Schema for GNF Atlas 2 - GNF Expression Atlas 2
  Database: hg38    Primary Table: gnfAtlas2    Row Count: 38,238   Data last updated: 2015-01-09
Format description: Browser extensible data with 15 fields including experiment values
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 14969int(10) unsigned range Start position in chromosome
chromEnd 15039int(10) unsigned range End position in chromosome
name gnf1h03908_s_atvarchar(255) values Name of item
score 1000int(10) unsigned range Score from 0-1000
strand -char(1) values + or -
thickStart 14969int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 15039int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned range Number of blocks
blockSizes 70,longblob   Comma separated list of block sizes
chromStarts 0,longblob   Start positions relative to chromStart
expCount 79int(10) unsigned range Number of experiment values
expIds 0,1,2,3,4,5,6,7,8,9,10,11,1...longblob   Comma separated list of experiment IDs
expScores 0.77,-0.508,0.222,0.081,-0....longblob   Comma separated list of experiment scores

Connected Tables and Joining Fields
        hgFixed.gnfHumanAtlas2Median.expScores (gnfAtlas2.expScores and gnfHumanAtlas2Median.expScores are arrays sharing an index)
      hgFixed.gnfHumanAtlas2MedianExps.id (which is an array index into gnfAtlas2.expScores)
      hgFixed.gnfHumanAtlas2MedianRatio.expScores (gnfAtlas2.expScores and gnfHumanAtlas2MedianRatio.expScores are arrays sharing an index)
      hg38.affyGnf1h.qName (via gnfAtlas2.name)
      hg38.knownToGnfAtlas2.value (via gnfAtlas2.name)
      hgFixed.gladHumESOtherData.name (via gnfAtlas2.name)
      hgFixed.gnfHumanAtlas2All.name (via gnfAtlas2.name)
      hgFixed.gnfHumanAtlas2AllRatio.name (via gnfAtlas2.name)
      hgFixed.gnfHumanAtlas2Median.name (via gnfAtlas2.name)
      hgFixed.gnfHumanAtlas2MedianRatio.name (via gnfAtlas2.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStartsexpCountexpIdsexpScores
585chr11496915039gnf1h03908_s_at1000-14969150390170,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.77,-0.508,0.222,0.081,-0.041,0.685,-0.11,-0.265,-0.021,-0.58,0.684,0.209,-0.53,0.326,-0.407,-0.007,-0.033,0.164,0.458,-2.659,- ...
585chr11693417273gnf1h01690_s_at996-169341727301339,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.114,0.418,-0.121,-0.084,-0.075,0.305,-0.379,0.726,-0.064,0.091,-0.123,-0.588,-0.434,0.319,-0.236,-0.09,0.091,0.248,0.112,-0.57 ...
585chr12141121998gnf1h07742_at968+21411219980525,77,48,25,77,0,56,238,326,510,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.007,0.415,-0.019,-0.324,-0.436,-0.753,-0.6,0.185,-0.174,-0.004,-0.102,-1.014,-0.361,-0.7,-0.806,-0.688,-0.873,-0.466,-0.535,-0 ...
585chr12434724723gnf1h03342_at996-243472472301376,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.186,-0.401,-0.019,-0.168,-1.087,-0.837,-0.16,0.375,0.576,-0.41,-0.36,-0.948,0.192,-1.441,-0.241,0.207,0.074,-0.279,-0.632,0.14 ...
585chr16333263788gnf1h04689_at1000+633326378801456,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-0.281,0.323,-0.014,-0.285,-0.389,-0.034,0.361,0.541,0.087,-0.083,-0.267,-0.89,0.573,0.222,0.342,0.319,0.259,0.036,0.059,-0.263, ...
586chr1132022132195gnf1h11145_s_at984+1320221321950274,38,0,135,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-0.585,1.732,-0.585,0.254,-0.585,-0.585,-0.585,-0.585,0.516,-0.085,-0.585,0.319,-0.585,-0.585,2.283,0.551,-0.585,-0.585,0.433,0. ...
586chr1132947133643gnf1h03516_x_at980-13294713364302116,74,0,622,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-0.352,-0.002,0.163,-0.399,-0.091,-0.238,-0.28,-0.163,0.369,-0.291,-0.16,-1.022,-0.477,-0.44,0.154,-0.16,0.019,-0.529,-2.014,0.7 ...
586chr1183694186385gnf1h03907_at990-18369418638503397,69,69,0,1796,2622,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...-1.792,-0.37,-0.178,-1.059,1.201,-1.091,0.006,-0.429,-0.184,-1.036,0.028,0.132,0.954,-1.637,2.245,0.618,-0.236,-0.242,-1.075,0.6 ...
586chr1185490185560gnf1h03908_s_at1000-1854901855600170,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.77,-0.508,0.222,0.081,-0.041,0.685,-0.11,-0.265,-0.021,-0.58,0.684,0.209,-0.53,0.326,-0.407,-0.007,-0.033,0.164,0.458,-2.659,- ...
586chr1187456187795gnf1h01690_s_at990-18745618779501339,0,790,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45, ...0.114,0.418,-0.121,-0.084,-0.075,0.305,-0.379,0.726,-0.064,0.091,-0.123,-0.588,-0.434,0.319,-0.236,-0.09,0.091,0.248,0.112,-0.57 ...

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GNF Atlas 2 (gnfAtlas2) Track Description
 

Description

This track shows expression data from the GNF Gene Expression Atlas 2. This contains two replicates each of 79 human tissues run over Affymetrix microarrays. By default, averages of related tissues are shown. Display all tissues by selecting "All Arrays" from the "Combine arrays" menu on the track settings page. As is standard with microarray data red indicates overexpression in the tissue, and green indicates underexpression. You may want to view gene expression with the Gene Sorter as well as the Genome Browser.

Credits

Thanks to the Genomics Institute of the Novartis Research Foundation (GNF) for the data underlying this track.

References

Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. PMID: 15075390; PMC: PMC395923