Duplicate gene symbols converted from UCSC gene id

Question

[gndy90]

Hi,

I am a beginner in RNASeq. I am running Cufflinks on my human cell transcriptome analysis. Finally, CummeRund gave me the UCSC gene id of differentiallyexpressed genes, not the gene symbols. So I converted the gene id to gene symbols by UCSC Genome Browser. My question is:

1. I submitted 2900 gene ids, it gave me about 3000 gene_id-gene_symbol pairs. About 100 new gene ids were added. What's the reason for this?

2. My downstream analysis do not allow for duplicate gene symbols. What should I do about the duplicates? I searched in Biostars, found that the different gene ids corresponding to one common gene symbol are different haplotypes of the gene. Should I just add up the expression values with the same gene symbol?

Thanks.

[GouthamAtla]

Would it be possible to post an example gene_id with multiple gene_symbols?

[gndy90]

Sure. But I think It should be 'gene symbol with multiple gene IDs'.

Here is two examples:

gene id       gene symbol
uc001ajr.3    TNFRSF14
uc001ajt.1    TNFRSF14
uc001aju.3    FAM213B
uc001ajw.2    FAM213B

[andrew.j.skelton73]

Could they not be transcript variants (isoforms) of the same gene?

[gndy90]

But I did gene level differential expression analysis in cuffdiff and cummeRbund.

Here is my hg19 GTF file format:

chr1 hg19_knownGene exon 11874 12227 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
chr1 hg19_knownGene exon 12613 12721 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
chr1 hg19_knownGene exon 13221 14409 0.000000 + . gene_id "uc001aaa.3"; transcript_id "uc001aaa.3";
chr1 hg19_knownGene exon 11874 12227 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";
chr1 hg19_knownGene exon 12646 12697 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";
chr1 hg19_knownGene exon 13221 14409 0.000000 + . gene_id "uc010nxr.1"; transcript_id "uc010nxr.1";

No gene symbol within it. Is that correct?

Answer 1

[GouthamAtla]

For this particular example,the gene_id is same as transcript_id. The gene_id column in mandatory for a gtf format, hence ucsc just added the transcript_id as gene_id. So they are different transcripts of a Gene.

[gndy90]

Solved! I used the incomplete gtf file exported from table browser. Thank you !