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Sample GSM65263 Query DataSets for GSM65263
Status Public on Jul 23, 2005
Title MCF7-UCLA X MCF7+6um Tamoxifen 48hrs #1
Sample type RNA
 
Channel 1
Source name MCF7-UCLA
Organism Homo sapiens
Characteristics MCF7-UCLA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MCF7+6um Tamoxifen 48hrs
Organism Homo sapiens
Characteristics MCF7+6um Tamoxifen 48hrs
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Breast
Image: http://boussard-smd.stanford.edu:8000/MicroArray/gifs/2000-08/8996.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jul 22, 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 GPL2671
Series (1)
GSE2987 RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 1559 1839 166 218 1393 1621 null null 167 222 null null null null null null null null 100 100 null null null null .859 1.164 null null 1.164 null 52 312 1.059 .94 null null null 80 89 121 130 0 1895 224 1671 1.2 null null .834 null .263 null
2 2350 2561 169 237 2181 2324 null null 172 240 null null null null null null null null 100 100 null null null null .938 1.066 null null 1.069 null 52 301 1.034 .94 null null null 79 88 136 145 0 2640 244 2396 1.099 null null .91 null .136 null
3 862 1266 160 224 702 1042 null null 163 231 null null null null null null null null 91 91 null null null null .674 1.484 null null 1.487 null 80 325 1.321 .93 null null null 79 89 151 161 0 1305 230 1075 1.531 null null .653 null .615 null
4 211 250 161 225 50 25 null null 167 232 null null null null null null null null 57 33 null null null null 2 .5 null null 1.614 null 80 314 .002 0 null null null 80 90 163 173 0 257 231 26 .52 null null 1.923 null -.943 null
5 210 213 151 206 59 7 null null 157 211 null null null null null null null null 56 17 null null null null 8.429 .119 null null .509 null 120 518 .199 .2 null null null 75 88 180 193 0 219 212 7 .119 null null 8.429 null -3.075 null
6 2932 4609 156 198 2776 4411 null null 158 201 null null null null null null null null 92 98 null null null null .629 1.589 null null 1.579 null 80 292 1.485 .96 null null null 78 88 197 207 0 4751 204 4547 1.638 null null .611 null .712 null
7 683 1043 161 207 522 836 null null 161 208 null null null null null null null null 100 100 null null null null .624 1.602 null null 1.579 null 52 255 1.4 .93 null null null 78 87 212 221 0 1075 213 862 1.651 null null .606 null .724 null
8 183 217 153 205 30 12 null null 154 205 null null null null null null null null 37 22 null null null null 2.5 .4 null null .968 null 120 557 .089 .08 null null null 74 87 224 237 0 223 211 12 .4 null null 2.5 null -1.322 null
9 4675 4291 152 196 4523 4095 null null 154 199 null null null null null null null null 91 100 null null null null 1.105 .905 null null .901 null 80 338 .846 .96 null null null 78 88 242 252 0 4423 202 4221 .933 null null 1.072 null -.1 null
10 334 331 158 200 176 131 null null 160 204 null null null null null null null null 88 73 null null null null 1.344 .744 null null .762 null 52 307 .555 .65 null null null 77 86 256 265 0 341 206 135 .767 null null 1.304 null -.383 null
11 379 487 162 216 217 271 null null 163 218 null null null null null null null null 98 96 null null null null .801 1.249 null null 1.183 null 52 259 1.07 .83 null null null 77 86 272 281 0 502 222 280 1.29 null null .775 null .368 null
12 827 1042 170 224 657 818 null null 169 223 null null null null null null null null 87 92 null null null null .803 1.245 null null 1.262 null 80 296 1.183 .95 null null null 77 87 286 296 0 1074 230 844 1.285 null null .778 null .361 null
13 2739 4078 169 233 2570 3845 null null 172 238 null null null null null null null null 96 98 null null null null .668 1.496 null null 1.471 null 80 325 1.425 .97 null null null 77 87 301 311 0 4204 240 3964 1.542 null null .648 null .625 null
14 7983 5919 164 211 7819 5708 null null 167 219 null null null null null null null null 96 97 null null null null 1.37 .73 null null .742 null 80 377 .71 .97 null null null 76 86 316 326 0 6102 217 5885 .753 null null 1.329 null -.41 null
15 764 597 144 174 620 423 null null 149 180 null null null null null null null null 100 98 null null null null 1.466 .682 null null .698 null 52 289 .604 .91 null null null 76 85 331 340 0 615 179 436 .703 null null 1.422 null -.508 null
16 571 612 131 134 440 478 null null 560 401 null null null null null null null null 0 0 null null null null .921 1.086 null null 1.068 null 80 330 .979 .94 null null null 76 86 346 356 0 630 138 492 1.118 null null .894 null .161 null
17 13225 11540 135 134 13090 11406 null null 591 415 null null null null null null null null 81 80 null null null null 1.148 .871 null null .857 null 80 311 .668 .77 null null null 75 85 360 370 0 11896 138 11758 .898 null null 1.113 null -.155 null
18 263 218 132 134 131 84 null null 137 140 null null null null null null null null 90 73 null null null null 1.56 .641 null null .586 null 52 235 .322 .36 null null null 76 85 376 385 0 224 138 86 .656 null null 1.523 null -.607 null
19 6329 7199 137 161 6192 7038 null null 143 164 null null null null null null null null 98 97 null null null null .88 1.137 null null 1.12 null 80 298 1.086 .96 null null null 75 85 390 400 0 7421 165 7256 1.172 null null .853 null .229 null
20 3813 5169 165 197 3648 4972 null null 163 201 null null null null null null null null 98 97 null null null null .734 1.363 null null 1.358 null 80 306 1.289 .97 null null null 75 85 405 415 0 5328 203 5125 1.405 null null .712 null .49 null

Total number of rows: 24192

Table truncated, full table size 5798 Kbytes.




Supplementary data files not provided
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