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 ? 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 ? 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 ? Can I assume gnfHumanU95Alland gnfHumanU95AllExps are the chip similar results for humans ? 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
