Question: about source to make HGU133plus2 package
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gravatar for gregory voisin
12.3 years ago by
Canada
gregory voisin430 wrote:
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ADD COMMENTlink modified 12.3 years ago by Nianhua Li870 • written 12.3 years ago by gregory voisin430
Answer: about source to make HGU133plus2 package
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gravatar for Nianhua Li
12.3 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Hi, Greg, We first map probeset IDs to Entrez Gene IDs and then extract other annotations by using the Entrez Gene IDs. Here are some details for hgu133plus2 v1.16.0 (the one in bioc2.0 release). The ACCNUM environment (hgu133plus2ACCNUM) was extracted from Affymetrix's annotation file (dated 11/15/2006, the "Representative Public ID" column). It is used to get probeset to Entrez Gene mapping via data from Entrez Gene (GenBank to Entrez mapping, dated 2/28/2007) and UniGene (GenBank to UniGene mapping and UniGene to Entrez mapping, dated 2/26/2007). For unmapped probeset IDs, we use the probeset to Entrez mapping in Affymetrix's annotation file as a suppliment. The result is the ENTREZID environment. We then search for other annotations by using the Entrez IDs. The table below lists all the source data. table columns: --------------- Environment--name of the environment, e.g. CHRLOC represents hgu133plus2CHRLOC Source Name--name of the source database Source URL--URL of the source data directory Source Date--date of the source data ------------------------------------------------------ CHRLOC UCSC Genome Bioinformatics (Homo sapiens) ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapiens 2006-Apr14 CHR Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 ENZYME KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes 2007-Feb28 GENENAME Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 GO Gene Ontology http://archive.godatabase.org/latest 200702 MAP Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 OMIM Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 PATH KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes 2007-Feb28 PMID Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 REFSEQ Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 SYMBOL Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 UNIGENE Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 ENZYME2PROBE KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes 2007-Feb28 GO2PROBE Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 GO2ALLPROBES Gene Ontology http://archive.godatabase.org/latest 200702 GO2ALLPROBES Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 PATH2PROBE KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes 2007-Feb28 PFAM The International Protein Index ftp://ftp.ebi.ac.uk/pub/databases/IPI/current 2007-Feb21 PROSITE The International Protein Index ftp://ftp.ebi.ac.uk/pub/databases/IPI/current 2007-Feb21 PMID2PROBE Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA 2007-Feb28 ------------------------------------------------------- hope this helps nianhua
ADD COMMENTlink written 12.3 years ago by Nianhua Li870
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