Gene starts with "LOC" prefix ?
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3.8 years ago
sunnykevin97 ▴ 980

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!

RNA-Seq gene sequence • 4.4k views
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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.

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The number after the LOC is the EntrezID. You can access these entries by the URL https://www.ncbi.nlm.nih.gov/gene/{number}

For your examples,

LOC117740983    117740983    https://www.ncbi.nlm.nih.gov/gene/117740983
LOC117726460    117726460    https://www.ncbi.nlm.nih.gov/gene/117726460
LOC117746502    117746502    https://www.ncbi.nlm.nih.gov/gene/117746502
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I thought the same, thanks for the suggestions.

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Hi, this is very useful, thanks. How would I go about running GO enrichment analysis with this list?

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Since LOC genes are uncharacterized there is likely no way to do GO enrichment analysis on those.

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3.8 years ago
vkkodali_ncbi ★ 3.7k

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
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Most LOC entries are uncharacterized locations, at least on human and mouse genomes.

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How do I run a batchmode using esearch ? I had morethan 1000 geneID's in a file, using the above command. Suggestions please.

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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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