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Sample GSM81495 Query DataSets for GSM81495
Status Public on Nov 03, 2005
Title GC (SNU1 cells)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name SNU1 cells
Organism Homo sapiens
Characteristics SNU1 cells
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16558.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 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
1 348 390 105 70 243 320 339 386 105 73 234 316 0 0 75 80 23 26 100 100 100 100 563 550 .759 1.317 1.35 1.349 1.243 1.518 52 361 1.367 .85 90 1520 7740 86 95 79 88 0 386 69 317 1.304 382 313 .767 1.337 .383 .419
2 891 904 105 74 786 830 796 697 110 77 691 623 0 0 493 675 32 23 100 96 100 96 1616 1314 .947 1.056 .902 .949 1.045 2.024 32 128 1.221 .86 60 1680 7750 89 95 97 103 0 895 73 822 1.046 690 617 .956 .893 .064 -.164
3 3858 4839 101 68 3757 4771 4139 5079 104 76 4038 5011 0 0 1349 1537 36 39 100 100 98 100 8528 9049 .787 1.27 1.241 1.405 1.248 2.136 80 322 1.273 .92 110 1810 7740 85 96 107 118 0 4791 67 4724 1.257 5029 4961 .795 1.229 .33 .297
4 272 457 101 68 171 389 117 100 109 76 16 32 0 0 340 790 59 46 31 41 27 35 560 48 .44 2.275 2 1.115 1.481 5.199 80 267 2.878 .72 100 1930 7740 86 96 120 130 -50 452 67 385 2.252 99 32 .444 1.98 1.171 .986
5 1387 6428 105 66 1282 6362 1517 6761 405 120 1412 6695 0 0 399 1729 2369 321 0 100 0 100 7644 8107 .202 4.963 4.742 5.069 4.728 1.558 80 350 2.604 .23 100 2070 7730 85 95 134 144 0 6364 65 6299 4.913 6694 6629 .204 4.695 2.297 2.231
6 570 1393 106 72 464 1321 458 1143 137 80 352 1071 0 0 307 945 181 51 75 100 50 100 1785 1423 .351 2.847 3.043 2.705 2.385 2.391 12 104 2.921 .66 50 2210 7750 89 94 150 155 -100 1379 71 1308 2.819 1132 1060 .355 3.012 1.495 1.591
7 1600 2426 100 69 1500 2357 1643 2452 103 71 1543 2383 0 0 491 893 24 26 100 100 100 100 3857 3926 .636 1.571 1.544 1.493 1.55 1.768 80 349 1.662 .93 100 2350 7730 85 95 162 172 0 2402 68 2334 1.556 2428 2359 .643 1.529 .638 .613
8 755 560 106 66 649 494 770 537 120 87 664 471 0 0 196 163 79 135 100 98 100 93 1143 1135 1.314 .761 .709 .76 .743 1.58 80 293 .742 .89 100 2490 7730 85 95 176 186 0 554 65 489 .754 532 466 1.327 .702 -.408 -.51
9 955 1046 107 70 848 976 839 891 123 94 732 821 0 0 599 798 82 144 96 90 88 73 1824 1553 .869 1.151 1.122 1.067 1.156 2.077 52 210 1.268 .87 80 2630 7740 87 95 191 199 -100 1036 69 966 1.14 882 813 .878 1.11 .188 .151
10 320 314 100 66 220 248 311 314 101 67 211 248 0 0 97 97 21 18 100 100 100 100 468 459 .887 1.127 1.175 1.115 1.237 1.603 52 245 1.512 .74 90 2760 7730 85 94 203 212 0 311 65 246 1.116 311 246 .896 1.164 .158 .219
11 4835 453 99 63 4736 390 4983 456 102 67 4884 393 0 0 1087 164 23 19 100 97 100 97 5126 5277 12.144 .082 .08 .078 .082 1.446 80 286 .082 .93 100 2900 7730 85 95 217 227 0 449 62 386 .082 451 389 12.265 .08 -3.616 -3.65
12 654 1149 105 69 549 1080 633 1208 109 71 528 1139 0 0 267 394 25 22 100 100 100 100 1629 1667 .508 1.967 2.157 2.094 1.984 1.449 52 226 1.916 .89 90 3030 7730 85 94 230 239 0 1138 68 1069 1.948 1196 1128 .513 2.136 .962 1.095
13 622 910 110 70 512 840 601 908 113 75 491 838 0 0 141 309 26 28 100 98 100 98 1352 1329 .61 1.641 1.707 1.512 1.567 1.854 80 321 1.847 .89 110 3170 7730 84 95 243 254 0 901 69 832 1.624 899 830 .616 1.69 .7 .757
14 1227 1572 109 70 1118 1502 1258 1604 111 75 1149 1534 0 0 227 418 25 28 100 98 100 98 2620 2683 .744 1.343 1.335 1.27 1.391 1.787 80 246 1.423 .91 100 3310 7720 84 94 258 268 0 1556 69 1487 1.33 1588 1519 .752 1.322 .412 .403
15 173 181 104 71 69 110 120 85 106 74 16 14 0 0 189 316 22 23 41 38 23 27 179 30 .627 1.594 .875 1.052 1.003 4.595 80 220 2.03 .68 100 3430 7730 85 95 270 280 -50 179 70 109 1.578 84 14 .634 .866 .658 -.207
16 172 164 106 65 66 99 123 80 109 72 17 15 0 0 243 378 24 30 37 32 13 13 165 32 .667 1.5 .882 .847 .878 4.518 80 252 2.137 .54 100 3560 7730 85 95 283 293 -50 162 64 98 1.485 79 15 .673 .874 .571 -.195
17 768 955 106 64 662 891 837 977 108 68 731 913 0 0 243 234 23 23 97 100 97 100 1553 1644 .743 1.346 1.249 1.451 1.329 1.818 80 265 1.309 .92 100 3700 7730 85 95 297 307 0 946 63 882 1.333 967 904 .75 1.237 .414 .306
18 797 706 106 68 691 638 836 714 108 72 730 646 0 0 216 170 24 23 100 100 100 100 1329 1376 1.083 .923 .885 .979 .891 1.806 80 259 .894 .88 100 3840 7730 85 95 311 321 0 699 67 632 .914 707 640 1.094 .876 -.129 -.191
19 421 502 109 69 312 433 425 503 111 72 316 434 0 0 85 132 24 22 100 100 100 100 745 750 .721 1.388 1.373 1.351 1.36 1.506 80 289 1.478 .88 100 3980 7720 84 94 325 335 0 497 68 429 1.374 498 430 .728 1.36 .458 .443
20 2116 4077 115 73 2001 4004 2081 4177 117 76 1966 4104 0 0 454 1232 26 24 100 100 100 100 6005 6070 .5 2.001 2.087 1.857 2.033 1.747 80 309 2.179 .93 100 4120 7720 84 94 339 349 0 4037 72 3964 1.981 4136 4063 .505 2.067 .986 1.047

Total number of rows: 44544

Table truncated, full table size 9775 Kbytes.




Supplementary data files not provided
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