What are accession numbers starting with PIR e.g. PIR60289?
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4 months ago
Dataman ▴ 350

Hi! While using GeneHancer, I have encountered accession numbers starting with PIR such as PIR60289. What are these and where can I get more information about them?

For example

chr1    16607335    16609589    Enhancer;genehancer_id=GH01I016607;connected_gene=PIR60289;score=550.77;connected_gene=PIR35349;score=0.77;connected_gene=NBPF1;score=0.44  1.13    .   1


These accession number should refer to genes as GeneHancer reports Gene–enhancer associations. A quick search on the Web was not informative. Searching FANTOM, VISTA, and ENCODE for answer was not successful either. These were checked, since they are the basis for GeneHancer. Searching GeneCards also did not help. GeneCards was searched because, GeneHancer is integrated in the GeneCards.

There is a PIR file format, but I am do not believe this is what I am looking for.

accession_number • 298 views
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4 months ago

those are PIR protein identifiers as they are used by the Protein Information Resource (https://proteininformationresource.org/) .

In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases.

those are now also part of UNIprot and thus you can find protein IDs starting with PIR in uniprot (just as well as you will encounter sp , from swissprot, ... )

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Great! Thanks! I am now puzzled about the results I get e.g. for PIR60289. Since GeneHancer is a database about human enhancers, I expect these protein identifiers are human-related! But PIR60289 refers to Candidatus Pacebacteria bacterium (source)! Am I missing something here?

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yeah, good question and I do see your point but I'm not so familiar with those DBs ... Perhaps ask the GeneHancer DB folks?