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Sample GSM81471 Query DataSets for GSM81471
Status Public on Nov 03, 2005
Title GC (HUVEC2)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name HUVEC, plastic 4 hrs
Organism Homo sapiens
Characteristics HUVEC, plastic 4 hrs
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Stomach cancer
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18757.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 GPL3041
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
1 381 252 107 71 274 181 403 239 108 73 296 168 0 0 154 94 22 16 88 98 88 96 455 464 1.514 .661 .568 .715 .658 1.769 52 340 .591 .88 90 1990 8870 66 75 70 79 0 245 69 176 .641 232 163 1.559 .551 -.641 -.86
2 579 774 104 70 475 704 658 765 107 70 554 695 0 0 369 455 20 15 83 100 75 100 1179 1249 .675 1.482 1.255 1.852 1.515 2.327 12 92 1.417 .93 50 2140 8880 69 74 87 92 0 751 68 683 1.439 743 675 .695 1.218 .525 .284
3 1707 1398 107 68 1600 1330 1818 1433 108 71 1711 1365 0 0 681 456 21 16 100 100 100 100 2930 3076 1.203 .831 .798 .894 .808 1.519 80 353 .788 .96 100 2290 8860 65 75 100 110 0 1357 66 1291 .807 1391 1325 1.239 .775 -.309 -.369
4 128 88 110 69 18 19 111 76 111 70 1 7 0 0 61 47 22 14 25 34 15 21 37 8 .947 1.056 7 .512 .585 4.395 52 243 .946 .74 80 2410 8850 65 73 113 121 -50 85 67 18 1.025 74 7 .976 6.796 .035 2.765
5 1001 2452 105 69 896 2383 1115 2597 107 71 1010 2528 0 0 486 1002 22 15 91 100 91 100 3279 3538 .376 2.66 2.503 2.783 2.51 1.473 80 335 2.565 .95 100 2580 8860 65 75 129 139 0 2381 67 2314 2.582 2521 2454 .387 2.43 1.369 1.281
6 113 80 109 70 4 10 108 78 109 71 -1 8 0 0 38 22 21 14 21 30 9 13 14 7 .4 2.5 null .486 .4 4.223 52 223 .382 .45 80 2700 8850 65 73 142 150 -50 78 68 10 2.427 76 8 .412 null 1.279 null
7 1181 1454 111 70 1070 1384 1301 1473 114 71 1190 1403 0 0 576 553 24 15 96 100 95 100 2454 2593 .773 1.293 1.179 1.52 1.282 1.9 80 331 1.201 .94 100 2870 8860 65 75 158 168 0 1412 68 1344 1.256 1430 1362 .796 1.145 .329 .195
8 606 1044 110 72 496 972 595 1105 114 76 485 1033 0 0 181 258 35 35 98 100 98 100 1468 1518 .51 1.96 2.13 1.982 1.922 1.353 52 275 1.923 .94 90 3000 8850 64 73 171 180 0 1014 70 944 1.903 1073 1003 .526 2.068 .928 1.048
9 438 786 106 69 332 717 314 468 108 74 208 399 0 0 357 611 20 28 81 100 75 100 1049 607 .463 2.16 1.918 2.565 2.161 2.252 32 165 1.944 .94 60 3150 8860 67 73 188 194 0 763 67 696 2.097 454 387 .477 1.862 1.068 .897
10 336 238 106 72 230 166 330 240 108 73 224 168 0 0 119 66 22 17 94 100 94 96 396 392 1.386 .722 .75 .757 .689 1.797 52 304 .659 .89 90 3290 8850 64 73 200 209 0 231 70 161 .701 233 163 1.427 .728 -.513 -.458
11 1688 265 111 73 1577 192 1614 264 113 73 1503 191 0 0 1044 136 22 15 94 88 94 84 1769 1694 8.214 .122 .127 .125 .117 1.994 52 255 .115 .9 80 3440 8860 66 74 216 224 0 257 71 186 .118 256 185 8.46 .123 -3.081 -3.019
12 441 302 116 75 325 227 390 302 131 87 274 227 0 0 277 143 91 53 71 84 68 78 552 501 1.432 .698 .828 .828 .75 1.96 32 192 .582 .88 70 3580 8860 66 73 230 237 0 293 73 220 .678 293 220 1.475 .804 -.56 -.314
13 1423 2044 112 72 1311 1972 1534 2139 122 80 1422 2067 0 0 597 645 68 39 95 100 92 100 3283 3489 .665 1.504 1.454 1.794 1.48 2.162 80 375 1.421 .96 100 3730 8850 64 74 244 254 0 1984 70 1915 1.46 2077 2007 .685 1.411 .546 .497
14 534 479 108 71 426 408 527 465 110 73 419 394 0 0 262 200 24 16 94 96 88 94 834 813 1.044 .958 .94 1.016 .986 2.127 52 253 .87 .91 80 3870 8850 65 73 259 267 0 465 69 396 .93 451 383 1.075 .913 -.105 -.131
15 425 245 109 68 316 177 403 243 297 72 294 175 0 0 181 64 2321 18 0 100 0 96 493 469 1.785 .56 .595 .637 .554 2.031 32 201 .421 .81 70 4020 8840 64 71 274 281 0 238 66 172 .544 236 170 1.839 .578 -.879 -.791
16 974 1246 112 69 862 1177 1083 1305 219 72 971 1236 0 0 401 460 1752 17 0 100 0 100 2039 2207 .732 1.365 1.273 1.409 1.34 1.38 80 353 .055 .17 100 4170 8850 64 74 288 298 0 1210 67 1143 1.326 1267 1200 .754 1.236 .407 .305
17 540 743 109 71 431 672 563 743 111 72 454 672 0 0 220 259 21 15 94 100 94 100 1103 1126 .641 1.559 1.48 1.639 1.601 1.55 52 265 1.498 .92 90 4310 8850 64 73 302 311 0 721 69 652 1.514 721 652 .661 1.437 .598 .523
18 487 382 110 73 377 309 510 425 110 75 400 352 0 0 213 139 23 16 91 95 88 95 686 752 1.22 .82 .88 .866 .813 1.799 80 301 .746 .93 100 4460 8860 65 75 317 327 0 371 71 300 .796 413 342 1.257 .854 -.33 -.227
19 371 1223 108 74 263 1149 392 1343 111 78 284 1269 0 0 153 434 24 27 90 100 90 100 1412 1553 .229 4.369 4.468 4.843 4.218 1.654 52 300 4.044 .92 90 4600 8840 63 72 331 340 0 1187 72 1116 4.242 1304 1232 .236 4.338 2.085 2.117
20 743 986 107 75 636 911 748 983 107 78 641 908 0 0 383 444 22 28 94 100 90 100 1547 1549 .698 1.432 1.417 1.748 1.403 2.33 52 267 1.382 .92 90 4760 8860 65 74 347 356 0 957 73 884 1.391 954 882 .719 1.375 .476 .46

Total number of rows: 43008

Table truncated, full table size 9134 Kbytes.




Supplementary data files not provided
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