I am doing a good deal of RNAseq analysis on Saccharomyces. I found your results that rounds RPKM values can be used to produce reliable gene lists interesting given the amount of time money and effort spend by so many of the problem. I am going to give this method a try. I am wondering if you could let me know what type of information I would need to make a functional enrichment for Saccharomyces cerevisiae as well. Looking forward to hearing from you. I am currently using CLC genomics workbench and I would like to compare the results of your approach to CLC's DEG pipeline (one that was not included in your study). Thanks for your time.
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sRAP (and I assume CLC Bio) will be giving you a list of differentially expressed genes in a table.
I think the easiest solution is to copy and paste that list of differentially expressed genes web-based functional enrichment tool. For example, GATHER should work for you if you set the organism to "yeast":
In the future, I'll considering adding GO terms for yeast to use in BD-Func. However, the new Bioconductor release is coming soon, so I won't be able to make changes for a bit. So, I think this is the best immediate solution.
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UPDATE: The yeast GO terms are pretty different than the human and mouse GO terms. I tried to create a BD-Func signature file for yeast, but I found that there was only one term with both positively and negatively regulated genes (genes in multiple nitrogen degradation pathways) and they didn't both meet the requirement of containing a minimum of genes in each GO term.
For this reason, I will not be adding a yeast BD-Func file to the standalone or Bioconductor (in the sRAP package) versions. I apologize for the inconvenience, but there are a lot of tools out there that can analyze yeast GO terms.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I am doing a good deal of RNAseq analysis on Saccharomyces. I found your results that rounds RPKM values can be used to produce reliable gene lists interesting given the amount of time money and effort spend by so many of the problem. I am going to give this method a try. I am wondering if you could let me know what type of information I would need to make a functional enrichment for Saccharomyces cerevisiae as well. Looking forward to hearing from you. I am currently using CLC genomics workbench and I would like to compare the results of your approach to CLC's DEG pipeline (one that was not included in your study). Thanks for your time.
Thank you for using sRAP.
sRAP (and I assume CLC Bio) will be giving you a list of differentially expressed genes in a table.
I think the easiest solution is to copy and paste that list of differentially expressed genes web-based functional enrichment tool. For example, GATHER should work for you if you set the organism to "yeast":
http://gather.genome.duke.edu/
In the future, I'll considering adding GO terms for yeast to use in BD-Func. However, the new Bioconductor release is coming soon, so I won't be able to make changes for a bit. So, I think this is the best immediate solution.
UPDATE: The yeast GO terms are pretty different than the human and mouse GO terms. I tried to create a BD-Func signature file for yeast, but I found that there was only one term with both positively and negatively regulated genes (genes in multiple nitrogen degradation pathways) and they didn't both meet the requirement of containing a minimum of genes in each GO term.
For this reason, I will not be adding a yeast BD-Func file to the standalone or Bioconductor (in the sRAP package) versions. I apologize for the inconvenience, but there are a lot of tools out there that can analyze yeast GO terms.