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Sample GSM3817 Query DataSets for GSM3817
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 57
Sample type RNA
 
Channel 1
Source name Non-transformed plants
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Plants that overexpress PK12
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description RNA was extracted from plants that overexpress PK12 and from non-transformed plants. Plants were grown for 10 days under long day conditions. Hybridization was performed on an array from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K Arabidopsis ESTs. Data in this platform contains 4 repetitions including 2 independent biological experiments.
Keywords = alternative splicing
Keywords = phosphorylation
 
Submission date Feb 02, 2003
Last update date May 27, 2005
Contact name Robert Fluhr
E-mail(s) robert.fluhr@weizmann.ac.il
Phone 972-8-9342175
Organization name Weizmann Institute of Science
Department Plant Sciences
Street address
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL242
Series (1)
GSE274 Overexpression of the plant LAMMER kinase PK12

Data table header descriptions
ID_REF
VALUE log ratio of PRE_VALUE
ch1 Intensity Channel 1 average (mean) of intensities
ch1 Background Channel1 background
ch1 Intensity Std Dev Channel 1 Intensity standard deviation
ch1 Background Std Dev Channel 1 background standard deviation
ch1 Diameter Channel 1 diameter of the spot
ch1 Area Number of pixels used when calculating spot intensity
ch1 Footprint Channel 1 distance between the expect position of a spot and its actual measurment position
ch1 Circularity The degree to which a spot matches a perfect circle in channel 1
ch1 Spot Uniformity The uniformity of pixels used in the spot intensity calculation in channel 1
ch1 Bkg. Uniformity The uniformity of pixels used in the local background intensity calculation in channel 1
ch1 Signal Noise Ratio The ratio of the spot intensity to the standart deviation of the local background of all spots
ch1 Confidence channel1 Confidence
ch2 Intensity Channel 2 average (mean) of intensities
ch2 Background Channel2 background
ch2 Intensity Std Dev Channel 2 Intensity standard deviation
ch2 Background Std Dev Channel 2 background standard deviation
ch2 Diameter Channel 2 diameter of the spot
ch2 Area Number of pixels used when calculating spot intensity
ch2 Footprint Channel 2 distance between the expect position of a spot and its actual measurment position
ch2 Circularity The degree to which a spot matches a perfect circle in channel 2
ch2 Spot Uniformity The uniformity of pixels used in the spot intensity calculation in channel 2
ch2 Bkg. Uniformity The uniformity of pixels used in the local background intensity calculation in channel 2
ch2 Signal Noise Ratio The ratio of the spot intensity to the standart deviation of the local background of all spots
ch2 Confidence channel2 Confidence
Ignore Filter Ignore Filter
PRE_VALUE Each gene's measured intensity was divided by its control channel value in each sample. When the control channel value was below 10.0 the data point was considered bad. The 50th percentile of all measurements was used as a positive control for each sample. Each measurement for each gene was divided by this synthetic positive control, assuming that this was at least 0.01. The bottom tenth percentile was used as a test for correct background subtraction.

Data table
ID_REF VALUE ch1 Intensity ch1 Background ch1 Intensity Std Dev ch1 Background Std Dev ch1 Diameter ch1 Area ch1 Footprint ch1 Circularity ch1 Spot Uniformity ch1 Bkg. Uniformity ch1 Signal Noise Ratio ch1 Confidence ch2 Intensity ch2 Background ch2 Intensity Std Dev ch2 Background Std Dev ch2 Diameter ch2 Area ch2 Footprint ch2 Circularity ch2 Spot Uniformity ch2 Bkg. Uniformity ch2 Signal Noise Ratio ch2 Confidence Ignore Filter PRE_VALUE
1 0.3310223 109.707184 0 152.495163 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 250.276245 0 298.969391 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 1 2.143
2 0.2780673 279.823212 0 277.977905 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 564.928162 0 401.738861 0 198.511383 18100 2.510102 0.885381 0.986313 1 3.40E+38 1 1 1.897
3 -0.2806693 29881.52539 0 6734.082031 0 153.683441 18100 2.510102 0.982049 0.87529 1 3.40E+38 1 16670.64648 0 4227.969238 0 153.683441 18100 2.510102 0.975802 0.89325 1 3.40E+38 1 1 0.524
4 -0.0467243 13639.86719 0 3274.918945 0 153.890411 18100 2.510102 0.933177 0.888214 1 3.40E+38 1 13031.09961 0 3193.486084 0 155.536346 18100 2.510102 0.955307 0.892792 1 3.40E+38 1 1 0.898
5 0.1734783 192.331497 0 238.623993 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 305.265198 0 343.892334 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 1 1.491
6 0.2132523 1789.237549 7.309091 553.028503 19.110664 176.799423 18100 2.510102 0.944837 0.978088 1 93.625084 1 3141.016602 42.763638 923.098572 63.594772 173.34491 18100 2.510102 0.955893 0.953674 0.99971 49.391113 1 1 1.634
7 -0.2380723 444.773468 0 320.896851 0 191.49231 18100 2.510102 0.920656 0.993256 1 3.40E+38 1 273.828735 0 300.822998 0 203.108276 18100 2.510102 0.785398 1 1 3.40E+38 1 1 0.578
8 0.3585063 961.762451 0 649.924194 0 189.487106 18100 2.510102 0.924964 0.971146 1 3.40E+38 1 2339.663086 2.818182 1522.675903 9.355313 182.992371 18100 2.510102 0.937882 0.903595 1 250.089229 1 1 2.283
9 -0.3279023 54790.0625 8.218182 9911.192383 21.657854 153.268631 18100 2.510102 0.963564 0.873215 1 2529.801073 1 27432.93359 7.345455 8273.819336 17.082825 156.556274 18100 2.510102 0.936378 0.661469 1 1605.878071 1 1 0.47
10 0.1061913 13660.74609 0 4114.32373 0 158.576431 18100 2.510102 0.92079 0.862808 1 3.40E+38 1 18562.25391 0 5111.381348 0 163.712234 18100 2.510102 0.929001 0.826675 1 3.40E+38 1 1 1.277
11 0.0759123 7022.59668 0 1604.700806 0 161.952896 18100 2.510102 0.938155 0.946655 1 3.40E+38 1 8902.756836 0 2196.560303 0 156.962387 18100 2.510102 0.960456 0.920746 1 3.40E+38 1 1 1.191
12 -0.0109953 1735.646362 46.418182 687.401917 71.263641 182.469788 18100 2.510102 0.942758 0.959045 0.999451 24.355286 1 1762.856323 9.872727 752.66748 25.582874 185.583237 18100 2.510102 0.929074 0.962448 1 68.907672 1 1 0.975
13 -0.4412913 10131.47559 276.927277 1330.766724 352.8992 172.054718 18100 2.510102 0.966451 0.939194 0.986481 28.709262 1 3940.425293 142.363632 887.441284 178.825836 177.159134 18100 2.510102 0.962766 0.956268 0.994949 22.034989 1 1 0.362
14 -0.0241093 3250.74585 63.854546 735.222961 101.408859 182.64415 18100 2.510102 0.933565 0.965591 0.996689 32.055837 1 3284.790039 76.054543 1000.63446 118.897156 182.295258 18100 2.510102 0.943847 0.948868 0.999313 27.627154 1 1 0.946
15 0.1212313 6282.149414 17.654545 1182.016602 34.25407 159.776276 18100 2.510102 0.949198 0.947372 1 183.398626 1 8819.253906 2.218182 1715.762085 5.886868 157.367447 18100 2.510102 0.916378 0.933975 1 1498.123143 1 1 1.322
16 -0.3362993 2711.044189 0 988.262207 0 166.794159 18100 2.510102 0.918859 0.976791 1 3.40E+38 1 1330 0 735.333496 0 192.982544 18100 2.510102 0.811735 0.973709 1 3.40E+38 1 1 0.461
17 0.0476643 1063.325928 0 570.432129 0 187.630173 18100 2.510102 0.85209 0.989182 1 3.40E+38 1 1263.060791 0 801.248596 0 190.492355 18100 2.510102 0.852127 0.979111 1 3.40E+38 1 1 1.116
18 -0.1301823 6548.348145 0 2473.069092 0 169.256897 18100 2.510102 0.900457 0.940079 1 3.40E+38 1 5167.519531 0 1899.244751 0 175.896927 18100 2.510102 0.858631 0.951492 1 3.40E+38 1 1 0.741
19 0.3261313 2247.441895 0 1166.704712 0 168.124725 18100 2.510102 0.91813 0.948593 1 3.40E+38 1 5067.790039 0 2485.893311 0 161.756226 18100 2.510102 0.885138 0.911194 1 3.40E+38 1 1 2.119
20 -0.4100503 2499.160156 0 981.214417 0 177.876389 18100 2.510102 0.926538 0.960464 1 3.40E+38 1 1034.066284 0 665.601013 0 191.990341 18100 2.510102 0.924557 0.975616 1 3.40E+38 1 1 0.389

Total number of rows: 11964

Table truncated, full table size 2329 Kbytes.




Supplementary data files not provided

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