HI
I'm working with RNA_Seq data from non-model organisms after differential gene expression analysis I find out their are lot of genes starting with prefix "LOC" and further searched in web I found out that these are genes which don't have any orthologs. I further performed downstream analysis I unable to convert LOC's into ENTREZID's/ENSEMBL ID's using clusterprofiler(bitr function). How do I proceed further for downstream analysis something line GO/KEGG analysis. Should I ignore them completely ? I had total of 7 samples after differential gene expression analysis they found to be 4501 for each sample.
If I search these ID's in NCBI I getting the gene information.
suggestions please!
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written
by
sunnykevin97
1 answer
These don't appear to have useful gene symbols. But you can get names for these using Entrez Direct as follows:
esearch -db gene -query 'LOC117740983' | esummary | xtract -pattern DocumentSummary -element Id,Name,Description
How do I run a batchmode using esearch ? I had morethan 1000 geneID's in a file, using the above command. Suggestions please.
Use epost method. Put your queries in a file, one per line.
$ more tt
117740983
117726460
117746502
$ epost -db gene -input tt | esummary | xtract -pattern DocumentSummary -element Id,Name,Description
117746502 LOC117746502 neuropilin-1a-like
117740983 LOC117740983 transmembrane protein 230-like
117726460 LOC117726460 NADH-cytochrome b5 reductase 3
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Can you provide an example or two? Sometimes LOCs have informative aliases that you can use. If you have the Entrez Gene IDs you can fetch a list of all aliases for each of them.
https://www.ncbi.nlm.nih.gov/search/all/?term=LOC117740983 https://www.ncbi.nlm.nih.gov/gene/117726460 https://www.ncbi.nlm.nih.gov/search/all/?term=LOC117746502
The number after the
LOCis the EntrezID. You can access these entries by the URLhttps://www.ncbi.nlm.nih.gov/gene/{number}For your examples,
I thought the same, thanks for the suggestions.
Hi, this is very useful, thanks. How would I go about running GO enrichment analysis with this list?
Since
LOCgenes are uncharacterized there is likely no way to do GO enrichment analysis on those.