[Genome] Incorrectly annotated link

[Fan Hsu]

Hi Michael,

Thanks for pointing this out.

I looked into it and found that the pathway link of this gene,
PGRMC1 (NM_006667/O00264) was based on data downloaded from
CGAP,

ftp://ftp1.nci.nih.gov/pub/CGAP/Hs_GeneData.dat

I believe CGAP/NCI gets this data from BioCarta.  

As Mike Mitchell points out, for data we obtained from
3rd parties, we do not manually curate them.  Please contact
the original data source, CGAP (and/or BioCarta) directly 
to correct their downloadable data file(s). 

We are in the process of building our next release of
UCSC Known Genes (KG).  If CGAP updates their file soon,
the correction might make it to our next KG release.
Otherwise, it should show up on the following release.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of Michael A. Cahill
Sent: Monday, February 05, 2007 4:22 AM
To: genome at soe.ucsc.edu
Subject: [Genome] Incorrectly annotated link


Dear Sir/Madam,

I would like to report an error in your bioinformatics 'UCSC Proteome
Browser' server for the entry of Protein O00264 (aka PGRC1_HUMAN or
PGC1_HUMAN) Membrane associated progesterone receptor component 1 (mPR).

http://harvester.embl.de/harvester/Q6IB/Q6IB11.htm#PROTEOME

The above page concerns the HGNC protein designated PGRMC1. The
following link is erroneous.

"Pathways: 

BioCarta -  h_mPRPathway
(http://cgap.nci.nih.gov/Pathways/BioCarta/h_mPRPathway) - How
Progesterone Initiates the Oocyte Maturation"

This linked 'mPR' pathway refers to a seven membrane receptor G-coupled
protein also called mPR (membrane progestin receptor), which is NOT the
cytochrome B5-containing Membrane Progesterone Receptor (mPR/PGRMC1).
See the following text from a review I have written on PGRMC1.  

Cahill MA. 2007. Progesterone Receptor Membrane Component 1: an
integrative review. J. Ster. Biochem. Mol. Biol. in press (probably to
appear in the April 2007 edition).

mPR: nomenclatural booby trap
Note that another protein (in addition to mPR/PGRMC1), termed membrane
progestin receptor, has also been denoted as mPR in the literature. This
different gene product is a G-protein coupled seven membrane domain
progestin receptor found from fish to mammals that conveys non-genomic
effects of progesterone, and is otherwise not at all related to PGRMC1
or PR [16]. There are currently eleven mammalian members belonging to
this separate gene family, which has been named the PAQR family, after
two of the initially described ligands (progestin and adipoQ receptors)
[17].

References:
16. Y. Zhu, J. Bond, P. Thomas, Identification, classification, and
partial characterization of
genes in humans and other vertebrates homologous to a fish membrane
progestin receptor,
Proc. Natl. Acad. Sci. U. S. A. 100 (5) (2003) 2237-2242.
17. Y.T. Tang, T. Hu, M. Arterburn, B. Boyle, J.M. Bright, P.C. Emtage,
W.D. Funk, PAQR
proteins: a novel membrane receptor family defined by an ancient
7-transmembrane pass
motif, J. Mol. Evol. 61 (3) (2005) 372-380.


Kind regards,
Mike Cahill.


________________________________________________________
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Michael Cahill,
Chief Research Officer,
tel: +49(0)61 31-50 192 25.
fax: +49(0)61 31-50 192 11.
www.proteosys.com.



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