I'm working on a 2006 public microarray dataset ( https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/ ).
I've reanalysed the data to get differentially expressed transcripts, and now I'm trying to test pathway enrichment for some gene sets.
The problem I'm facing is that I need to identify which probes of the chip correspond to the genes in the sets I want to test. Considering the chip probes are annotated with old EMBL transcript ID (most of the id are like AAXXXXXX, AIXXXXXX, HXXXXX, NXXXXX, RXXXXX, TXXXXX, with numbers for Xs, for example I know that "AI375736" corresponds to CD28 gene).
I'm not really sure how to find a correspondance between the genes I want to study and these transcripts IDs.
If anyone has any advice on how to do that it would be very helpful.