Schema for GNF Atlas 2 - GNF Expression Atlas 2 |
|---|
| |
Database: hg38 Primary Table: gnfAtlas2 Row Count: 38,238
Format description: Browser extensible data with 15 fields including experiment values
| field | example | SQL type | info | description |
|---|
| bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 14969 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 15039 | int(10) unsigned | range | End position in chromosome |
| name | gnf1h03908_s_at | varchar(255) | values | Name of item |
| score | 1000 | int(10) unsigned | range | Score from 0-1000 |
| strand | - | char(1) | values | + or - |
| thickStart | 14969 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 15039 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| reserved | 0 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
| blockCount | 1 | int(10) unsigned | range | Number of blocks |
| blockSizes | 70, | longblob | | Comma separated list of block sizes |
| chromStarts | 0, | longblob | | Start positions relative to chromStart |
| expCount | 79 | int(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 |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | expCount | expIds | expScores |
|---|
| 585 | chr1 | 14969 | 15039 | gnf1h03908_s_at | 1000 | - | 14969 | 15039 | 0 | 1 | 70, | 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, ... | 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,- ... |
| 585 | chr1 | 16934 | 17273 | gnf1h01690_s_at | 996 | - | 16934 | 17273 | 0 | 1 | 339, | 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, ... | 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 ... |
| 585 | chr1 | 21411 | 21998 | gnf1h07742_at | 968 | + | 21411 | 21998 | 0 | 5 | 25,77,48,25,77, | 0,56,238,326,510, | 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, ... | 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 ... |
| 585 | chr1 | 24347 | 24723 | gnf1h03342_at | 996 | - | 24347 | 24723 | 0 | 1 | 376, | 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, ... | 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 ... |
| 585 | chr1 | 63332 | 63788 | gnf1h04689_at | 1000 | + | 63332 | 63788 | 0 | 1 | 456, | 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, ... | -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, ... |
| 586 | chr1 | 132022 | 132195 | gnf1h11145_s_at | 984 | + | 132022 | 132195 | 0 | 2 | 74,38, | 0,135, | 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, ... | -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. ... |
| 586 | chr1 | 132947 | 133643 | gnf1h03516_x_at | 980 | - | 132947 | 133643 | 0 | 2 | 116,74, | 0,622, | 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, ... | -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 ... |
| 586 | chr1 | 183694 | 186385 | gnf1h03907_at | 990 | - | 183694 | 186385 | 0 | 3 | 397,69,69, | 0,1796,2622, | 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, ... | -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 ... |
| 586 | chr1 | 185490 | 185560 | gnf1h03908_s_at | 1000 | - | 185490 | 185560 | 0 | 1 | 70, | 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, ... | 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,- ... |
| 586 | chr1 | 187456 | 187795 | gnf1h01690_s_at | 990 | - | 187456 | 187795 | 0 | 1 | 339, | 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, ... | 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
| |
|
|
|