drosphila2PATH question
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@ariel-chernomoretz-1863
Last seen 5.7 years ago
Dear list, I want to know how affy probesets map to kegg pathways in drosophila2 arrays. However I realized that no such mappings are included in drosophila2 v1.12 annotation package. Is there a reason for this? Where can I find that information? Thanks Ariel Chernomoretz
Pathways affy Pathways affy • 481 views
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Dear Ariel, The short answer is: this is a bug/missing feature. The package drosophila2 was built by using ABPkgBuilder, which is designed for human, mouse and rat, not for fly. To get probe to KEGG mapping, the function first gets probe to Entrez Gene mapping, and then use ftp://ftp.genome.jp/pub/kegg/pathways/dme/dme_gene_map.tab to get KEGG pathway IDs. dem_gene_map.tab contains two columns: KEGG gene IDs and KEGG pathway IDs. KEGG has similar files for each organism. For human, mouse and rat, KEGG Gene IDs happen to be the same as Entrez Gene ID. Therefore, function ABPkgBuilder can use this file to get probe to KEGG pathway mapping right away. But for other organisms KEGG gene IDs are in a different format. Therefore ABPkgBuilder will fail to get KEGG pathway IDs. One solution is to modify ABPkgBuilder to get Entrez Gene to KEGG gene ID mapping from ftp://ftp.genome.jp/pub/kegg/genomes/dme/dme_ncbi-geneid.list The other solution is to write specific builder functions for fly, just like what happened to Arabidopsis and yeast. It is because ABPkgBuilder uses Entrez Gene ID as the base identifier for gene. But most people may perfer flybase (rather than Entrez Gene). Therefore, it is more appealling to write a fly specific builder function. But this is also time consuming... sorry there is no direct answer, but hope it provides some background information. nianhua
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