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Sample GSM3816 Query DataSets for GSM3816
Status Public on Feb 05, 2003
Title Overexpression of the plant LAMMER kinase PK12 56
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 28, 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 -0.44 79.41 0 127.17 0 203.1 16300 14.66 0.78 1 1 3.40E+38 1 18.29 0 40.37 0 203.1 16300 14.66 0.78 1 1 3.40E+38 1 1 0.35
2 0.01 163.53 0 208.46 0 203.1 16300 11.1 0.78 1 1 3.40E+38 1 126.49 0 167.59 0 203.1 16300 11.1 0.78 1 1 3.40E+38 1 1 1.02
3 -0.02 10970.2 0 2726.47 0 162.73 16300 41.16 0.86 0.94 1 3.40E+38 1 8313.5 0 1736.1 0 157.36 16300 41.16 0.93 0.96 1 3.40E+38 1 1 0.94
4 -0.03 9605.93 68.98 1815.91 108.58 164.29 16300 41.26 0.94 0.92 0.99 88.46 1 6653.4 5.18 1307.59 14.53 160.76 16300 41.26 0.95 0.95 1 457.67 1 1 0.91
5 -0.24 565.64 0 751.78 0 203.1 16300 41.16 0.78 1 1 3.40E+38 1 245.65 0 368.38 0 202.95 16300 41.16 0.79 1 1 3.40E+38 1 1 0.57
6 -0.02 1228.01 0 479.04 0 191.15 16300 22.15 0.87 0.98 1 3.40E+38 1 918.51 0 363.66 0 183.51 16300 22.15 0.9 0.98 1 3.40E+38 1 1 0.95
7 -0.5 245.2 0 249.9 0 203.1 16300 14.66 0.78 1 1 3.40E+38 1 44.85 0 81.24 0 203.1 16300 14.66 0.78 1 1 3.40E+38 1 1 0.31
8 0.04 920.77 0 641.65 0 194.95 16300 11.1 0.85 0.97 1 3.40E+38 1 749.01 0 586.89 0 191.65 16300 11.1 0.87 0.98 1 3.40E+38 1 1 1.12
9 -0.26 21554.34 783.34 6308.07 1002.02 170 16300 11.73 0.95 0.74 0.98 21.51 1 8426.36 234.49 2587.83 348.24 183.86 16300 11.73 0.9 0.81 0.98 24.19 1 1 0.54
10 0.16 7024.62 115.23 1183.75 164.26 176.97 16300 11.61 0.95 0.95 0.99 42.76 1 7456.77 189.92 1362.32 251.61 172.23 16300 11.61 0.94 0.94 0.99 29.63 1 1 1.44
11 0.16 3428.3 0 899.34 0 173.89 16300 27.96 0.91 0.97 1 3.40E+38 1 3794.6 0 884.41 0 164.48 16300 27.96 0.93 0.97 1 3.40E+38 1 1 1.44
12 -0.11 846.75 0 461.65 0 184.03 16300 31.46 0.87 0.98 1 3.40E+38 1 538.96 0 278.74 0 188.13 16300 31.46 0.91 0.99 1 3.40E+38 1 1 0.76
13 -0.4 6342.66 1.61 1379.77 5.54 158.97 16300 27.96 0.94 0.95 1 1142.94 1 1941.67 0 583.11 0 162.14 16300 27.96 0.96 0.98 1 3.40E+38 1 1 0.39
14 -0.15 1452.81 0 753.09 0 195.92 16300 24.97 0.86 0.98 1 3.40E+38 1 692.52 0 444.71 0 182.64 16300 24.97 0.94 0.99 1 3.40E+38 1 1 0.7
15 0.04 4003.68 0 1246.53 0 153.26 16300 13.89 0.95 0.97 1 3.40E+38 1 3464.87 0 976.33 0 155.33 16300 13.89 0.94 0.98 1 3.40E+38 1 1 1.1
16 -0.37 1365.66 0 678.74 0 187.12 16300 11.61 0.89 0.98 1 3.40E+38 1 438.07 0 256.04 0 180.71 16300 11.61 0.87 0.99 1 3.40E+38 1 1 0.42
17 -0.08 487.27 0 356.46 0 194.13 16300 11.25 0.91 0.99 1 3.40E+38 1 317.45 0 254.21 0 203.1 16300 11.25 0.78 1 1 3.40E+38 1 1 0.83
18 -0.19 3878.76 0 1272.07 0 158.77 16300 9.47 0.95 0.96 1 3.40E+38 1 1815.36 0 600.61 0 162.14 16300 9.47 0.94 0.98 1 3.40E+38 1 1 0.63
19 0.1 1062.12 0 607.66 0 190.82 16300 9.02 0.91 0.98 1 3.40E+38 1 965.81 0 480.11 0 172.23 16300 9.02 0.92 0.98 1 3.40E+38 1 1 1.26
20 -0.57 2205.84 0.78 922.63 4.45 194.78 16300 26.7 0.84 0.96 1 495.22 1 593.4 0 518.8 0 191.82 16300 26.7 0.86 0.99 1 3.40E+38 1 1 0.26

Total number of rows: 11964

Table truncated, full table size 1610 Kbytes.




Supplementary data files not provided
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