[Genome] Genome Browser Questions

[Brooke Rhead]

Hello Jiyeon,

There are currently two sets of Conservation / Most Conserved tracks on 
our human March 2006 (hg18) browser.  One set consists a 17-way 
alignment, and the other (newer) set consists of a 28-way alignment. 
The 28-way alignment tracks are simply called "Conservation" and "Most 
Conserved", while the 17-way has "17-way" in the titles.  The 28-way 
tracks have two sets of scores: one for all 28 species, and one for only 
the placental mammals.

I looked at your region of interest, chr7:154945993-154947619.  While 
there is nothing in the 17-way Most Conserved track, there is a highly 
conserved region visible in the 28-way Most Conserved track, in both the 
placental mammals and the full 28-way subtracks.

If you would like to get this data from the Table Browser hit the 
"Tables" link at the top of the page and make the following selections:

clade: vertebrate
genome: human
assembly: mar. 2006
group: comparative genomics
track: most conserved
table: choose either mammal (phastConsElements28wayPlacMammal) or 
vertebrate (phastConsElements28way)
region: choose "position" and enter your region of interest
output format: all fields from selected table

Hit "get output".  You should get the region visible in the Most 
Conserved track in the Genome Browser.  Note that coordinates retrieved 
from the Table Browser have a 0-based start, not a 1-based start, as 
explained here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1.

I hope this information is helpful.  If you have further questions, 
please do not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



choi at cabm.rutgers.edu wrote:
> Dear colleague:
> 
> We are requesting help in attaining some bioinformatic information about
> sequence surrounding two human SNPs, rs1861972, and rs1861973.  These SNPs
> map to distal chromosome 7 in the intron of the ENGRAILED 2 (EN2) gene.
> 
> We have previously demonstrated that these 2 SNPs are significantly
> associated with Autism Spectrum Disorder (Gharani et al. Mol Psychiatry.
> 2004 May;9(5):474-84, Benayed et al. Am J Hum Genet. 2005
> Nov;77(5):851-68).
> 
> We are now preparing a manuscript that demonstrates these two SNPs are
> functional, affecting the transcriptional regulation of EN2. A part of the
> manuscript explores the evolutionary conservation of the area surrounding
> these SNPs.
> 
>>From "17-Way Most Cons Track Settings" at genome.ucsc.edu, it is possible
> to attain lod and score values for different portions of EN2 that are
> evolutionarily conserved.  For example, there is one area of the intron
> that is ~2kb 5’ of rs1861972 and rs1861973 that is highly conserved
> between 11 mammalian species (chr7:154945604-154945685; score = 483;
> lod=147).
> 
> We would like to attain similar values for the ~1.6kb chromosomal region
> encompassing rs1861972 and rs1861973 (chr7:154945993-154947619).  Is this
> possible?
> 
> Thank you for your time
> 
> Jiyeon Choi
> Dr. Millonig lab, UMDNJ
> 
> 
> 
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