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Sample GSM90276 Query DataSets for GSM90276
Status Public on Dec 31, 2005
Title AT2_VEGF_10ng
Sample type RNA
 
Channel 1
Source name Huvec treated with 5ng VEGF
Organism Homo sapiens
Characteristics Huvec treated with 5ng VEGF
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/2002-05/28510.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 1425 1610 728 558 697 1052 1509 1518 746 573 781 960 0 0 575 525 133 174 84 98 82 88 1749 1741 .663 1.509 1.229 1 1 1 52 318 1 .54 90 2080 7570 56 65 47 56 0 1643 569 1073 1.54 1549 980 .649 1.254 .623 .327
2 8772 11468 734 540 8038 10928 10078 13448 743 543 9344 12908 0 0 4225 5492 116 173 93 98 92 98 18966 22252 .736 1.36 1.381 1 1 1 80 378 1 .78 100 2230 7580 57 67 62 72 0 11702 551 11151 1.387 13722 13171 .721 1.41 .472 .495
3 7800 17909 739 527 7061 17382 8528 18529 743 534 7789 18002 0 0 3327 7081 110 164 94 98 94 96 24443 25791 .406 2.462 2.311 1 1 1 52 320 1 .85 90 2380 7580 57 66 77 86 0 18274 538 17737 2.512 18907 18369 .398 2.358 1.329 1.238
4 2045 3837 723 525 1322 3312 2441 4013 730 556 1718 3488 0 0 908 1669 132 210 81 93 78 90 4634 5206 .399 2.505 2.03 1 1 1 32 200 1 .74 70 2520 7580 58 65 92 99 0 3915 536 3380 2.556 4095 3559 .391 2.072 1.354 1.051
5 28329 17593 682 478 27647 17115 28748 15884 617 491 28066 15406 0 0 20796 11461 282 234 82 98 82 94 44762 43472 1.615 .619 .549 1 1 1 52 339 1 .82 90 2660 7570 56 65 105 114 0 17952 488 17464 .632 16208 15720 1.583 .56 -.663 -.836
6 2238 3018 693 467 1545 2551 2731 3151 627 468 2038 2684 0 0 1040 1340 248 175 82 90 73 90 4096 4722 .606 1.651 1.317 1 1 1 52 255 1 .81 80 2810 7580 58 66 121 129 0 3080 477 2603 1.685 3215 2739 .594 1.344 .753 .426
7 14713 17411 729 493 13984 16918 16289 18654 745 506 15560 18161 0 0 7924 7257 156 173 96 100 96 98 30902 33721 .827 1.21 1.167 1 1 1 80 352 1 .89 100 2960 7580 57 67 135 145 0 17766 503 17263 1.235 19035 18532 .81 1.191 .304 .252
8 3279 2363 728 469 2551 1894 3630 2661 744 495 2902 2192 0 0 1491 1095 285 191 91 93 88 90 4445 5094 1.347 .742 .755 1 1 1 80 354 1 .84 100 3110 7580 57 67 150 160 0 2411 479 1933 .758 2715 2237 1.32 .771 -.4 -.376
9 1382 2142 730 482 652 1660 1503 2429 744 493 773 1947 0 0 654 1022 309 179 69 86 65 82 2312 2720 .393 2.546 2.519 1 1 1 52 254 1 .67 80 3260 7580 58 66 166 174 0 2186 492 1694 2.598 2479 1987 .385 2.57 1.377 1.362
10 2164 3549 723 471 1441 3078 2448 3725 733 489 1725 3254 0 0 972 1878 144 175 84 92 84 92 4519 4979 .468 2.136 1.886 1 1 1 52 305 1 .82 90 3410 7570 56 65 180 189 0 3621 481 3141 2.18 3801 3320 .459 1.925 1.124 .945
11 4193 11710 716 478 3477 11232 4451 12002 735 496 3735 11524 0 0 1603 5037 134 173 98 100 98 100 14709 15259 .31 3.23 3.085 1 1 1 80 419 1 .86 110 3550 7580 56 67 193 204 0 11949 488 11461 3.296 12247 11759 .303 3.148 1.721 1.655
12 9311 14471 711 474 8600 13997 9432 14609 727 500 8721 14135 0 0 6416 11562 116 159 92 98 92 96 22597 22856 .614 1.628 1.621 1 1 1 52 245 1 .78 80 3690 7570 57 65 209 217 0 14766 484 14283 1.661 14907 14423 .602 1.654 .732 .726
13 6448 4051 745 491 5703 3560 7129 4388 754 523 6384 3897 0 0 3082 2131 142 194 92 94 92 86 9263 10281 1.602 .624 .61 1 1 1 52 336 1 .88 90 3840 7570 56 65 223 232 0 4134 501 3633 .637 4478 3977 1.57 .623 -.651 -.683
14 1777 1709 747 459 1030 1250 1897 1812 769 510 1150 1353 0 0 509 543 219 233 90 93 87 93 2280 2503 .824 1.214 1.177 1 1 1 32 210 1 .67 70 4000 7570 57 64 240 247 0 1744 468 1276 1.238 1849 1381 .808 1.201 .308 .264
15 1522 2211 740 453 782 1758 1654 2264 764 471 914 1811 0 0 772 1033 208 166 73 92 67 90 2540 2725 .445 2.248 1.981 1 1 1 52 310 1 .53 90 4130 7570 56 65 252 261 0 2256 462 1794 2.294 2310 1848 .436 2.022 1.198 1.016
16 9142 13220 752 464 8390 12756 11549 15113 781 482 10797 14649 0 0 6298 7321 161 212 78 94 76 92 21146 25446 .658 1.52 1.357 1 1 1 52 312 1 .79 90 4280 7570 56 65 267 276 0 13490 473 13016 1.551 15421 14948 .645 1.384 .634 .469
17 8662 7992 733 446 7929 7546 10587 8843 755 468 9854 8397 0 0 5357 3913 159 223 86 92 84 92 15475 18251 1.051 .952 .852 1 1 1 52 312 1 .84 90 4420 7570 56 65 281 290 0 8155 455 7700 .971 9023 8568 1.03 .87 -.042 -.202
18 1546 1932 723 431 823 1501 1482 1736 736 459 759 1305 0 0 839 1314 134 217 71 73 63 67 2324 2064 .548 1.824 1.719 1 1 1 52 252 1 .75 80 4580 7570 57 65 298 306 -50 1971 440 1532 1.861 1771 1332 .537 1.754 .896 .811
19 12657 19777 727 447 11930 19330 14247 22450 754 482 13520 22003 0 0 5934 11016 280 266 100 100 100 100 31260 35523 .617 1.62 1.627 1 1 1 80 466 1 .9 110 4720 7570 55 66 310 321 0 20181 456 19724 1.653 22908 22452 .605 1.661 .725 .732
20 10001 13096 732 463 9269 12633 10866 14301 773 516 10134 13838 0 0 4785 6375 388 352 87 100 87 96 21902 23972 .734 1.363 1.366 1 1 1 32 212 1 .85 70 4870 7570 57 64 327 334 0 13363 472 12891 1.391 14593 14120 .719 1.393 .476 .479

Total number of rows: 43008

Table truncated, full table size 9386 Kbytes.




Supplementary data files not provided
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