gene list for RNA seq

Question

[pshubhamoy]

Hi, I need a list of all the protein coding genes from mouse with gene name and corresponding Entrez Gene ID. can somebody help.

thanks

Answer 1

[EagleEye]

1) simple way:

Example, Mus musculus

http://rest.kegg.jp/list/mmu

For other organism/species use codes from following link,

http://rest.kegg.jp/list/organism

2) With some effort using UCSC (Select Mus musculus as reference in your case):

A: I need to download a list of all human genes with their respective Esemble gene

[steve]

This is a dumb question but I just wanted to double check, this is independent of reference genome (mm9, mm10), correct?

[pshubhamoy]

Hi Steve,

good point, yes I am using mm10

Answer 2

[unksci]

the most up-to-date and comprehensive reference for Entrez Gene ID, which also contains the status of the genes, is:

http://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz (which you have to filter by taxon ID 10090 for Mus muscululs)

or, conveniently : http://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz

The table also contains the gene name (or more correctly: gene names separated by naming institution), and the gene-type (which you have to filter for "protein-coding")

Answer 3

[pshubhamoy]

Thanks all,

actually I have a RNA-seq data set and I would like to remove all the non-coding genes. is there any available tool for that?

[steve]

This is something that you could accomplish fairly easily in any programming language e.g. R or Python. However the specific implementation would be heavily dependent on the structure of your data

[WouterDeCoster]

Strategy for R:

Assuming you have a count table with genes on rows and samples on columns you can easily read this table in as a data.frame counts. Analogous you can read in the list of genes you want to keep (or remove, doesn't matter) into a vector keepgenes.

Then you can easily slice the counts data.frame by something like newdata <- counts[counts$gene %in% keepgenes, ]

If this strategy/pseudocode is unclear for you I can expand on this, but this is really basic R and you'll make your RNA-seq analysis far less painful if you dive in a R tutorial and learn yourself how to perform these tasks. Knowledge of at least one programming language is an enormous advantage.

Answer 4

[ebrahimiet]

Hi

You can easily use Ensembl Biomart

http://www.ensembl.org/biomart/martview/3e6bde1e77a85c663750a6367619f66f Regards

Esmaeil