Dear all,
I've been recently trying make some orthologous conversion. Generally, I’m using biomart, org.Hs.eg.db and org.Mm.eg.db, sort of things to do orthologous mapping. The usual approach worked well for me in the past. Basically I find organism specific gene ID, either entrez or ensemble. then, using biomart to get cross species reference. But I’ve come across a paper which was terribly bad in terms of gene annotation. I don’t think I’ve convinced myself if the genes described in their paper was actually expressed, or if that’s the gene that they mean.
Just want to ask if any of you would happen to have a better method that helps to identify the genes in their native organisms? Table below illustrate my difficulties.
ID Gene Name.Description
AK022594 AK022594 Homo sapiens cDNA FLJ12532 fis, clone NT2RM4000200
AK130878 AK130878 Homo sapiens cDNA FLJ27368 fis, clone UBA03195
BC030102 BC030102 cDNA clone IMAGE:4796690
BX647159 BX647159 DKFZp686H14196 (from clone DKFZp686H14196)
THC2624002 THC2624002 HUMAN (Q9BXR7) Interleukin 10 (Fragment
THC2634713 THC2634713 Unknown
THC2699065 THC2699065 DTDP-glucose 4,6-dehydratase (Fragment), partial (9%)
THC2708669 THC2708669 Dihydropteroate synthase (DHPS) (Dihydropteroatepyrophosphorylase) , partial (5%)
BX427767 BX427767 cDNA clone CS0DM012YK01 3-PRIME
BX647159 BX647159 cDNA DKFZp686H14196
CR616309 CR616309 LIMF1-lipase maturation factor 1
thank you very much for your input!
Cheers, Tongtong
The first column looks like GenBank accession for clones (I don't recognize the THCxxxxx though). You may be able to find which gene they map to with the Ensembl API (I don't think BioMart takes clone IDs as input). Alternatively, retrieve the clone sequences from NCBI and map them yourself to your reference gene set.