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Sample GSM81472 Query DataSets for GSM81472
Status Public on Nov 03, 2005
Title GC (SNU5 cells)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SNU5 cells vs CRG
Organism Homo sapiens
Characteristics SNU5 cells vs CRG
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14720.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 (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
1 449 458 118 64 331 394 436 436 126 79 318 372 0 0 166 174 88 94 96 96 78 86 725 690 .84 1.19 1.17 1.163 1.251 1.783 52 322 1.249 .8 90 1630 8160 51 60 126 135 0 636 89 547 1.653 606 517 .605 1.625 .725 .7
2 763 356 114 62 649 294 627 323 121 69 513 261 0 0 404 258 51 47 100 84 100 71 943 774 2.207 .453 .509 .346 .38 2.953 32 146 .495 .69 70 1770 8170 53 60 141 148 0 494 86 408 .629 449 363 1.589 .707 -.668 -.501
3 3031 3172 114 63 2917 3109 3175 3411 118 68 3061 3348 0 0 861 1040 30 22 100 100 100 100 6026 6409 .938 1.066 1.094 1.031 1.077 1.59 80 270 1.091 .94 100 1890 8150 50 60 152 162 0 4406 88 4318 1.48 4738 4650 .676 1.519 .566 .603
4 208 208 116 66 92 142 130 89 118 68 14 23 0 0 205 331 29 22 40 51 28 35 234 37 .648 1.543 1.643 .94 .932 3.525 80 254 1.833 .74 100 2010 8160 51 61 164 174 -50 289 92 197 2.144 124 32 .466 2.282 1.1 1.19
5 1416 3179 118 66 1298 3113 1447 3243 123 77 1329 3177 0 0 408 1121 35 47 100 100 100 100 4411 4506 .417 2.398 2.391 2.311 2.428 1.558 80 343 2.574 .93 100 2160 8150 50 60 179 189 0 4415 92 4324 3.331 4504 4413 .3 3.32 1.736 1.731
6 632 900 135 85 497 815 592 823 148 113 457 738 0 0 379 491 55 72 87 96 78 93 1312 1195 .61 1.64 1.615 2.024 1.986 2.447 32 121 1.602 .8 60 2300 8180 55 61 195 201 0 1250 118 1132 2.278 1143 1025 .439 2.243 1.187 1.165
7 1618 3067 125 71 1493 2996 1697 3036 131 81 1572 2965 0 0 618 1035 44 37 100 100 100 100 4489 4537 .498 2.007 1.886 2.074 2.05 1.555 80 304 2.008 .95 100 2430 8150 50 60 206 216 0 4260 99 4161 2.787 4217 4118 .359 2.62 1.479 1.389
8 793 1244 122 66 671 1178 788 1130 126 71 666 1064 0 0 303 490 35 24 100 100 100 100 1849 1730 .57 1.756 1.598 1.766 1.769 1.563 80 295 1.797 .92 100 2560 8150 50 60 219 229 0 1728 92 1636 2.438 1569 1478 .41 2.219 1.286 1.15
9 1540 1211 131 72 1409 1139 1399 1233 135 76 1268 1161 0 0 794 584 38 24 100 100 100 100 2548 2429 1.237 .808 .916 .845 .876 1.641 32 167 .755 .89 70 2710 8170 53 60 235 242 0 1682 100 1582 1.123 1713 1613 .891 1.272 .167 .347
10 441 552 125 72 316 480 374 448 127 76 249 376 0 0 205 328 33 25 100 100 100 98 796 625 .658 1.519 1.51 1.458 1.555 1.808 52 269 1.565 .84 90 2830 8140 49 58 246 255 0 767 100 667 2.11 622 522 .474 2.097 1.077 1.069
11 3889 1533 124 73 3765 1460 3980 1513 127 75 3856 1440 0 0 1244 499 33 23 100 100 100 100 5225 5296 2.579 .388 .373 .392 .392 1.354 80 334 .37 .95 110 2970 8160 50 61 259 270 0 2129 101 2028 .539 2101 2000 1.857 .519 -.893 -.947
12 1325 1477 119 70 1206 1407 1198 1364 125 72 1079 1294 0 0 583 870 32 21 100 100 100 100 2613 2373 .857 1.167 1.199 1.061 1.229 1.732 52 245 1.287 .91 90 3110 8140 49 58 274 283 0 2051 97 1954 1.62 1894 1797 .617 1.666 .696 .736
13 677 993 119 70 558 923 626 892 124 73 507 822 0 0 250 435 30 22 100 100 98 100 1481 1329 .605 1.654 1.621 1.68 1.637 1.478 80 316 1.73 .93 110 3250 8150 49 60 287 298 0 1379 97 1282 2.297 1239 1142 .435 2.252 1.2 1.171
14 1065 1068 121 70 944 998 1031 1021 123 72 910 951 0 0 345 359 29 23 100 100 100 100 1942 1861 .946 1.057 1.045 1.075 1.074 1.419 80 286 1.048 .95 110 3390 8150 49 60 301 312 0 1483 97 1386 1.468 1418 1321 .681 1.451 .554 .538
15 171 144 122 72 49 72 136 89 123 73 14 17 0 0 157 207 28 24 35 43 25 25 121 31 .681 1.469 1.214 .998 1.07 4.576 80 236 1.438 .72 100 3510 8160 51 61 314 324 -50 200 100 100 2.041 124 24 .49 1.687 1.029 .754
16 132 75 128 73 4 2 132 70 130 74 4 -3 0 0 36 26 32 23 20 17 3 5 6 1 2 .5 null .74 .674 2.937 80 258 .063 .04 100 3650 8160 51 61 328 338 -50 104 101 3 .694 97 null 1.44 null -.526 null
17 875 953 129 73 746 880 902 979 130 76 773 906 0 0 253 230 33 23 100 100 100 100 1626 1679 .848 1.18 1.172 1.242 1.179 1.402 80 289 1.148 .94 110 3790 8160 50 61 341 352 0 1324 101 1222 1.638 1360 1258 .61 1.628 .712 .703
18 671 342 128 71 543 271 674 332 132 76 546 261 0 0 163 126 33 23 100 98 100 97 814 807 2.004 .499 .478 .46 .477 1.693 80 275 .506 .9 100 3930 8150 50 60 356 366 0 475 99 376 .693 461 363 1.443 .664 -.529 -.591
19 381 288 129 72 252 216 334 249 131 76 205 177 0 0 121 132 33 21 100 100 98 100 468 382 1.167 .857 .863 .816 .869 1.685 80 286 .911 .81 100 4070 8150 50 60 370 380 0 400 100 300 1.19 346 246 .84 1.199 .252 .262
20 1468 2034 136 76 1332 1958 1453 1992 139 80 1317 1916 0 0 411 591 36 27 100 100 100 100 3290 3233 .68 1.47 1.455 1.472 1.474 1.414 80 368 1.512 .94 110 4210 8150 49 60 383 394 0 2825 106 2719 2.042 2767 2661 .49 2.021 1.03 1.015

Total number of rows: 44544

Table truncated, full table size 9774 Kbytes.




Supplementary data files not provided

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