Hi. Is there someone who can please help me? So I annotated RNAseq data of several samples with MG Rast. I then got an extensive list of gene names on which I did statistical analyses. After this, I ended up with a selective list of gene names with which I want to work further. I only have the gene names, not the sequences of these selected genes. I want to know to which categories these genes belong (e.g virulence, cell wall, co-enzymes) etc I do not have the sequences of these selected genes, only their names. Can I use MG Rast to find this? Or any other database that I can use to get the (broad) category to which these genes belong? Or will one need their sequences? Any help would be really appreciated.
Dear Margot
There are different annotation databases you can use e.g. GO, Reactome etc. Most however are based on human or mouse biology and the gene symbols from your organism will need to be same. Once we accept that assumption, you can either use a web based database e.g. innate db or string are easy to use. You can however also use R and Bioconductor platform but will need some programming skills. I am sure some other people will also post their useful suggestions. Here is one tutorial in R https://datacatz.wordpress.com/2018/01/19/gene-set-enrichment-analysis-with-topgo-part-1/
Good luck
Hi,
As Umar said. You can use web based tools toi enrich tour dataset with Gêne Ontology (GO), Pfam, KEGG, etc. Usually, you need to use the sequences toi blastx them against the databases that are of interest to you. But it is also radier to do it programmatically using R or another bioinformatics tool that you can use on a computer cluster.
Good luck.
Sorry for late answer, but you can also use biomaRt (https://bioconductor.org/packages/release/bioc/html/biomaRt.html), which is very useful to link functions/ontologies (e.g., GO) to specific gene symbols/names (e.g., Entrez, NCBI nomenclature, etc...).
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