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Sample GSM81483 Query DataSets for GSM81483
Status Public on Nov 03, 2005
Title GC (KATO 3 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 (KATO 3 cells)
Organism Homo sapiens
Characteristics GC (KATO 3 cells)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19047.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 GPL3038
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 2813 3580 801 469 2012 3111 2964 3602 809 507 2163 3133 0 0 741 880 166 277 100 100 100 100 5123 5296 .647 1.546 1.448 1.615 1.551 1.247 12 92 1.533 .94 50 1870 8520 43 48 93 98 0 3346 438 2907 1.445 3366 2928 .692 1.354 .531 .437
2 1675 1866 791 533 884 1333 1263 1676 790 525 472 1143 0 0 954 802 101 98 91 100 83 100 2217 1615 .663 1.508 2.422 1.929 1.778 1.852 12 54 1.175 .89 40 2020 8510 43 47 109 113 0 1744 498 1246 1.409 1566 1068 .71 2.263 .495 1.178
3 4732 5923 796 526 3936 5397 5131 6462 815 540 4335 5936 0 0 2069 2559 135 114 96 100 96 100 9333 10271 .729 1.371 1.369 1.454 1.337 1.309 32 161 1.362 .98 60 2130 8540 45 51 119 125 0 5536 492 5044 1.281 6039 5548 .78 1.28 .358 .356
4 931 863 786 533 145 330 830 582 794 537 44 49 0 0 392 700 122 96 30 41 17 27 475 93 .439 2.276 1.114 1.249 1.37 3.953 80 409 1.984 .77 100 2280 8520 41 51 132 142 -50 807 498 308 2.127 544 46 .47 1.041 1.089 .058
5 3382 6418 787 527 2595 5891 2668 6746 790 531 1881 6219 0 0 3552 2729 115 78 93 100 93 100 8486 8100 .441 2.27 3.306 2.985 2.97 1.62 32 144 1.512 .72 60 2400 8530 44 50 146 152 0 5998 493 5506 2.122 6305 5812 .471 3.09 1.085 1.628
6 802 702 764 521 38 181 782 562 1031 574 18 41 0 0 157 462 2795 1036 0 6 0 2 219 59 .21 4.763 2.278 2.087 2.392 4.051 80 434 3.873 .4 100 2560 8520 41 51 160 170 -50 656 487 169 4.452 525 38 .225 2.129 2.154 1.09
7 2013 2634 771 514 1242 2120 1950 2600 2149 819 1179 2086 0 0 255 441 6418 2402 0 16 0 0 3362 3265 .586 1.707 1.769 1.705 1.71 1.22 12 80 .353 .24 50 2660 8530 44 49 172 177 0 2462 480 1981 1.595 2430 1950 .627 1.654 .674 .726
8 2240 1992 772 446 1468 1546 1563 1662 788 455 791 1216 0 0 2375 1504 211 109 84 96 68 90 3014 2007 .95 1.053 1.537 1.371 1.672 2.869 32 172 .735 .93 60 2800 8530 44 50 186 192 -100 1862 417 1445 .984 1553 1136 1.016 1.437 -.023 .523
9 857 698 765 466 92 232 788 507 1066 692 23 41 0 0 329 559 3384 2170 0 2 0 0 324 64 .397 2.522 1.783 .869 1.103 3.279 80 402 1.806 .72 100 2970 8520 41 51 201 211 -100 652 436 217 2.357 474 38 .424 1.666 1.237 .736
10 1251 1635 766 513 485 1122 1232 1668 768 516 466 1155 0 0 334 688 104 79 84 96 78 90 1607 1621 .432 2.313 2.479 2.145 2.14 1.698 32 136 2.357 .81 60 3080 8530 44 50 214 220 0 1528 479 1049 2.162 1559 1079 .463 2.316 1.112 1.212
11 2461 10555 756 518 1705 10037 2618 11513 757 519 1862 10995 0 0 946 5181 116 79 90 100 87 100 11742 12857 .17 5.887 5.905 6.053 5.824 1.48 32 224 5.882 .96 70 3220 8530 43 50 227 234 0 9864 484 9380 5.502 10760 10276 .182 5.519 2.46 2.464
12 1273 1768 742 487 531 1281 1218 1737 751 494 476 1250 0 0 221 396 138 94 100 100 91 100 1812 1726 .415 2.412 2.626 2.502 2.64 1.54 12 68 2.377 .85 40 3350 8530 45 49 242 246 0 1652 455 1197 2.255 1623 1168 .444 2.454 1.173 1.295
13 1587 2281 763 511 824 1770 1592 2382 788 508 829 1871 0 0 568 605 118 96 91 100 91 100 2594 2700 .466 2.148 2.257 2.139 2.389 1.305 12 98 1.805 .88 50 3510 8520 43 48 257 262 0 2132 478 1654 2.008 2226 1749 .498 2.109 1.005 1.077
14 2783 2454 774 529 2009 1925 2802 2400 778 529 2028 1871 0 0 1134 1167 118 95 90 93 87 87 3934 3899 1.044 .958 .923 .884 .967 1.558 32 172 .967 .94 60 3640 8530 44 50 270 276 0 2293 494 1799 .896 2243 1749 1.117 .862 -.159 -.214
15 1377 2142 805 543 572 1599 1394 2224 784 536 589 1681 0 0 300 372 128 90 91 100 83 100 2171 2270 .358 2.795 2.854 3.551 2.877 2.856 12 68 2.419 .79 40 3770 8530 45 49 284 288 0 2002 507 1494 2.613 2079 1571 .383 2.667 1.385 1.415
16 3468 4669 781 553 2687 4116 3562 4682 783 560 2781 4129 0 0 979 1481 117 93 96 100 96 100 6803 6910 .653 1.532 1.485 1.496 1.607 1.405 32 227 1.527 .95 70 3910 8520 42 49 296 303 0 4364 517 3847 1.432 4376 3859 .699 1.388 .518 .473
17 2016 2767 782 567 1234 2200 1901 2637 783 586 1119 2070 0 0 453 461 144 127 100 100 100 100 3434 3189 .561 1.783 1.85 1.865 1.76 1.482 12 104 1.947 .86 50 4050 8520 43 48 311 316 0 2586 530 2056 1.666 2464 1935 .6 1.729 .737 .79
18 2332 2012 758 575 1574 1437 2277 2023 815 597 1519 1448 0 0 342 408 242 162 100 100 100 100 3011 2967 1.095 .913 .953 .893 .895 1.453 12 104 .826 .87 50 4180 8520 43 48 324 329 0 1880 537 1343 .853 1891 1353 1.172 .891 -.229 -.167
19 1952 3268 783 552 1169 2716 1451 3158 961 694 668 2606 0 0 1632 1384 938 648 34 93 21 90 3885 3274 .43 2.323 3.901 3.403 3.77 2.326 32 164 1.382 .8 60 4330 8520 43 49 339 345 -100 3054 516 2538 2.171 2951 2436 .461 3.646 1.119 1.866
20 2396 3087 772 597 1624 2490 2414 3252 1058 853 1642 2655 0 0 1282 1728 1219 902 61 73 28 57 4114 4297 .652 1.533 1.617 1.563 1.413 2.158 52 264 1.131 .82 80 4470 8520 42 50 352 360 -100 2885 558 2327 1.433 3039 2481 .698 1.511 .519 .596

Total number of rows: 41088

Table truncated, full table size 9269 Kbytes.




Supplementary data files not provided
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