Hi Gilad, Please see my answers to your questions below. If you have additional questions, please reply to [email protected].
Regards, --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 8/23/2011 7:14 AM, Gilad Finkelstein wrote: > Hi Brooke, > Thank you for the helpful insights. > > I would like to clarify some internal details (I will use > the gnfMouseU74aAll as an example): > > > gnfMouseU74aAllExps has the "id" field of each tissue > > gnfMouseU74aAll has various genes (the name field ? ) run with that chip > each gets its own record each uses the expScores filed (comma delimited > blob) to store expression level for each of the above id's (i.e. id=0 is the > first value id=1 is the second one etc..) > What do the -<value> score stand for ? what is the scale ? > A negative expScore denotes underexpression, and positive values over expression, more extreme values denoting more extreme over/under expression. > I also noticed that each tissue appears twice in the table (e.g. 'testis' > and 'testis 2' ) > Is it the same probe used on 2 different tests ? Is one different from the > other or is it just two different tests run ? different conditions ? > This means there are replicates of the same tissue. You can find more information about the methods and conditions used in the published article found in the track description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=affyGnfU74A (see under 'References'). > How do I connect the gene name with that of the UCSC gene name ? > e.g. > I run SELECT * FROM `hgFixed`.`gnfMouseU74aAll` limit 1; and get > ''AFFX-MurIL2_at'' what UCSC gene is this ? > > In general, the Table Browser is a useful tool for viewing relationships between tables. From the main page, click on 'Tables' located in the top blue navigation bar. Make the following selections: clade: Mammal genome: Mouse assembly: July 2007 (NCBI37/mm9) group: Expression and Regulation track: GNF U74A table: hgFixed.gnfMouseU74aAll If you click on the 'describe table schema' button, you will find a list of all the connected tables and their joining fields. This should help you retrieve the data you want. For more information on how to use the Table Browser, please refer to our help page: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html > Can I assume gnfHumanU95Alland gnfHumanU95AllExps are the > chip similar results for humans ? > The track description can be viewed by selecting the primary table from the Table Browser (affyGnfU74A in the above example), and clicking 'describe table schema'. > Sorry for asking so many questions in one email,If there is one place > that describes the internal relations between tables and their meaning I > would be happy to do it myself if you point it to the place. > I figured the SCOP part with your help, thanks > > Gilad Finkelstein > Erez Levanon Lab > Bar-Ilan University > > > On Tue, Aug 23, 2011 at 5:46 AM, Brooke Rhead <[email protected]> wrote: > > >> Hi Gilad, >> >> There are 3 tables that contain absolute microarray expression values on >> the mm9 UCSC Genes track for the adar gene. The tracks and corresponding >> tables (which are in the hgFixed database) are: >> >> For "GNF Expression Atlas 2 Data from GNF1M Mouse Chip": >> hgFixed.knownToGnfAtlas2All >> >> For "Rinn et. al Sex Gene Expression Data on MOE430A Chip": >> hgFixed.mouseRinnSex >> >> For "GNF Expression Atlas Data from U74a Mouse Chip": >> hgFixed.gnfMouseU74aAll >> >> The SCOP domain information comes from the ucscScop and scopDesc tables. >> >> I hope this is helpful. If you have further questions, please feel free to >> contact us again at [email protected]. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> >> On 08/21/11 01:20, Gilad Finkelstein wrote: >> >> >>> Hi >>> for a list of genes: >>> 1. grab the list of absolute Microarray Expression Data value per tissue >>> 2. Intersect any gene that belong to a specific SCOP domain >>> >>> What tables will contain such information >>> I can see all the data via a simple table browser query(example for mouse >>> adar1 gene) >>> http://genome.ucsc.edu/cgi-**bin/hgGene?hgg_gene=uc008pzx.** >>> 2&hgg_prot=Q99MU3&hgg_chrom=**chr3&hgg_start=89534639&hgg_** >>> end=89557377&hgg_type=**knownGene&db=mm9&hgsid=**208225823<http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=uc008pzx.2&hgg_prot=Q99MU3&hgg_chrom=chr3&hgg_start=89534639&hgg_end=89557377&hgg_type=knownGene&db=mm9&hgsid=208225823> >>> >>> Thanks >>> Gilad Finkelstein >>> Erez Levanon Lab >>> Bar-Ilan University >>> ______________________________**_________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >>> >>> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
