[Genome] UCSC homologene

[Fungazid]

Hi Ann,

I'm still contemplating to commit sin ( ;-) ): to use
the NCBI homologene database. I saw that in the case
of dog (for example) most genes and their products are
gene bank predictions like 
XP_544872.2 	XM_544872.2 
Can I find cross link to this specific sort of
annotations in UCSC tables? 

Many thanks, Avi


--- Ann Zweig <ann at soe.ucsc.edu> wrote:

> Hello again Avi,
> 
> 	We have only created BlastTab tables with pairwise
> orthologs between the seven 
> organisms that I listed in my previous email.  Your
> best bet for viewing the 
> relationship between the mouse and the dog (or
> opossum) is to use the Chain/Net 
> tracks.  In the mouse genome browser, turn on the
> Chain and Net tracks to the 
> Dog (or Opossum).
> 
> 	The Dog Chain track in the mouse browser shows
> alignments of dog (canFam2, May 
> 2005) to the mouse genome using a gap scoring system
> that allows longer gaps 
> than traditional affine gap scoring systems. It can
> also tolerate gaps in both 
> dog and mouse simultaneously. These "double-sided"
> gaps can be caused by local 
> inversions and overlapping deletions in both
> species.
> 
> 	You can read about the details behind this or any
> track (description, methods, 
> display, credits, references) by pressing on the
> 'mini-button' to the left of 
> the actual track display, or by clicking on the
> hyperlinked track name in the 
> track controls (below the display).
> 
> 	As for question 2, you are correct: query is the
> species in this database (in 
> this case, hg18), and target is the species to which
> it is aligned (in this 
> case, mm9).
> 
> 	The kgXref tables in each database give several
> aliases for each gene ID.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> 
> 
> Fungazid wrote:
> > Ann, 
> > thank you for your nice help, I must say .I have
> > another 2 related questions (I hope it is not too
> > detailed )
> > 
> > 1)
> > what do you mean by: "For more distant 
> > species reciprocal-best BLASTP hits are used." ??
> For
> > example how can I find the target gene of dog or
> > opossum, for a query mouse gene?
> > 
> > 2)
> > About the mmBlastTab table in hg18 database: 
> > As far as I understand:
> > a.	'query' field = the name of human gene, 
> > b.	'target' = the name of the homologous gene is
> mouse
> > c.	hg18 and mm8 kgXref  tables give aliases to the
> > query and taget gene names respectively.
> > I hope this is right
> > 
> > Thank you again, Avi
> > 
> > 
> > --- Ann Zweig <ann at soe.ucsc.edu> wrote:
> > 
> >> Hello Avi,
> >>
> >> 	We have several data sets available that show
> >> homologous genes.
> >>
> >> 	The BlastTab tables show pairwise orthologs
> between
> >> the following 
> >> organisms:
> >>
> >> organism	tableName
> >> --------	---------
> >> human		hgBlastTab
> >> mouse		mmBlastTab
> >> rat		rnBlastTab
> >> zebrafish	drBlastTab
> >> D. melanogaster	dmBlastTab
> >> C. elegans	ceBlastTab
> >> S. cerevisiae	scBlastTab
> >>
> >> 	Orthologies between human, mouse, and rat are
> >> computed by taking the 
> >> best BLASTP hit, and filtering out non-syntenic
> >> hits. For more distant 
> >> species reciprocal-best BLASTP hits are used.
> >>
> >> 	The Conservation tracks show multiple alignments
> of
> >> a number of species 
> >> along with measures of evolutionary conservation.
> 
> >> For example, the 
> >> Conservation track on the latest human assembly
> >> (hg18), shows alignment 
> >> with 27 other vertebrates.
> >>
> >> 	You can read about the details behind any track
> >> (description, methods, 
> >> display, credits, references) by pressing on the
> >> 'mini-button' to the 
> >> left of the actual track display, or by clicking
> on
> >> the hyperlinked 
> >> track name in the track controls (below the
> >> display).
> >>
> >> 	You can use the Table Browser tool on our
> website
> >> ('Tables' from the 
> >> top blue navigation bar) to view the contents of
> >> tables.  Alternatively, 
> >> you can download tables from our download sever
> >> here: 
> >> http://hgdownload.cse.ucsc.edu/downloads.html
> >>
> >> 	This should be enough to get you started. 
> Please
> >> don't hesitate to 
> >> contact the mail list again if you require
> further
> >> assistance.
> >>
> >>
> >> Regards,
> >>
> >> ----------
> >> Ann Zweig
> >> UCSC Genome Bioinformatics Group
> >> http://genome.ucsc.edu
> >>
> >> Please feel free to search the Genome mailing
> list
> >> archives by visiting 
> >> our home page, clicking on "Contact Us", then
> typing
> >> a word or phrase 
> >> into the search box.  On that same page 
> >> (http://genome.ucsc.edu/contacts.html), you can
> >> subscribe to the Genome 
> >> mailing list.
> >>
> >>
> >> Fungazid wrote:
> >>  > I would like to ask 2 questions:
> >>  >
> >>  > 1) Is there UCSC-tables that group homologous
> >> genes ?
> >>  > More specifically, tables that group together
> >> genes
> >>  > that their conservation is measured at the
> >> protein
> >>  > level, or mRNA level.
> >>  > for example, the table should look like:
> >>  >
> >>  > groupNumber gene species
> >>  > 1 NM_001011874 mm8
> >>  > 1 NM_001011971 rn4
> >>  > 1 NM_052898 gh18
> >>  > ...
> >>  >
> >>  > + some conservations measures
> >>  >
> >>  >
> >>  > 2) There are similar tables in homologene
> >> database:
> >>  >
> >>  >
> >>
> >
>
http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene&cmd=search&term=
> >>  >
> >>  > Is there a way to link these tables to UCSC
> >> refGene
> >>  > tables, or similar UCSC gene tables?
> >>  >
> >>  > Many thanks, Avi
> >>  >
> >>  >
> >>  >
> >>  > 
> >>
> 
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