Hi Raj, Thank you for the additional details. Here is a previously-answered mailing list question that explains how the values in the various UCSC gnfAtlas2 tables were calculated:
https://lists.soe.ucsc.edu/pipermail/genome/2007-January/012631.html If this does not answer your questions, please feel free to write back to [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 06/10/09 14:40, Raj wrote: > Hi Brooke, > > More info. This probe, which in UCSC data appears highly expressed in > some tissues, has "absent calls" in all 79 samples on the GNF site data. This probe is also shown diagramatically at the GNF site here: > http://biogps.gnf.org/?referer=symatlas#goto=genereport&id=3008, > which is generated from the original dataset. You can see from the diagram that the expression values for this probe are all generally smaller than 10, which means they do not express at all. This contrasts this probe's data on the UCSC site which is showing it to be highly expressed in some tissues (with expressed values in several hundreds). > > Thanks, > > Raj > > > --- On Thu, 6/11/09, Raj <[email protected]> wrote: > >> From: Raj <[email protected]> >> Subject: Re: [Genome] GNF Atlas 2 data >> To: "Brooke Rhead" <[email protected]> >> Cc: [email protected] >> Date: Thursday, June 11, 2009, 2:48 AM >> Thanks for reverting back Brooke. >> Here is the link of the original dataset (Human U133A + >> GNF1H (gcRMA-condensed) GeneAtlas (7M)): >> >> http://wombat.gnf.org/downloads/gnf1h,gcrma.zip or can >> be navigated from the main page: http://wombat.gnf.org/index.html >> >> In addition to my previous question, I don't quite >> understand what exact operations UCSC-GB has done to >> transform the original GNF data (in record #1 below) to >> various other forms (records #2, #3, #4 below) (for clarity >> I am copying the records again): >> >> 1. From GNF (Novartis) site (one value for each of the 79 >> tissues (probably avergaed over the two measurement?) - >> looks like raw scores?) >> 208553_at 8.3 6.3 6.55 5.35 6.35 6.55 5.1 8.05 6.4 6.9 7.8 >> 7.75 9.8 8.85 8.35 8 8.9 7.35 7.8 9.65 5.55 6.85 5 5.1 6.05 >> 6.7 4.6 6.7 6.75 5.7 5.9 5.4 6.5 7.15 4.8 8.1 6.5 6.45 6.5 >> 7.65 5.9 8.2 8.75 6.15 5.75 5.35 4.45 4.95 7 6.45 7.4 6.8 >> 6.2 7.65 7.4 5.9 6.9 5.4 7.65 6.65 6.4 5.7 6.05 6.25 5.3 >> 6.65 5.65 5.95 6.15 6.8 7.65 6.45 6.75 5.6 5.6 7.1 5.65 6.95 >> 5.6 >> >> 2. UCSC Table: gnfHumanAtlas2All (2 measurements each in 79 >> tissues) >> 208553_at 158 >> 38,15,27,48,201,25,361,23,156,491,383,420,49,328,76,68,664,406,330,139,331,224,58,42,217,53,62,28,38,23,25,100,324,191,53,30,29,49,15,56,67,29,96,72,93,54,25,34,110,81,118,24,38,25,25,69,17,15,82,36,59,32,13,55,22,29,76,70,16,32,120,29,208,18,86,37,26,42,31,23,48,24,30,38,66,48,63,45,53,68,31,30,38,44,59,28,22,31,38,95,25,26,34,21,18,85,58,29,17,28,17,38,35,13,75,81,47,23,253,23,55,131,88,18,82,18,24,46,40,95,19,61,16,32,60,28,24,91,19,79,29,50,47,53,29,68,55,34,110,60,69,108,26,43,23,22,72,83, >> >> 3. UCSC Table: gnfHumanAtlas2AllRatio (2 measurements each >> in 79 tissues) >> 208553_at 158 >> >> -0.291,-2.217,-0.784,0.046,2.112,-0.895,2.957,-1.016,1.746,3.400,3.042,3.175,0.076,2.818,0.709,0.548,3.836,3.126,2.827,1.580,2.832,2.268,0.319,-0.147,2.222,0.189,0.415,-0.732,-0.291,-1.016,-0.895,1.105,2.801,2.038,0.189,-0.632,-0.681,0.076,-2.217,0.268,0.527,-0.681,1.046,0.631,1.000,0.216,-0.895,-0.452,1.242,0.801,1.343,-0.954,-0.291,-0.895,-0.895,0.569,-2.217,-2.217,0.818,-0.369,0.343,-0.539,-2.217,0.242,-1.080,-0.681,0.709,0.590,-2.217,-0.539,1.368,-0.681,2.161,-2.217,0.887,-0.330,-0.839,-0.147,-0.585,-1.016,0.046,-0.954,-0.632,-0.291,0.505,0.046,0.438,-0.047,0.189,0.548,-0.585,-0.632,-0.291,-0.080,0.343,-0.732,-1.080,-0.585,-0.291,1.031,-0.895,-0.839,-0.452,-1.147,-2.217,0.870,0.319,-0.681,-2.217,-0.732,-2.217,-0.291,-0.410,-2.217,0.690,0.801,0.015,-1.016,2.444,-1.016,0.242,1.494,0.920,-2.217,0.818,-2.217,-0.954,-0.016,-0.217,1.031,-2.217,0.392,-2.217,-0.539,0.368,-0.732,-0.954,0.969,-2.217,0.765,-0.681,0.105,0.015,0.189,-0.681,0.548,0.242,-0.452,1. >> 242,0.368,0.569,1.216,-0.839,-0.113,-1.016,-1.080,0.631,0.836, >> >> 4. UCSC Table: gnfAtlas2 (one value for each of the 79 >> tissues (probably averaged over the two measurements in the >> same tissue)) >> 785 chr6 26264597 26265257 208553_at 998 + 26264597 >> 26265257 0 1 660, 0, 79 >> 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78, >> >> -0.454000,-2.217000,-0.673000,0.224000,0.649000,-0.881000,0.278000,-0.593000,0.195000,-0.988000,-1.378000,0.344000,-0.028000,-0.163000,1.022000,-1.048000,-0.493000,-0.098000,-0.800000,-0.726000,-0.288000,-0.105000,-0.067000,-0.222000,-0.303000,-0.975000,0.608000,0.839000,0.609000,2.204000,2.550000,-0.369000,2.573000,0.970000,3.108000,1.447000,0.629000,3.481000,0.086000,1.206000,-0.159000,-0.653000,0.105000,2.420000,-1.254000,-0.182000,0.008000,-1.254000,0.370000,-0.833000,0.734000,-0.462000,-0.913000,-0.185000,-0.485000,-1.314000,0.746000,0.102000,0.196000,-0.673000,0.805000,-0.476000,-0.181000,-0.194000,0.892000,0.407000,-1.474000,-0.867000,0.276000,-0.609000,-0.077000,0.369000,-0.799000,-0.501000,0.714000,0.868000,-0.649000,-0.700000,-1.378000, >> >> Thanks a lot, >> >> Raj >> >> >> >> --- On Thu, 6/11/09, Brooke Rhead <[email protected]> >> wrote: >> >>> From: Brooke Rhead <[email protected]> >>> Subject: Re: [Genome] GNF Atlas 2 data >>> To: "Raj" <[email protected]> >>> Cc: [email protected] >>> Date: Thursday, June 11, 2009, 12:30 AM >>> Hello Raj, >>> >>> Can you please point me to the location of the gene >>> expression record on the GNF site? >>> >>> -- >>> Brooke Rhead >>> UCSC Genome Bioinformatics Group >>> >>> >>> On 06/10/09 10:33, Raj wrote: >>>> Hi, >>>> >>>> Below are two gene expression records >> representing the >>> same probe. >>> However, the UCSC website record (shown below as >> record 1) >>> is completely >>> different from the original GNF website record (shown >> below >>> as record >>> 2). The two record values appear to be raw form. >> Looking at >>> this data, >>> the probe appears to be expressing in the UCSC >> record, >>> while it is not >>> in the GNF record. >>>> Can somebody explain why there is this >> discrepancy? >>>> 1. UCSC Table: >>>> clade: Mammal >>>> genome: Human >>>> assembly: Mar. 2006 >>>> group: Expression >>>> track: GNF Atlas 2 >>>> table: gnfHumanAtlas2All >>>> 208553_at 158 >> 38,15,27,48,201,25,361,23,156,491,383,420,49,328,76,68,664,406,330,139,331,224,58,42,217,53,62,28,38,23,25,100,324,191,53,30,29,49,15,56,67,29,96,72,93,54,25,34,110,81,118,24,38,25,25,69,17,15,82,36,59,32,13,55,22,29,76,70,16,32,120,29,208,18,86,37,26,42,31,23,48,24,30,38,66,48,63,45,53,68,31,30,38,44,59,28,22,31,38,95,25,26,34,21,18,85,58,29,17,28,17,38,35,13,75,81,47,23,253,23,55,131,88,18,82,18,24,46,40,95,19,61,16,32,60,28,24,91,19,79,29,50,47,53,29,68,55,34,110,60,69,108,26,43,23,22,72,83, >>>> >>>> 2. From GNF (Novartis) site >>>> 208553_at 8.3 >>> 6.3 6.55 >>> 5.35 6.35 >>> 6.55 5.1 >>> 8.05 6.4 >>> 6.9 7.8 >>> 7.75 9.8 >>> 8.85 8.35 >>> 8 8.9 >>> 7.35 7.8 >>> 9.65 5.55 >>> 6.85 5 >>> 5.1 6.05 >>> 6.7 4.6 >>> 6.7 6.75 >>> 5.7 5.9 >>> 5.4 6.5 >>> 7.15 4.8 >>> 8.1 6.5 >>> 6.45 6.5 >>> 7.65 5.9 >>> 8.2 8.75 >>> 6.15 5.75 >>> 5.35 4.45 >>> 4.95 7 >>> 6.45 7.4 >>> 6.8 6.2 >>> 7.65 7.4 >>> 5.9 6.9 >>> 5.4 7.65 >>> 6.65 6.4 >>> 5.7 6.05 >>> 6.25 5.3 >>> 6.65 5.65 >>> 5.95 6.15 >>> 6.8 7.65 >>> 6.45 6.75 >>> 5.6 5.6 >>> 7.1 5.65 >>> 6.95 5.6 >>>> Thanks, >>>> >>>> Raj >>>> >>>> >>>> >>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> >> > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
