Hello Kathleen, There are 76 distinct tissues with two replicates per experiment, which brings the number of values = 158 scores. The order of the tissues is in the gnfHumanAtlas2AllExps.id field, the tissue names are in the gnfHumanAtlas2AllExps.name field.
For example, gnfHumanAtlas2AllExps.id =0 or =1, the first two fields are: id name 0 ColorectalAdenocarcinoma 1 ColorectalAdenocarcinoma 2 This replication per-tissue is explained in the track's description page (open Assembly browser and click on track name - or - open the Table browser to the track, leave the primary table as-is, click on "describe table schema", then scroll to the bottom on the page. Hopefully this addresses your questions, but please let us know if you need more information, Jen --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/30/10 5:49 AM, kathleen askland wrote: > I have recently downloaded human expression data via UCSC genome Table > Browser using the following query parameters: Mammal, human, Assembly: > Feb 2009(GRCh37/hg19), Group: Expression, Track: GNFAtlas2, Table: > hgFixed.gnfHumanAtlas2All, as I wanted all available replicates > available for each probe. > > However, the file output is very difficult to understand. There were > 44775 probes (as expected) for which data are available. Each probe > has a corresponding 'hgFixed.gnfHumanAtlas2All.expCount' value= 158, > suggesting there should be 158 expression values per probe and, in > fact, the column headed 'hgFixed.gnfHumanAtlas2All.expScores' does in > fact contain 158 comma-separated absolute expression values. > > However, I am not able to obtain the EXP ids (i.e., tissue name) > associated with each of the 158 expression values in the sequence so > how is one supposed to figure out which tissue each of the 158 > expression scores corresponds to? > > I have attempted to obtain those expression IDs in several ways, by > selecting different associated tables to join and seemingly relevant > variables to no avail. Moreover, even more confusingly, when I select > from associated table gnfHumanAtlas2MedianExps the variables > 'hgFixed.gnfHumanAtlas2AllExps.id' and > 'hgFixed.gnfHumanAtlas2AllExps.name' which would seem like the desired > information, I get a series of comma-separated EXP ids and the > corresponding EXP id tissue names (e.g., 112 and Pancreas, > respectively), but there are generally not 158 entries in each of > these cells and many probes have 'n/a' in both columns. > > So, for example, probe '1007_s_at' has the following associated data: > hgFixed.gnfHumanAtlas2All.expCount='158', > hgFixed.gnfHumanAtlas2All.expScores= > '3621,3212,1078,1130,475,408,375,528,...' (158 distinct values > comma-separated) > hgFixed.gnfHumanAtlas2AllExps.id= '112' > hgFixed.gnfHumanAtlas2AllExps.name='Pancreas' > > While probe '117_at' gives: > hgFixed.gnfHumanAtlas2All.expCount='158', > hgFixed.gnfHumanAtlas2All.expScores= > '338,277,2383,2456,617,423,...'(158 comma-separated values) > hgFixed.gnfHumanAtlas2AllExps.id= '52,74,75,85,94,96,98,112,121,127,129,137,' > hgFixed.gnfHumanAtlas2AllExps.name='cerebellum,CingulateCortex,CingulateCortex > 2,Lung 2,Uterus,Thyroid,fetalThyroid,Pancreas,TestisGermCell > 2,salivarygland 2,trachea 2,skin 2,' > > Since the number of expression values listed under > 'hgFixed.gnfHumanAtlas2All.expScores' does not correspond to the > number of Expression IDs/names listed under > 'hgFixed.gnfHumanAtlas2AllExps.id' and > 'hgFixed.gnfHumanAtlas2AllExps.name', respectively, how is one > supposed to figure out which tissue each of the 158 expression scores > corresponds to? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
