Question: International Protein Index (Ipi)
0
gravatar for Varun Gupta
8.2 years ago by
Varun Gupta1.1k
United States
Varun Gupta1.1k wrote:

Hi Everyone

I have a list of ribosomal protein genes and i want to extract the corresponding IPI (International Protein Index) for it.

How can i get them for all the genes in one go?

Hope to hear from you guys soon.

Regards Varun

protein index • 3.6k views
ADD COMMENTlink modified 8.2 years ago by Ahill1.8k • written 8.2 years ago by Varun Gupta1.1k

I am wondering why you want to use IPI in your analysis ? IPI is deprecated by EBI, you could use an alternate resource for your analysis.

ADD REPLYlink written 8.2 years ago by Khader Shameer18k
1
gravatar for Vikas Bansal
8.2 years ago by
Vikas Bansal2.4k
Berlin, Germany
Vikas Bansal2.4k wrote:

Download IPI Gene Cross-References File Format from here. The description of file format is here. You can download the file. I think 6th or 7th column is gene name and 10th column is IPI. You can extract your interest of genes with IPI's.

ADD COMMENTlink written 8.2 years ago by Vikas Bansal2.4k

The last release is at ftp://ftp.ebi.ac.uk/pub/databases/IPI/last_release. That file format description has been taken down too, but was last archived here.

Column Summary Comments
1 Chromosome Values: 1-n (where n = 22 (human), 19 (mouse), 20 (rat), etc..), W, X, Y, Z, "M" for Mitochondrion, "C" for Chloroplast, "Un" for unknown.
2 Cosmid For some Ensembl genes, a location in the complete chromosome is not known owing to the incompletion of the underlying sequence assembly, and the co-ordinates provides are merely the local co-ordinates within a single cosmid. Where this is the case, the cosmid name is given in the second column
3 Start co-ordinate of gene (on Ensembl assembly). Given in base pairs, global (these are chromosomal co-ordinates, except in cases discussed previously). Data taken from Ensembl.
4 End co-ordinate of gene (on Ensembl assembly). Given in base pairs, global (these are chromosomal co-ordinates, except in cases discussed previously). Data taken from Ensembl.
5 Strand of gene (on Ensembl assembly) corresponding to these co-ordinates. 1 for FORWARD or SENSE and -1 for REVERSE or ANTISENSE.
6 Gene location Taken from species-specific gene resource (e.g. HUGO) if available or Entrez Gene if not.
7 Ensembl Gene ID  
8 Gene id, Gene symbol Taken from HUGO, MGD, RGD, ZFIN, TAIR Gene (as appropriate, dependent on the species).
9 Gene id, Gene symbol Taken from Entrez Gene.
10 IPI ACs All IPI ACs associated with this gene are given.
11 UniProtKB/Swiss-Prot ACs All UniProtKB/Swiss-Prot ACs associated with this gene are given.
12 UniProtKB/TrEMBL ACs All UniProtKB/TrEMBL ACs associated with this gene are given.
13 Ensembl peptide IDs All Ensembl peptide IDs associated with this gene are given. Havana curated transcripts preceeded by the key HAVANA: (e.g. ENSP00000341800;HAVANA:ENSP00000317992;).
14 RefSeq STATUS:ID couples All RefSeq STATUS:ID couples associated with this gene are given (RefSeq entry revision status details).
15 TAIR Protein IDs All TAIR Protein IDs associated with this gene are given.
16 H-InvDB Protein IDs All H-InvDB Protein IDs associated with this gene are given.
17 UniGene Gene IDs All UniGene Gene IDs associated with this gene are given.
18 CCDS IDs All CCDS IDs associated with this gene are given.
19 RefSeq GI protein IDs All GI protein IDs associated with this gene are given.
20 Vega Gene ID  
21 Vega peptide IDs All Vega peptide IDs associated with this gene are given.
ADD REPLYlink written 5.8 years ago by Louis140
0
gravatar for Ahill
8.2 years ago by
Ahill1.8k
United States
Ahill1.8k wrote:

Where do your ribosomal gene identifers come from (Genbank accessions, UniProt accessions, ...?). As noted by Varun, IPI is deprecated, but if you need IPI IDs for comparison with legacy data, one method is:

  1. Go to http://www.uniprot.org
  2. Select the ID Mapping Tab
  3. Paste or upload your ribosomal gene identifiers
  4. Select the type of your source identifiers in the "From" box
  5. Select IPI in the "To" box.
  6. Click Map. Download the resulting .list file of IPI identifiers

All inter-database identifier mappings should be checked for carefully for accuracy, depending on your application, since determining a "correct" mapping can be complicated.

ADD COMMENTlink written 8.2 years ago by Ahill1.8k

This no longer works

ADD REPLYlink written 5.8 years ago by Louis140
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