This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Gene names from NCBI is not able to use for overlapping in species comparison

Hi,

I want to check the overlapping genes between three species. I fetched all the Gene names from the GENE database of NCBI. The list had synonym names for several genes. I am confused which all synonyms should I remove before I plot Venn diagram. I fear that some synonyms may hit on the other list which can make an increase in the overlaps. If I remove the synonyms list and go with the genes names will I lose overlaps? Any Idea to make all the genes in a standard form independent to species?

Thanks in Advance,
Amk

ncbi overlap venn conversion comparison
• 2,563 views • link
updated by abascalfederico abascalfederico • written by Amk Amk

1 answer

I guess you mean orthologous genes not overlapping. You can use phylogenetic trees, for example from Ensembl Compara, or look at Genomicus and the synteny

• 0 views • link
updated by Ram Ram • written by abascalfederico abascalfederico

Hi abascalfederico,

Thank you for your suggestion.

• 0 views • link
updated by Ram Ram • written by Amk Amk

Log in to answer this question.

More posts like this