Schema for gnfAtlas2

Database: rn4 Primary Table: gnfAtlas2 Row Count: 7,663 Data last updated: 2006-04-11
Format description: Browser extensible data with 15 fields including experiment values
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	602	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	2286521	`int(10) unsigned`	range	Start position in chromosome
`chromEnd`	2287076	`int(10) unsigned`	range	End position in chromosome
`name`	rc_AA800177_at	`varchar(255)`	values	Name of item
`score`	962	`int(10) unsigned`	range	Score from 0-1000
`strand`	-	`char(1)`	values	+ or -
`thickStart`	2286521	`int(10) unsigned`	range	Start of where display should be thick (start codon)
`thickEnd`	2287076	`int(10) unsigned`	range	End of where display should be thick (stop codon)
`itemRgb`	0	`int(10) unsigned`	range	Used as itemRgb as of 2004-11-22
`blockCount`	2	`int(10) unsigned`	range	Number of blocks
`blockSizes`	122,433,	`longblob`		Comma separated list of block sizes
`chromStarts`	0,122,	`longblob`		Start positions relative to chromStart
`expCount`	44	`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`	0.248000,0.321000,-3.527000...	`longblob`		Comma separated list of experiment scores

To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.

Connected Tables and Joining Fields


	hgFixed.gnfRatAtlas2Median.expScores (gnfAtlas2.expScores and gnfRatAtlas2Median.expScores are arrays sharing an index) hgFixed.gnfRatAtlas2MedianExps.id (which is an array index into gnfAtlas2.expScores) hgFixed.gnfRatAtlas2MedianRatio.expScores (gnfAtlas2.expScores and gnfRatAtlas2MedianRatio.expScores are arrays sharing an index) hgFixed.gnfRatAtlas2All.name (via gnfAtlas2.name) hgFixed.gnfRatAtlas2AllRatio.name (via gnfAtlas2.name) hgFixed.gnfRatAtlas2Median.name (via gnfAtlas2.name) hgFixed.gnfRatAtlas2MedianRatio.name (via gnfAtlas2.name) rn4.affyU34A.qName (via gnfAtlas2.name)

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts	expCount	expIds	expScores
602	chr1	2286521	2287076	rc_AA800177_at	962	-	2286521	2287076	0,0,0	2	122,433,	0,122,	44	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,	0.248000,0.321000,-3.527000,-0.176000,-0.003000,-1.024000,-3.027000,0.516000,0.002000,-0.786000,-0.049000,-0.077000,0.464000,-3. ...
602	chr1	2289144	2304638	M26686_g_at	994	-	2289144	2304638	0,0,0	11	165,6,114,100,23,217,86,121,105,32,105,	0,166,173,287,387,4692,6523,7196,11243,14188,15389,	44	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,	0.021000,0.233000,-2.712000,0.699000,-2.040000,-1.095000,-2.055000,1.005000,0.018000,0.363000,0.009000,0.313000,0.505000,-0.0360 ...
602	chr1	2289144	2304638	M26686_at	994	-	2289144	2304638	0,0,0	11	165,6,114,100,23,217,86,121,105,32,105,	0,166,173,287,387,4692,6523,7196,11243,14188,15389,	44	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,	0.146000,-0.356000,-1.143000,0.755000,1.870000,-0.294000,-1.109000,-0.935000,-0.046000,-0.003000,0.266000,1.450000,-0.367000,-0. ...
603	chr1	2436934	2437433	rc_AA875420_at	1000	-	2436934	2437433	0,0,0	1	499,	0,	44	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,	0.895000,-1.051000,-1.091000,-0.783000,1.411000,-0.182000,-0.629000,0.077000,0.186000,-0.005000,0.294000,1.378000,-0.383000,0.65 ...
603	chr1	2438842	2439403	rc_AA799680_at	986	-	2438842	2439403	0,0,0	1	561,	0,	44	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,	-0.252000,0.406000,1.497000,0.165000,-2.973000,-0.666000,1.786000,-0.210000,0.007000,1.944000,-0.033000,-1.357000,-0.438000,1.57 ...
611	chr1	3435309	3435803	rc_AI639310_at	996	-	3435309	3435803	0,0,0	1	494,	0,	44	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,	0.071000,0.145000,-2.315000,-0.993000,1.933000,-0.696000,-1.072000,-0.196000,-1.112000,-1.034000,-0.043000,1.306000,-0.512000,1. ...
77	chr1	4428181	4579373	U92072_at	1000	-	4428181	4579373	0,0,0	27	180,221,112,166,370,240,51,66,152,17,33,179,221,41,68,148,73,155,79,124,84,64,135,101,82,98,503,	0,1971,6699,8350,8843,10038,17199,28915,38455,40519,40586,46662,47278,52925,53197,53484,57339,58575,70460,79931,81881,85837,8721 ...	44	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,	-0.013000,0.769000,-0.452000,0.447000,0.854000,0.259000,-0.995000,0.485000,-0.257000,-0.573000,-0.289000,0.652000,0.374000,0.454 ...
78	chr1	5318616	5744590	M61099_at	998	-	5318616	5744590	0,0,0	10	2818,960,931,127,169,247,236,250,1018,55,	0,2818,32689,48582,56890,62290,98679,296482,423556,425919,	44	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,	0.373000,1.086000,-2.293000,-0.123000,-0.091000,0.483000,-2.293000,-0.239000,2.163000,-2.293000,1.534000,0.255000,-0.839000,-2.2 ...
9	chr1	7099845	7614980	AJ002967_at	996	-	7099845	7614980	0,0,0	75	260,23,93,109,241,159,66,66,39,137,112,167,158,86,202,75,62,61,79,147,269,130,157,173,190,155,206,118,206,76,150,136,176,151,173 ...	0,3719,9282,10861,13646,14233,20663,21759,22028,27730,41430,44486,47090,51470,61535,69285,71123,81178,84730,88089,93320,113946,1 ...	44	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,	-0.211000,-0.292000,-0.272000,-0.198000,0.917000,0.151000,-0.532000,0.149000,0.023000,0.106000,-0.240000,0.686000,-0.227000,1.02 ...
639	chr1	7147008	7171026	AB011666_s_at	998	-	7147008	7171026	0,0,0	5	85,86,202,75,58,	0,4307,14372,22122,23960,	44	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,	1.012000,-0.730000,-0.357000,-0.382000,1.960000,-1.125000,-1.236000,0.167000,0.000000,0.239000,-0.444000,1.782000,-0.386000,0.63 ...

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

Description

Credits

References