell me of a tool that can do that? Supposedly Panther was able to do this, but the documentation describes links that do not exist in the software, so that I had no idea how to get to the right tool.
Thanks!
Benjamin
Contact Dr. Bionaz in Animal and Rangeland Sciences at Oregon State University. I think he may have what you're looking for.
Thanks for the help, Vahid and Heaven! I looked into David, but it doens't seem to do what I'm looking for. While iPathwayGuide is intriguing, and pools a lot of interetsing data together, it also doesn't quite seme to hit the mark. Heaven, I will contact Dr. Bionaz as per your advice. Thanks!
I don't know of anything that can call pathways for you but you can always try the deseq2 package in R to get significantly differentiated genes. Assuming you have some sort of genome sequence for the cells you can map your reads on to that using Bowtie and sort the output by position on the genome. If you have syntenic genes that are similarly regulated you can look them up to manually see if they are a pathway.
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Hi Vahid, thanks! I hadn't really looked much further into this anymore as I came across some other computuational emthods that might be, on the whole, mroe informative, but thanks for the link! I'll have a look.
Benjamin, it may be helpful for future researchers if you post a short outline of your answer to this problem.
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