Microarray track: Difference between revisions

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==Database Representation==
==Database Representation==
At the most basic level, the data for set of microarrays is stored in two tables:
Microarray tracks are are stored as BED 15 data.  A typical gapped BED item will have 12 fields.  The microarray, or "expRatio" BEDs are another three fields tacked on to the gapped BED. These fields are the '''expCount''', '''expIds''', and '''expScores''' fields.
#A bed 15 table, containing both the probe information and the experimental data.  The first 12 fields of this table are normal bed fields (excluding the bin field). These mainly describe the positioning of a gene or whatever item.  Fields 10-12 deal with exons.  Microarray tracks may have exons, but usually the convention is to set the blockCount=1, blockStarts=0, and blockSize=chromEnd-chromStart... i.e pretending there's only one exon.
 
##chrom
The following is an example BED 15:
##chromStart
 
##chromEnd
#chrom chromStart chromEnd name score strand thickStart thickEnd reserved blockCount blockSizes chromStarts expCount expIds expScores
##name
  chr1 159639972 159640031 2440848 500 - 159639972 159640031 0 1 59, 0, 33 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, 0.593000,1.196000,-0.190000,-1.088000,0.093000,-0.731000,0.130000,-0.008000,-1.087000,0.609000,-1.061000,-1.092000,0.807000,0.499000,-0.322000,-0.985000,0.309000,0.000000,0.812000,-0.457000,-0.560000,0.096000,0.186000,-1.092000,0.045000,0.573000,1.170000,1.336000,1.251000,1.919000,-0.056000,-0.189000,0.028000,
##score
chr1 159640161 159640190 2440849 500 - 159640161 159640190 0 1 29, 0, 33 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, -0.906000,-1.247000,0.111000,-0.515000,-0.057000,-0.892000,0.167000,1.278000,0.051000,-0.596000,-0.251000,-0.826000,0.487000,0.714000,0.674000,1.046000,0.694000,0.236000,-0.718000,-1.196000,-1.274000,-1.278000,-1.055000,0.838000,-0.494000,1.137000,0.000000,0.690000,0.166000,-0.232000,0.174000,-1.253000,1.363000,
##strand
  chr1 159640215 159640242 2440850 500 - 159640215 159640242 0 1 27, 0, 33 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, -0.465000,0.127000,1.215000,-0.073000,-0.465000,-0.141000,0.507000,-0.462000,-0.464000,0.570000,1.356000,0.559000,-0.459000,-0.464000,-0.458000,0.000000,0.322000,-0.454000,0.887000,-0.464000,1.196000,-0.463000,0.376000,-0.461000,0.547000,0.032000,-0.464000,0.066000,0.762000,-0.465000,-0.456000,0.919000,-0.464000,
##reserved/itemRGB
chr1 159640256 159640309 2440851 500 - 159640256 159640309 0 1 53, 0, 33 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, 1.779000,1.039000,-0.068000,-0.066000,-0.050000,0.665000,0.861000,-0.067000,0.000000,0.090000,-0.067000,1.240000,-0.018000,-0.068000,0.122000,0.478000,-0.068000,-0.068000,0.630000,-0.068000,0.092000,0.620000,-0.066000,-0.068000,1.601000,0.537000,1.103000,0.720000,1.959000,1.703000,-0.061000,-0.067000,1.097000,
##thickStart
chr1 159641139 159641250 2440852 300 - 159641139 159641250 0 1 111, 0, 33 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, 0.000000,1.569000,-0.090000,0.330000,-0.091000,-0.089000,0.634000,1.319000,-0.090000,-0.092000,-0.048000,-0.091000,-0.091000,0.815000,1.455000,1.127000,1.549000,0.337000,0.432000,-0.092000,-0.092000,-0.090000,0.397000,1.082000,-0.092000,-0.091000,1.780000,2.025000,1.988000,2.575000,0.224000,-0.092000,-0.092000,
##thickEnd
chr1 159642074 159642102 2440853 500 - 159642074 159642102 0 1 28, 0, 33 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, 2.204000,-1.053000,-0.756000,1.135000,0.393000,0.366000,-0.730000,-0.113000,-1.179000,1.079000,-1.194000,-1.195000,-0.675000,1.124000,0.382000,-1.196000,0.313000,-0.380000,0.244000,-0.258000,2.070000,1.312000,-1.195000,1.901000,-1.191000,0.438000,-1.195000,1.096000,1.635000,0.232000,-0.440000,0.528000,0.000000,
##blockCount
chr1 159642586 159642611 2363661 600 + 159642586 159642611 0 1 25, 0, 33 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, 0.486000,0.065000,0.897000,-0.566000,-1.169000,-1.547000,-0.266000,0.370000,-0.864000,-0.802000,1.214000,-0.240000,0.269000,-0.067000,0.375000,0.258000,0.366000,-0.275000,0.965000,0.785000,0.571000,0.511000,0.759000,0.658000,-0.196000,-0.055000,-0.017000,-0.411000,-0.450000,-1.028000,0.104000,-0.228000,-0.000000,
##blockSizes
chr1 159642702 159642762 2363662 600 + 159642702 159642762 0 1 60, 0, 33 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, -0.772000,-0.532000,0.061000,-1.913000,-2.283000,-1.696000,-0.062000,0.200000,-0.609000,-2.054000,-1.184000,-2.465000,0.746000,0.673000,0.316000,0.041000,1.147000,0.590000,0.963000,0.919000,0.914000,0.000000,0.224000,-0.077000,0.395000,1.124000,0.690000,-0.369000,-1.427000,-0.970000,0.297000,0.335000,1.471000,
##blockStarts
chr1 159642857 159642883 2363663 200 + 159642857 159642883 0 1 26, 0, 33 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, 0.434000,-1.679000,-1.102000,0.529000,0.435000,0.614000,0.000000,0.175000,-1.517000,-1.148000,-0.180000,-1.379000,-0.798000,-0.163000,-0.219000,-1.936000,0.183000,0.627000,-0.933000,0.446000,1.150000,-2.162000,-0.018000,0.191000,1.351000,1.378000,-0.941000,0.743000,-1.632000,-0.415000,0.800000,-0.165000,1.257000,
##'''expCount'''
chr1 159642959 159642988 2363664 600 + 159642959 159642988 0 1 29, 0, 33 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, 0.000000,0.018000,-0.061000,-1.540000,-1.477000,-1.977000,-0.058000,-0.430000,-0.293000,-1.256000,-1.060000,-1.701000,0.715000,0.978000,0.980000,1.190000,1.248000,0.974000,0.907000,1.145000,0.782000,-0.152000,0.218000,-0.109000,1.550000,1.126000,1.537000,0.023000,-0.140000,-0.728000,0.520000,0.605000,0.597000,
##'''expIds'''
chr1 159643028 159643054 2363665 600 + 159643028 159643054 0 1 26, 0, 33 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, 0.291000,-0.093000,0.000000,-1.483000,-1.041000,-1.644000,0.219000,-0.189000,-0.466000,-0.942000,-0.832000,-1.026000,0.565000,0.868000,0.813000,0.786000,0.793000,0.574000,0.773000,0.764000,0.568000,-0.291000,-0.055000,-0.103000,0.916000,0.970000,0.993000,-0.106000,-0.230000,-0.402000,0.310000,0.433000,0.563000,
##'''expScores'''
 
#An [[expRecord]] table containing details concerning each of the experiments outlined in the bed 15 table.
The '''expCount''' field says how many microarrays the track is using.  The '''expIds''' field is used to link microarray labels to the microarray measurements in the '''expScores''' field.  The microarray labeling information is not found in the BED 15 at all, rather it's part of the microarray configuration.  Also, the '''expCount''' and '''expIds''' fields are constant across all rows, which may seem like a waste of space, but in theory the BED 15 spec allows more flexibility than it is actually given by its implementation in the browser.


==trackDb Settings==
==trackDb Settings==
==Example==
Microarray tracks in the browser must have several specific trackDb settings.  The following is an example trackDb entry of a microarray track:
 
track affyHumanExon
shortLabel Affy All Exon
longLabel Affymetrix All Exon Chips
group regulation
priority 79.1
visibility hide
type expRatio
expScale 3.0
expStep 0.5
groupings affyHumanExonGroups
 
The important settings are:'''type''', '''expScale''', '''expStep''', and '''groupings'''.  "type expRatio" is what indicates to the browser that the track's data is a microarray.  The expScale is a reflection of the dynamic range of the data, and is an absolute value.  This effects the coloring of the track.  An expScale of 3.0 will mean that most of the data is between -3.0 and 3.0 and that the brightest green will be used for values less than or equal to -3.0 and the brightest red for values greater than or equal to 3.0.  The expStep value controls the color key step values on the deatils page.  '''groupings''' sets the specific set of configurations to load from the '''microarrayGroups.ra''' file(s). 
 
==micrarrayGroups.ra==
==Microarray Custom Tracks==
==Microarray Custom Tracks==
The microarray custom track format is similar to a normal BED custom track format with the addition of some parameters to the "track" header.
The microarray custom track format is similar to a normal BED custom track format with the addition of some parameters to the "track" header.


[[Category:Technical FAQ]]
[[Category:Technical FAQ]]

Revision as of 01:00, 24 October 2006

This document attempts to explain the microarray tracks on the browser in pretty extensive detail. The gene sorter has a somewhat different strategy for microarrays.

Database Representation

Microarray tracks are are stored as BED 15 data. A typical gapped BED item will have 12 fields. The microarray, or "expRatio" BEDs are another three fields tacked on to the gapped BED. These fields are the expCount, expIds, and expScores fields.

The following is an example BED 15: 

#chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts	expCount	expIds	expScores
chr1	159639972	159640031	2440848	500	-	159639972	159640031	0	1	59,	0,	33	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,	0.593000,1.196000,-0.190000,-1.088000,0.093000,-0.731000,0.130000,-0.008000,-1.087000,0.609000,-1.061000,-1.092000,0.807000,0.499000,-0.322000,-0.985000,0.309000,0.000000,0.812000,-0.457000,-0.560000,0.096000,0.186000,-1.092000,0.045000,0.573000,1.170000,1.336000,1.251000,1.919000,-0.056000,-0.189000,0.028000,
chr1	159640161	159640190	2440849	500	-	159640161	159640190	0	1	29,	0,	33	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,	-0.906000,-1.247000,0.111000,-0.515000,-0.057000,-0.892000,0.167000,1.278000,0.051000,-0.596000,-0.251000,-0.826000,0.487000,0.714000,0.674000,1.046000,0.694000,0.236000,-0.718000,-1.196000,-1.274000,-1.278000,-1.055000,0.838000,-0.494000,1.137000,0.000000,0.690000,0.166000,-0.232000,0.174000,-1.253000,1.363000,
chr1	159640215	159640242	2440850	500	-	159640215	159640242	0	1	27,	0,	33	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,	-0.465000,0.127000,1.215000,-0.073000,-0.465000,-0.141000,0.507000,-0.462000,-0.464000,0.570000,1.356000,0.559000,-0.459000,-0.464000,-0.458000,0.000000,0.322000,-0.454000,0.887000,-0.464000,1.196000,-0.463000,0.376000,-0.461000,0.547000,0.032000,-0.464000,0.066000,0.762000,-0.465000,-0.456000,0.919000,-0.464000,
chr1	159640256	159640309	2440851	500	-	159640256	159640309	0	1	53,	0,	33	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,	1.779000,1.039000,-0.068000,-0.066000,-0.050000,0.665000,0.861000,-0.067000,0.000000,0.090000,-0.067000,1.240000,-0.018000,-0.068000,0.122000,0.478000,-0.068000,-0.068000,0.630000,-0.068000,0.092000,0.620000,-0.066000,-0.068000,1.601000,0.537000,1.103000,0.720000,1.959000,1.703000,-0.061000,-0.067000,1.097000,
chr1	159641139	159641250	2440852	300	-	159641139	159641250	0	1	111,	0,	33	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,	0.000000,1.569000,-0.090000,0.330000,-0.091000,-0.089000,0.634000,1.319000,-0.090000,-0.092000,-0.048000,-0.091000,-0.091000,0.815000,1.455000,1.127000,1.549000,0.337000,0.432000,-0.092000,-0.092000,-0.090000,0.397000,1.082000,-0.092000,-0.091000,1.780000,2.025000,1.988000,2.575000,0.224000,-0.092000,-0.092000,
chr1	159642074	159642102	2440853	500	-	159642074	159642102	0	1	28,	0,	33	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,	2.204000,-1.053000,-0.756000,1.135000,0.393000,0.366000,-0.730000,-0.113000,-1.179000,1.079000,-1.194000,-1.195000,-0.675000,1.124000,0.382000,-1.196000,0.313000,-0.380000,0.244000,-0.258000,2.070000,1.312000,-1.195000,1.901000,-1.191000,0.438000,-1.195000,1.096000,1.635000,0.232000,-0.440000,0.528000,0.000000,
chr1	159642586	159642611	2363661	600	+	159642586	159642611	0	1	25,	0,	33	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,	0.486000,0.065000,0.897000,-0.566000,-1.169000,-1.547000,-0.266000,0.370000,-0.864000,-0.802000,1.214000,-0.240000,0.269000,-0.067000,0.375000,0.258000,0.366000,-0.275000,0.965000,0.785000,0.571000,0.511000,0.759000,0.658000,-0.196000,-0.055000,-0.017000,-0.411000,-0.450000,-1.028000,0.104000,-0.228000,-0.000000,
chr1	159642702	159642762	2363662	600	+	159642702	159642762	0	1	60,	0,	33	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,	-0.772000,-0.532000,0.061000,-1.913000,-2.283000,-1.696000,-0.062000,0.200000,-0.609000,-2.054000,-1.184000,-2.465000,0.746000,0.673000,0.316000,0.041000,1.147000,0.590000,0.963000,0.919000,0.914000,0.000000,0.224000,-0.077000,0.395000,1.124000,0.690000,-0.369000,-1.427000,-0.970000,0.297000,0.335000,1.471000,
chr1	159642857	159642883	2363663	200	+	159642857	159642883	0	1	26,	0,	33	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,	0.434000,-1.679000,-1.102000,0.529000,0.435000,0.614000,0.000000,0.175000,-1.517000,-1.148000,-0.180000,-1.379000,-0.798000,-0.163000,-0.219000,-1.936000,0.183000,0.627000,-0.933000,0.446000,1.150000,-2.162000,-0.018000,0.191000,1.351000,1.378000,-0.941000,0.743000,-1.632000,-0.415000,0.800000,-0.165000,1.257000,
chr1	159642959	159642988	2363664	600	+	159642959	159642988	0	1	29,	0,	33	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,	0.000000,0.018000,-0.061000,-1.540000,-1.477000,-1.977000,-0.058000,-0.430000,-0.293000,-1.256000,-1.060000,-1.701000,0.715000,0.978000,0.980000,1.190000,1.248000,0.974000,0.907000,1.145000,0.782000,-0.152000,0.218000,-0.109000,1.550000,1.126000,1.537000,0.023000,-0.140000,-0.728000,0.520000,0.605000,0.597000,
chr1	159643028	159643054	2363665	600	+	159643028	159643054	0	1	26,	0,	33	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,	0.291000,-0.093000,0.000000,-1.483000,-1.041000,-1.644000,0.219000,-0.189000,-0.466000,-0.942000,-0.832000,-1.026000,0.565000,0.868000,0.813000,0.786000,0.793000,0.574000,0.773000,0.764000,0.568000,-0.291000,-0.055000,-0.103000,0.916000,0.970000,0.993000,-0.106000,-0.230000,-0.402000,0.310000,0.433000,0.563000,

The expCount field says how many microarrays the track is using. The expIds field is used to link microarray labels to the microarray measurements in the expScores field. The microarray labeling information is not found in the BED 15 at all, rather it's part of the microarray configuration. Also, the expCount and expIds fields are constant across all rows, which may seem like a waste of space, but in theory the BED 15 spec allows more flexibility than it is actually given by its implementation in the browser.

trackDb Settings

Microarray tracks in the browser must have several specific trackDb settings. The following is an example trackDb entry of a microarray track: 

track affyHumanExon
shortLabel Affy All Exon
longLabel Affymetrix All Exon Chips
group regulation
priority 79.1
visibility hide
type expRatio
expScale 3.0
expStep 0.5
groupings affyHumanExonGroups

The important settings are:type, expScale, expStep, and groupings. "type expRatio" is what indicates to the browser that the track's data is a microarray. The expScale is a reflection of the dynamic range of the data, and is an absolute value. This effects the coloring of the track. An expScale of 3.0 will mean that most of the data is between -3.0 and 3.0 and that the brightest green will be used for values less than or equal to -3.0 and the brightest red for values greater than or equal to 3.0. The expStep value controls the color key step values on the deatils page. groupings sets the specific set of configurations to load from the microarrayGroups.ra file(s).

micrarrayGroups.ra

Microarray Custom Tracks

The microarray custom track format is similar to a normal BED custom track format with the addition of some parameters to the "track" header.

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