Clip: Gene ID conversion with BioMart

[@Dr.Jia_Liu]

Very helpful. Typically we use updated gene ID or ensembl ID for pathway analysis from proteomic or genomic analyses. I am wondering if you know any analysis tools will group genes/proteins from different species, e.g., human and viruses, to show the interactions in one specific study.

[@Dr.Jia_Liu]

Biomart is not too helpful in one of my studies. The bioinformatic core provided me with gene names in different formats from my proteomic data; when I tried BioMart, it was only able to show 2 or 3 updated gene names out of 70 total. Do you have any suggestions on tools that allow conversion into uniformed format from multiple resources of naming system?

[@hhhh56hh545]

HELP HI I have a question. I have a small list of kegg ids that I obtained from KOBAS now I want to change them to gene names using biomart but biomart is giving no output. ids look like this bna03010 (organism is brassica napus) so can you help me find a solution please?

[@niharika1493]

If my data has Probe Ids alongwith Ensembl Id should I remove the probe Ids before using biomaRt package in R. Also, Ensembl Id has a suffix too, is there a need to remove them as well?

[@dr.neloferjan685]

I want to convert gene accession no.s of chickpea i.e, a plant species. But in data set it shows only animal species... Kindly let me know how to do that.

[@EnsemblHelpdesk]

You can do this using BioMart on plants.ensembl.org

[@smsmnona6634]

If I have input as a lot of exons from affymetrix HuEx 1.0 st v2 probe , could I know gene names by using biomart?

[@smsmnona6634]

And how I can uploaded exons on biomart

[@EnsemblHelpdesk]

If you have the array probe names you can use them as BioMart filters under "Input microarray probes/probesets ID list"

[@cintiamassillo4953]

I want to convert the gene name to Gene stable ID. However when I enter around 24,000 genes (RNA-seq data) the output is approximately 21,000 genes, why does that happen and how can I solve it?

[@EnsemblHelpdesk]

Please send a list of the missing gene names and details of your BioMart query to [e-mail].

[@eeroth42]

Why does this never pull the EntrezGene transcript name, is it because I have gene names as the input (ie: ENSMUSG)? Trying to convert to Entrez gene names.

[@EnsemblHelpdesk]

Hi there, thanks for your question. The equivalent is the NCBI gene ID now, as Entrez is deprecated. The 'EntrezGene transcript name' is redundant now, but has not been removed. We'll make sure it is updated soon. If you have any further questions please do let us know.

[@eeroth42]

Thanks!

[@pankajsharma2855]

I want to know gene coordinates of E.coli. can we do that using any tool??

[@EnsemblHelpdesk]

Unfortunately we don't have BioMart for bacteria, however if you search for your strain of interest on bacteria.ensembl.org, you should find a link to download GTF/GFF files.

[@kamranshah7498]

i want to do it in Malus domestica genes. . then?

[@EnsemblHelpdesk]

You would need to use our plants BioMart plants.ensembl.org/index.html

[@joshuamex100]

What kind of file can I use to import my list?

[@EnsemblHelpdesk]

Lists of IDs can be separated commas, tabs, new lines, spaces, whatever. If you do input a large file with other stuff in it, BioMart just can't read the other stuff so will ignore it, but will still find the IDs so long as they are separated from other items.

[@Ice84letters]

I have a really lon list of genes with the accesion number NM_...how can I do to convert them in Gene ID? can i do it with BIomart? I am trying with Rstudio but still I do not have enough knowledge and I really need help. I could only find this script geneIDs1

[@EnsemblHelpdesk]

Yes, BioMart is the ideal way to do this. Filter by RefSeq transcript IDs.

[@ahmedhashim5783]

Whene I used it to convert list of 5000 genes that have ensembl IDs, LOC IDs and gene name IDs to NCBI gene, I have 600000 genes!! Evry gene repited for more then 100 times!! Whay? I dont know 🤷‍♂️🤷‍♂️

[@ahmedhashim5783]

I tried allso with just 100 genes and the output wos 9363 genes, evry gene ripeted meny times !!!!