Schema for Sestan Brain - Sestan Lab Human Brain Atlas Microarrays |
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Database: hg19 Primary Table: sestanBrainAtlas Row Count: 877,469 Data last updated: 2010-08-05
Format description: Browser extensible data with 15 fields including experiment values
On download server: MariaDB table dump directory
| field | example | SQL type | description |
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| bin | 585 | smallint(5) unsigned | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | Reference sequence chromosome or scaffold |
| chromStart | 17120 | int(10) unsigned | Start position in chromosome |
| chromEnd | 17183 | int(10) unsigned | End position in chromosome |
| name | 2390568 | varchar(255) | Name of item |
| score | 0 | int(10) unsigned | Score from 0-1000 |
| strand | - | char(1) | + or - |
| thickStart | 17120 | int(10) unsigned | Start of where display should be thick (start codon) |
| thickEnd | 17183 | int(10) unsigned | End of where display should be thick (stop codon) |
| reserved | 0 | int(10) unsigned | Used as itemRgb as of 2004-11-22 |
| blockCount | 1 | int(10) unsigned | Number of blocks |
| blockSizes | 63 | longblob | Comma separated list of block sizes |
| chromStarts | 0, | longblob | Start positions relative to chromStart |
| expCount | 95 | int(10) unsigned | 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 | 0.418087,0.0955225,-0.47721... | longblob | Comma separated list of experiment scores |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | expCount | expIds | expScores |
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| 585 | chr1 | 17120 | 17183 | 2390568 | 0 | - | 17120 | 17183 | 0 | 1 | 63 | 0, | 95 | 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, ... | 0.418087,0.0955225,-0.477212,0.048923,-0.11261,-0.00196759,-0.776883,-0.314675,-0.195021,-0.743863,-0.295264,0.246773,1.24955,0. ... |
| 585 | chr1 | 17773 | 17910 | 2390574 | 0 | - | 17773 | 17910 | 0 | 1 | 137 | 0, | 95 | 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, ... | 0.690635,0.486202,0.423499,0.884233,0.404309,0.331875,1.22238,0.301079,-1.20858,-0.590146,0.877455,0.446346,1.09318,1.03443,0.27 ... |
| 585 | chr1 | 20238 | 20569 | 2390583 | 0 | - | 20238 | 20569 | 0 | 1 | 331 | 0, | 95 | 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, ... | 0.46975,-0.0634109,-0.764968,-0.134139,-0.582812,0.12378,-0.411052,-0.24772,-0.231436,-0.0418302,0.00751018,-0.466981,-0.133858, ... |
| 585 | chr1 | 52937 | 53068 | 2315131 | 0 | + | 52937 | 53068 | 0 | 1 | 131 | 0, | 95 | 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, ... | 0.15461,0.153974,0.0585965,0.152897,0.289199,0.0544073,0.0269655,0.0782757,0.170236,0.0551895,0.0102747,-0.00221387,0.307787,0.0 ... |
| 585 | chr1 | 63655 | 63697 | 2315133 | 0 | + | 63655 | 63697 | 0 | 1 | 42 | 0, | 95 | 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, ... | -0.480028,-1.40917,1.02369,0.124988,-0.790176,-0.614593,0.80978,0.259849,-0.632662,-0.630657,-0.314529,1.06793,-1.05945,-0.49194 ... |
| 585 | chr1 | 65535 | 65562 | 2315127 | 0 | + | 65535 | 65562 | 0 | 1 | 27 | 0, | 95 | 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, ... | 0.199905,0.0705677,0.0714879,-0.0983097,1.0886,0.0768147,-0.157092,0.714312,-0.0502537,0.0415264,0.0293931,0.144555,1.02098,0.37 ... |
| 585 | chr1 | 72304 | 72329 | 2390608 | 0 | - | 72304 | 72329 | 0 | 1 | 25 | 0, | 95 | 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, ... | -0.744522,-0.444655,-0.660479,1.05819,-0.35042,-0.643859,-0.168487,-0.146599,-0.0573659,-0.0717206,-0.726033,-0.933364,-0.252574 ... |
| 585 | chr1 | 96016 | 96637 | 2390641 | 0 | - | 96016 | 96637 | 0 | 1 | 621 | 0, | 95 | 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, ... | -1.12888,0.0686169,0.252342,1.2987,0.438521,0.0983189,0.00691155,-0.376695,0.423217,0.206014,0.346476,0.798898,0.855954,-0.50327 ... |
| 585 | chr1 | 98718 | 98982 | 2390643 | 0 | - | 98718 | 98982 | 0 | 1 | 264 | 0, | 95 | 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, ... | 0.0790222,-0.0536098,-0.274069,-0.00633079,0.267683,0.26805,0.28586,0.629358,0.0556511,0.00499217,-0.456561,-0.150463,0.397546,0 ... |
| 585 | chr1 | 115847 | 115991 | 2315146 | 0 | + | 115847 | 115991 | 0 | 1 | 144 | 0, | 95 | 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, ... | 0.00248418,-0.493508,0.902987,1.21268,0.802198,-1.2349,-1.32232,-1.4095,0.636576,0.352459,0.369951,0.482456,0.256,-0.476361,-0.3 ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Sestan Brain (sestanBrainAtlas) Track Description
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Description
This track displays exon microarray expression data from the late mid-fetal
human brain, generated by the Sestan Lab at Yale University. The data represent
13 brain regions, including nine areas of neocortex, and both hemispheres. By
default, arrays are grouped by the median for each brain region, including each
neocortical area. Alternatively, neocortex areas can be grouped together;
arrays can be grouped by mean; or all 95 arrays can be shown individually.
Methods
RNA was isolated from 13 brain regions, from both hemispheres, of four late
mid-fetal human brains, with a total PMI of less than one hour, and hybridized
to Affymetrix Human Exon 1.0 ST arrays. Affymetrix CEL files were imported into
Partek GS using Robust Multichip Average (RMA) background correction, quantile
normalization, and GC content correction. The normalized data were then
converted to log-ratios, relative to arrays hybridized with RNA pooled from all
regions of the same brain. Signal log-ratios are displayed here as green for
negative (underexpression) and red for positive (overexpression).
The probe set for this microarray track can be displayed by turning on the
Affy HuEx 1.0 track. Core, extended, and full probe sets are shown.
"Bounded" probe sets - exons that lie within the intron of more than
one gene - and potentially cross-hybridizing probe sets were filtered from this
dataset, leaving ~875K probe sets.
Credits
The data for this track were generated and analyzed by Matthew B. Johnson,
Yuka Imamura Kawasawa, Christopher Mason, and the
Yale Neuroscience Microarray Center.
Links
The raw microarray data are available via the
NCBI Gene Expression
Omnibus.
More information is available at
https://hbatlas.org/.
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