I have a list of ncRNA from miccroarray data annotated or represented by muliplte ID types for eg Genbank,Refseq,Ensemble some even from literature I want to convert them into on ID formate for gene ontology analysis can you please tell me any tool or method ? i tried biomart David etc but not worked do not convert most of the IDs
If your focus is to understand Gene Ontology (Biological Process, Molecular Function and Cellular Component), I would recommend to collect the sequences from all respective Ids, which you have collected from different sources (can be done by NCBI Enterz). Collected sequences can be put into BLAST2Go software and you will get results for same.
http://www.ncbi.nlm.nih.gov/sites/batchentrez
https://www.blast2go.com/free-b2g-trial
I also always use BioDBnet for this type of task
https://biodbnet-abcc.ncifcrf.gov/db/db2db.php
Cleaning/converting the data is a hard work, like any other type of cleaning :) No magic solutions, unless you are Hercules cleaning Augean stables ;)
Biomart is my favourite tool, preferably via webservices in R. Anyway, it has to be done carefully, looking at the size of results for each converted identifier, as often those are not 1-to-1 relationships:
# example for EnsemblID to GO
library(biomaRt)
ensembl = useMart("ensembl",dataset="mmusculus_gene_ensembl")
filters = listFilters(ensembl)
attributes = listAttributes(ensembl)
out
A word of caution ... don't expect that every identifier has a counterpart in all other databases. Annotation is a huge problem and even if all biologists would focus their work just on annotation and transfer of annotation among similar entities it would be futile.
In your case, DAVID would tell you which IDs it didn't 'know' and in my experience GO while being well annotated for the entities listed, it simply lacks many entries from other databases. Worst when looking at pathways where organization (like GO) is required and, therefore, less of the IDed entities will be available there.
Thanks to all of you people for very us-full advice and comments , i was thinking another thing can as Jens Allmer i was thinking if i can use these IDs directly for gene ontology analysis and then collect the information sort the information manually
Eg. GeneGo/Metacore does it that sort of way - converts everything you feed it with (one type of ID in one data column) and coverts internally to EntrezID, then GO enrichment is run on this (human, mouse, rat)
Dear,
You can try database : AbIDconvert.
Hoping it will be helpful
Marius
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