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Sample GSM90279 Query DataSets for GSM90279
Status Public on Dec 31, 2005
Title AT2_Natvie_Vegf
Sample type RNA
 
Channel 1
Source name VEGF_NATIVE
Organism Homo sapiens
Characteristics VEGF_NATIVE
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name REF
Organism Homo sapiens
Characteristics REF
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: HUVEC, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27493.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 Dec 30, 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 GPL3284
Series (1)
GSE3956 Antiangiogenic Antithrombin

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 1402 620 631 251 771 369 1380 502 638 262 749 251 0 0 297 374 102 86 100 86 100 63 1140 1000 2.089 .479 .335 .351 .361 2.512 52 336 .484 .62 90 2160 7910 78 87 47 56 0 1550 628 923 1.196 1255 628 .836 .838 .259 -.255
2 7072 2481 643 249 6429 2232 6747 2340 649 261 6104 2091 0 0 1766 933 108 89 100 100 100 100 8661 8195 2.88 .347 .343 .337 .329 1.305 52 300 .328 .9 90 2300 7910 78 87 61 70 0 6203 623 5580 .868 5850 5228 1.152 .856 -.204 -.224
3 5348 2775 627 257 4721 2518 5182 2487 639 263 4555 2230 0 0 1637 1333 114 74 100 100 100 100 7239 6785 1.875 .533 .49 .479 .532 1.853 52 313 .529 .87 90 2440 7910 78 87 75 84 0 6938 643 6295 1.333 6218 5575 .75 1.224 .415 .292
4 2137 1762 624 245 1513 1517 1750 1021 630 252 1126 776 0 0 947 1650 93 56 100 96 100 96 3030 1902 .997 1.003 .689 .705 .675 2.049 52 326 1.322 .87 90 2590 7910 78 87 90 99 0 4405 613 3793 2.507 2553 1940 .399 1.723 1.326 .785
5 21756 3423 622 240 21134 3183 22000 3266 629 245 21378 3026 0 0 7421 1454 94 55 100 100 100 100 24317 24404 6.64 .151 .142 .145 .145 1.575 80 362 .148 .94 100 2740 7920 79 89 105 115 0 8558 600 7958 .377 8165 7565 2.656 .354 -1.409 -1.499
6 3263 2806 626 240 2637 2566 3132 2153 632 247 2506 1913 0 0 1336 1936 102 57 100 98 100 98 5203 4419 1.028 .973 .763 .743 .837 2.1 52 322 1.118 .9 90 2890 7910 78 87 120 129 0 7015 600 6415 2.433 5383 4783 .411 1.908 1.283 .932
7 12104 3562 620 243 11484 3319 11536 2703 626 249 10916 2460 0 0 3283 1753 97 60 100 100 100 100 14803 13376 3.46 .289 .225 .263 .244 1.582 52 325 .296 .88 90 3030 7910 78 87 134 143 0 8905 608 8298 .723 6758 6150 1.384 .563 -.469 -.828
8 4117 1799 629 255 3488 1544 3531 1254 633 260 2902 999 0 0 1474 1256 103 62 100 98 100 94 5032 3901 2.259 .443 .344 .333 .353 2.248 52 325 .54 .83 90 3180 7910 78 87 149 158 0 4498 638 3860 1.107 3135 2498 .904 .861 .146 -.217
9 2286 2565 641 267 1645 2298 1720 1190 646 273 1079 923 0 0 1313 2531 113 65 100 94 98 92 3943 2002 .716 1.397 .855 .838 .881 2.935 52 256 1.751 .89 80 3320 7910 79 87 164 172 0 6413 668 5745 3.492 2975 2308 .286 2.139 1.804 1.097
10 3192 2135 657 273 2535 1862 3172 1646 662 281 2515 1373 0 0 1088 1335 101 71 98 98 98 98 4397 3888 1.361 .735 .546 .616 .542 2.165 52 313 .78 .84 90 3470 7910 78 87 178 187 0 5338 683 4655 1.836 4115 3433 .545 1.365 .877 .449
11 4495 5408 645 268 3850 5140 4694 5266 649 277 4049 4998 0 0 1037 1719 103 70 100 100 100 100 8990 9047 .749 1.335 1.234 1.318 1.28 1.371 80 383 1.461 .9 100 3620 7920 79 89 193 203 0 13520 670 12850 3.338 13165 12495 .3 3.086 1.739 1.626
12 10547 4855 637 260 9910 4595 10348 3791 639 263 9711 3531 0 0 4403 2903 98 57 100 100 100 100 14505 13242 2.157 .464 .364 .44 .451 2.06 52 289 .458 .87 90 3760 7920 79 88 207 216 0 12138 650 11488 1.159 9478 8828 .863 .909 .213 -.138
13 6184 1973 626 259 5558 1714 5947 1572 641 263 5321 1313 0 0 2987 1500 128 65 98 96 94 96 7272 6634 3.243 .308 .247 .239 .245 2.704 52 320 .32 .85 90 3910 7920 79 88 222 231 0 4933 648 4285 .771 3930 3283 1.297 .617 -.375 -.697
14 2460 2035 622 252 1838 1783 2421 1840 646 263 1799 1588 0 0 811 1252 139 74 96 100 96 100 3621 3387 1.031 .97 .883 .763 .905 1.91 32 213 1.067 .86 70 4070 7920 80 87 239 246 0 5088 630 4458 2.425 4600 3970 .412 2.207 1.278 1.142
15 3513 2196 625 240 2888 1956 3609 2032 633 246 2984 1792 0 0 1199 1240 97 53 100 100 100 100 4844 4776 1.476 .677 .601 .579 .668 1.92 52 306 .69 .82 90 4200 7910 78 87 251 260 0 5490 600 4890 1.693 5080 4480 .591 1.501 .76 .586
16 9342 1638 622 235 8720 1403 10150 1692 632 243 9528 1457 0 0 3199 740 133 98 100 93 98 91 10123 10985 6.215 .161 .153 .141 .158 1.709 80 387 .161 .91 100 4350 7910 78 88 266 276 0 4095 588 3508 .402 4230 3643 2.486 .382 -1.314 -1.387
17 9865 1815 632 231 9233 1584 10934 1936 642 231 10302 1705 0 0 3359 608 97 47 100 100 100 100 10817 12007 5.829 .172 .166 .17 .168 1.582 52 301 .151 .9 90 4490 7910 78 87 280 289 0 4538 578 3960 .429 4840 4263 2.332 .414 -1.221 -1.273
18 2150 986 633 235 1517 751 2247 944 644 236 1614 709 0 0 812 667 93 57 93 93 93 90 2268 2323 2.02 .495 .439 .369 .393 2.473 32 160 .48 .68 60 4640 7910 80 86 297 303 0 2465 588 1878 1.238 2360 1773 .808 1.098 .308 .135
19 15278 4113 643 236 14635 3877 15346 3868 653 240 14703 3632 0 0 6878 2087 102 53 100 100 100 100 18512 18335 3.775 .265 .247 .265 .236 1.691 80 383 .248 .89 100 4790 7920 79 89 310 320 0 10283 590 9693 .662 9670 9080 1.51 .618 -.594 -.695
20 7467 1936 634 230 6833 1706 7765 2100 637 233 7131 1870 0 0 3063 858 102 53 98 94 96 92 8539 9001 4.005 .25 .262 .235 .257 2.028 52 295 .23 .89 90 4940 7920 79 88 325 334 0 4840 575 4265 .624 5250 4675 1.602 .656 -.68 -.609

Total number of rows: 43008

Table truncated, full table size 9902 Kbytes.




Supplementary data files not provided
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