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Sample GSM81480 Query DataSets for GSM81480
Status Public on Nov 03, 2005
Title GC (SW620 cells)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name GC (SW620 cells)
Organism Homo sapiens
Characteristics GC (SW620 cells)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20206.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 02, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3041
Series (1)
GSE3547 Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 1644 3327 220 136 1424 3191 1241 2511 225 140 1021 2375 0 0 1434 2613 52 31 92 100 88 100 4615 3396 .446 2.241 2.326 2.743 2.483 1.925 52 307 2.02 .93 90 2240 8540 24 33 106 115 0 4159 170 3989 2.801 3139 2969 .357 2.908 1.486 1.54
2 648 1076 219 133 429 943 281 273 226 135 62 140 0 0 1041 1880 61 29 50 71 32 63 1372 202 .455 2.198 2.258 1.848 1.379 4.871 52 224 2.183 .75 80 2410 8550 26 34 124 132 -50 1345 166 1179 2.748 341 175 .364 2.823 1.458 1.497
3 5779 7841 210 134 5569 7707 6166 7923 216 137 5956 7789 0 0 3021 3599 63 38 93 100 93 100 13276 13745 .723 1.384 1.308 1.704 1.363 2.077 80 441 1.316 .97 110 2540 8530 22 33 135 146 0 9801 168 9634 1.73 9904 9736 .578 1.635 .791 .709
4 1016 2421 222 160 794 2261 792 1341 225 162 570 1181 0 0 1039 2338 61 29 83 100 75 100 3055 1751 .351 2.848 2.072 3.438 3.213 2.144 12 62 2.69 .86 40 2680 8540 27 31 153 157 -100 3026 200 2826 3.56 1676 1476 .281 2.59 1.832 1.373
5 3183 4310 213 154 2970 4156 2764 4089 225 166 2551 3935 0 0 1937 2569 127 107 96 100 95 100 7126 6486 .715 1.399 1.543 1.503 1.392 1.612 80 461 1.358 .96 110 2830 8530 22 33 164 175 0 5388 193 5195 1.749 5111 4919 .572 1.928 .807 .947
6 339 535 222 157 117 378 274 301 243 175 52 144 0 0 287 718 172 144 15 50 7 28 495 196 .31 3.231 2.769 1.563 2.519 5.227 52 229 2.844 .84 80 2990 8550 26 34 182 190 -50 669 196 473 4.038 376 180 .248 3.462 2.014 1.791
7 2593 4303 215 143 2378 4160 2412 4103 222 147 2197 3960 0 0 1686 2574 58 37 92 100 90 100 6538 6157 .572 1.749 1.802 1.893 1.767 1.557 80 321 1.657 .96 110 3130 8530 22 33 194 205 0 5379 179 5200 2.187 5129 4950 .457 2.253 1.129 1.172
8 3114 4237 211 138 2903 4099 2570 3673 217 142 2359 3535 0 0 2260 2505 58 43 98 100 98 100 7002 5894 .708 1.412 1.499 1.64 1.483 1.893 80 335 1.285 .95 100 3270 8530 23 33 209 219 0 5296 173 5124 1.765 4591 4419 .567 1.873 .82 .905
9 1315 3334 213 131 1102 3203 727 1984 217 138 514 1853 0 0 1317 3286 55 35 87 100 84 100 4305 2367 .344 2.907 3.605 3.609 2.883 2.12 32 196 2.727 .96 70 3430 8540 25 32 226 233 -100 4168 164 4004 3.633 2480 2316 .275 4.506 1.861 2.172
10 2125 3627 199 129 1926 3498 929 2013 206 143 730 1884 0 0 2334 3352 57 92 91 98 88 96 5424 2614 .551 1.816 2.581 2.427 2.147 1.912 80 395 1.616 .94 110 3560 8530 22 33 237 248 0 4534 161 4373 2.27 2516 2355 .44 3.226 1.183 1.69
11 4153 6935 202 144 3951 6791 3394 5835 211 159 3192 5691 0 0 3505 5262 60 100 93 98 92 97 10742 8883 .582 1.719 1.783 1.911 1.797 1.479 80 323 1.628 .97 100 3720 8550 25 35 254 264 0 8669 180 8489 2.149 7294 7114 .465 2.229 1.103 1.156
12 2706 5695 222 167 2484 5528 1855 5548 224 178 1633 5381 0 0 2339 3890 61 64 96 100 94 100 8012 7014 .449 2.225 3.295 2.884 2.452 2.172 52 194 1.984 .89 80 3870 8520 23 31 270 278 0 7119 209 6910 2.782 6935 6726 .359 4.119 1.476 2.042
13 3745 5213 217 154 3528 5059 3341 4718 222 163 3124 4564 0 0 2660 3179 62 56 98 100 97 100 8587 7688 .697 1.434 1.461 1.643 1.449 1.64 120 451 1.342 .96 120 4010 8530 22 34 282 294 0 6516 193 6324 1.792 5898 5705 .558 1.826 .842 .869
14 4189 6875 214 151 3975 6724 3526 7874 224 159 3312 7723 0 0 3270 4304 66 61 96 100 96 100 10699 11035 .591 1.692 2.332 2.272 1.987 2.127 32 172 1.548 .94 70 4150 8540 25 32 298 305 0 8594 189 8405 2.114 9843 9654 .473 2.915 1.08 1.543
15 2903 5524 206 133 2697 5391 2003 3841 217 146 1797 3708 0 0 2697 4334 62 58 96 100 94 98 8088 5505 .5 1.999 2.063 2.255 2.048 1.857 52 232 1.846 .93 80 4300 8540 25 33 313 321 0 6905 166 6739 2.499 4801 4635 .4 2.579 1.321 1.367
16 4332 6178 211 138 4121 6040 3960 6118 230 160 3749 5980 0 0 2609 3075 149 226 97 100 97 98 10161 9729 .682 1.466 1.595 1.702 1.553 1.763 80 342 1.383 .97 110 4430 8530 22 33 324 335 0 7723 173 7550 1.832 7648 7475 .546 1.994 .873 .996
17 4671 5267 214 155 4457 5112 2887 3957 234 179 2673 3802 0 0 4387 4440 157 240 92 97 88 90 9569 6475 .872 1.147 1.422 1.464 1.272 1.76 80 297 1.072 .97 100 4570 8540 24 34 339 349 0 6584 194 6390 1.434 4946 4753 .697 1.778 .52 .83
18 2394 4712 195 151 2199 4561 1366 3274 204 153 1171 3123 0 0 2433 3726 58 37 93 100 93 100 6760 4294 .482 2.074 2.667 2.66 2.482 1.709 80 341 1.788 .96 110 4720 8540 23 34 353 364 0 5890 189 5701 2.593 4093 3904 .386 3.334 1.374 1.737
19 2784 5310 181 133 2603 5177 2290 4172 189 143 2109 4039 0 0 2393 3478 57 70 97 100 97 100 7780 6148 .503 1.989 1.915 2.487 2.263 1.706 80 359 1.762 .95 100 4860 8540 24 34 368 378 0 6638 166 6471 2.486 5215 5049 .402 2.394 1.314 1.259
20 2286 5176 176 131 2110 5045 1161 3165 180 136 985 3034 0 0 2420 4992 44 66 86 96 77 87 7155 4019 .418 2.391 3.08 3.247 2.684 2.222 80 329 2.083 .94 100 5020 8540 24 34 384 394 0 6470 164 6306 2.989 3956 3793 .335 3.85 1.58 1.945

Total number of rows: 43008

Table truncated, full table size 9460 Kbytes.




Supplementary data files not provided
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