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Sample GSM81488 Query DataSets for GSM81488
Status Public on Nov 03, 2005
Title GC (HFI-1 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 (HFI-1 cells)
Organism Homo sapiens
Characteristics GC (HFI-1 cells)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19049.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) array@genome.stanford.edu
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 GPL3039
Series (2)
GSE3547 Comprehensive analysis of the gene expression profiles in human gastric cancer cell lines
GSE3921 Embryonic stem cells and pluripotent germ cell tumors

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
1 790 895 359 193 431 702 777 877 366 195 418 684 0 0 227 221 86 42 93 100 81 100 1133 1102 .614 1.629 1.636 1.802 1.552 1.722 80 406 1.548 .85 100 2010 8630 106 116 104 114 0 861 186 675 1.566 843 658 .639 1.573 .647 .654
2 1912 1171 372 189 1540 982 1675 969 386 193 1303 780 0 0 957 767 111 42 100 100 93 100 2522 2083 1.568 .638 .599 .582 .683 2.064 32 123 .665 .86 60 2160 8640 109 115 121 127 0 1126 182 944 .613 932 750 1.631 .576 -.706 -.797
3 7460 9425 375 197 7085 9228 7731 9675 377 202 7356 9478 0 0 2114 2817 66 51 100 100 100 100 16313 16834 .768 1.302 1.288 1.293 1.307 1.158 80 286 1.323 .98 110 2290 8630 105 116 131 142 0 9063 189 8873 1.252 9303 9113 .798 1.239 .325 .309
4 671 690 368 188 303 502 396 240 370 194 28 52 0 0 696 945 67 49 38 51 23 36 805 80 .604 1.657 1.857 1.04 1.057 3.515 80 236 1.42 .93 100 2400 8620 105 115 143 153 -50 663 181 483 1.593 231 50 .628 1.786 .672 .837
5 3518 4155 342 182 3176 3973 3737 4403 349 186 3395 4221 0 0 958 1173 69 43 100 100 100 100 7149 7616 .799 1.251 1.243 1.255 1.267 1.237 80 342 1.262 .98 110 2540 8620 104 115 156 167 0 3995 175 3820 1.203 4234 4059 .831 1.195 .266 .258
6 1801 2110 325 182 1476 1928 1663 2238 335 186 1338 2056 0 0 869 1129 62 43 100 100 100 100 3404 3394 .766 1.306 1.537 1.224 1.126 1.569 12 87 1.301 .92 50 2680 8630 108 113 173 178 0 2029 175 1854 1.256 2152 1977 .796 1.478 .329 .563
7 4085 4071 342 176 3743 3895 4237 4138 345 186 3895 3962 0 0 1080 1039 68 71 100 100 100 100 7638 7857 .961 1.041 1.017 1.061 1.03 1.256 80 291 1.021 .97 100 2810 8620 105 115 184 194 0 3914 169 3745 1.001 3979 3810 .999 .978 .001 -.032
8 1783 739 334 175 1449 564 1819 779 345 181 1485 604 0 0 461 188 74 51 100 98 100 98 2013 2089 2.569 .389 .407 .381 .39 1.47 80 271 .373 .92 100 2940 8620 105 115 197 207 0 711 168 542 .374 749 581 2.672 .391 -1.418 -1.354
9 2119 2074 350 169 1769 1905 2145 1882 359 174 1795 1713 0 0 1160 1124 81 51 100 100 96 100 3674 3508 .929 1.077 .954 1.191 1.042 1.679 52 195 1.039 .95 80 3080 8630 107 115 212 220 0 1994 163 1832 1.035 1810 1647 .966 .918 .05 -.124
10 678 501 334 161 344 340 700 499 339 166 366 338 0 0 161 129 73 46 95 98 88 95 684 704 1.012 .988 .923 1.037 .98 1.752 80 276 .883 .84 100 3210 8610 104 114 224 234 0 482 155 327 .95 480 325 1.052 .888 -.073 -.171
11 8806 1124 332 156 8474 968 8723 1096 336 161 8391 940 0 0 1743 246 71 39 100 100 100 100 9442 9331 8.754 .114 .112 .113 .111 1.279 80 293 .111 .95 110 3350 8620 104 115 237 248 0 1081 150 931 .11 1054 904 9.104 .108 -3.187 -3.215
12 1446 1952 337 164 1109 1788 1329 1850 343 165 992 1686 0 0 549 756 74 39 97 100 97 100 2897 2678 .62 1.612 1.7 1.73 1.593 1.516 80 263 1.574 .95 100 3490 8620 105 115 252 262 0 1877 158 1719 1.55 1779 1621 .645 1.634 .633 .709
13 1141 1071 335 162 806 909 1149 1084 338 164 814 922 0 0 274 234 66 38 100 100 100 100 1715 1736 .887 1.128 1.133 1.166 1.138 1.47 80 297 1.081 .91 110 3630 8620 104 115 265 276 0 1030 156 874 1.084 1042 887 .922 1.089 .117 .123
14 2159 2498 341 155 1818 2343 2141 2483 351 159 1800 2328 0 0 557 622 80 41 100 100 100 100 4161 4128 .776 1.289 1.293 1.312 1.258 1.257 80 308 1.267 .96 100 3770 8610 104 114 280 290 0 2402 149 2253 1.239 2388 2238 .807 1.244 .309 .315
15 2437 2883 380 174 2057 2709 2485 2684 406 209 2105 2510 0 0 1003 1092 113 157 100 100 100 100 4766 4615 .759 1.317 1.192 1.422 1.429 1.431 12 70 1.372 .93 50 3880 8610 106 111 293 298 0 2772 167 2605 1.266 2581 2413 .79 1.147 .341 .197
16 770 334 341 159 429 175 442 276 344 162 101 117 0 0 1296 165 64 34 65 90 43 68 604 218 2.451 .408 1.158 .927 1.174 3.92 32 151 .031 .15 60 4020 8630 108 114 307 313 -100 321 153 168 .392 265 113 2.549 1.114 -1.35 .156
17 1559 2124 325 156 1234 1968 1555 2111 328 158 1230 1955 0 0 362 428 65 35 100 100 100 100 3202 3185 .627 1.595 1.589 1.637 1.55 1.334 80 344 1.585 .94 110 4170 8620 104 115 319 330 0 2042 150 1892 1.533 2030 1880 .652 1.528 .617 .612
18 1170 464 325 154 845 310 1195 482 324 157 870 328 0 0 289 120 66 38 100 98 100 97 1155 1198 2.726 .367 .377 .364 .346 1.446 80 289 .34 .89 110 4290 8630 105 116 331 342 0 446 148 298 .353 463 315 2.835 .363 -1.503 -1.464
19 753 311 339 177 414 134 749 303 340 185 410 126 0 0 166 62 71 57 100 90 96 61 548 536 3.09 .324 .307 .311 .302 1.963 80 286 .284 .72 100 4450 8620 105 115 348 358 0 299 170 129 .311 291 121 3.213 .295 -1.684 -1.759
20 3072 4997 347 194 2725 4803 3131 5150 358 225 2784 4956 0 0 780 1351 82 141 100 100 100 100 7528 7740 .567 1.763 1.78 1.756 1.725 1.185 80 284 1.81 .97 110 4580 8630 105 116 360 371 0 4805 187 4618 1.695 4952 4765 .59 1.712 .761 .775

Total number of rows: 44544

Table truncated, full table size 10133 Kbytes.




Supplementary data files not provided
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