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Sample GSM93647 Query DataSets for GSM93647
Status Public on Jan 25, 2006
Title HUVEC exposure 1 ug/ml colchicine 120'_1
Sample type RNA
 
Channel 1
Source name Stratagene reference
Organism Homo sapiens
Characteristics Stratagene reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 ug/ml colchicine 120'_1
Organism Homo sapiens
Characteristics 1 ug/ml colchicine 120'_1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Drug treatment
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56595.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 Jan 24, 2006
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 GPL3386
Series (1)
GSE4090 Mechanism of the anti-inflammatory effect of colchicine in rheumatic diseases

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 437 313 107 83 330 230 426 279 109 83 319 196 0 0 106 132 24 28 100 98 100 95 560 515 1.435 .697 .614 .632 .65 1.591 68 273 .777 .88 90 1720 5940 69 78 99 108 0 348 92 256 .775 310 218 1.291 .683 -.368 -.55 -.55
2 7205 565 107 82 7098 483 7200 552 108 86 7093 470 0 0 2473 199 22 30 100 100 100 98 7581 7563 14.696 .068 .066 .066 .07 1.456 72 213 .067 .95 90 1880 5930 68 77 115 124 0 628 91 537 .076 614 522 13.222 .074 -3.725 -3.763 -3.763
3 3186 1871 105 82 3081 1789 3467 1930 108 85 3362 1848 0 0 1588 1011 24 29 100 100 100 100 4870 5210 1.722 .581 .55 .558 .567 1.394 72 210 .588 .97 90 2020 5930 68 77 129 138 0 2080 91 1988 .645 2145 2054 1.549 .611 -.632 -.711 -.711
4 421 344 114 89 307 255 412 331 119 94 298 242 0 0 112 116 29 32 100 100 100 98 562 540 1.204 .831 .812 .796 .805 1.607 69 220 .862 .88 90 2170 5930 68 77 144 153 0 382 99 283 .923 368 269 1.083 .903 -.115 -.148 -.148
5 1050 947 118 94 932 853 1081 909 121 99 963 815 0 0 307 412 32 37 100 100 100 100 1785 1778 1.093 .915 .846 .854 .871 1.539 73 273 .973 .93 100 2320 5940 69 79 159 169 0 1053 104 948 1.017 1010 906 .983 .941 .025 -.088 -.088
6 289 180 109 92 180 88 277 174 110 98 168 82 0 0 77 58 26 43 100 77 98 48 268 250 2.045 .489 .488 .402 .467 2.797 58 228 .489 .63 90 2470 5930 68 77 174 183 0 200 102 98 .543 193 91 1.84 .543 -.88 -.882 -.882
7 1149 1103 110 90 1039 1013 1154 1113 113 97 1044 1023 0 0 376 429 27 44 100 100 100 100 2052 2067 1.026 .975 .98 .943 .923 1.444 73 231 1.006 .95 90 2610 5930 68 77 188 197 0 1226 100 1126 1.084 1237 1137 .923 1.089 .116 .123 .123
8 425 532 112 83 313 449 425 525 111 89 313 442 0 0 105 196 23 31 100 100 100 100 762 755 .697 1.435 1.412 1.376 1.424 1.477 70 220 1.531 .92 90 2760 5930 68 77 203 212 0 591 92 499 1.594 584 491 .627 1.57 .673 .65 .65
9 268 158 111 88 157 70 256 146 112 94 145 58 0 0 66 56 23 32 100 74 97 46 227 203 2.243 .446 .4 .416 .429 2.127 99 281 .468 .6 110 2900 5940 68 79 216 227 0 176 98 78 .496 162 64 2.018 .445 -1.013 -1.169 -1.169
10 1899 343 110 90 1789 253 1938 335 112 94 1828 245 0 0 479 115 24 32 100 97 100 97 2042 2073 7.071 .141 .134 .133 .137 1.498 111 272 .141 .89 110 3050 5930 67 78 231 242 0 381 100 281 .157 372 272 6.362 .149 -2.669 -2.747 -2.747
11 3152 155 108 84 3044 71 3265 149 109 90 3157 65 0 0 671 57 22 35 100 70 100 46 3115 3222 42.873 .023 .021 .019 .022 2.35 86 233 .021 .58 100 3210 5940 69 79 248 258 0 172 93 79 .026 166 72 38.573 .023 -5.27 -5.449 -5.449
12 1828 4848 107 84 1721 4764 1904 5031 108 89 1797 4947 0 0 608 1676 20 36 100 100 100 100 6485 6744 .361 2.768 2.753 2.791 2.822 1.376 86 224 2.842 .96 100 3360 5940 69 79 263 273 0 5389 93 5295 3.077 5592 5499 .325 3.06 1.621 1.613 1.613
13 2587 3899 106 84 2481 3815 2613 3906 108 90 2507 3822 0 0 763 1114 22 31 100 100 100 100 6296 6329 .65 1.538 1.525 1.569 1.52 1.387 104 258 1.548 .96 110 3490 5940 68 79 275 286 0 4334 93 4240 1.709 4342 4248 .585 1.695 .773 .761 .761
14 311 199 108 91 203 108 308 186 110 96 200 95 0 0 52 65 22 32 100 92 100 68 311 295 1.88 .532 .475 .481 .467 1.913 83 239 .591 .67 100 3640 5940 69 79 291 301 0 221 101 120 .591 207 106 1.691 .528 -.758 -.921 -.921
15 691 137 113 102 578 35 694 116 115 104 581 14 0 0 146 67 25 36 100 37 100 20 613 595 16.514 .061 .024 .064 .08 3.5 77 234 .072 .38 100 3790 5940 69 79 306 316 0 152 113 39 .067 129 16 14.858 .027 -3.893 -5.223 -5.223
16 2383 2740 106 95 2277 2645 2377 2553 109 98 2271 2458 0 0 953 1089 23 32 100 100 100 100 4922 4729 .861 1.162 1.082 1.21 1.145 1.508 96 262 1.164 .96 110 3940 5940 68 79 320 331 0 3045 106 2940 1.291 2838 2732 .775 1.203 .369 .267 .267
17 2498 4203 104 89 2394 4114 2571 4158 108 93 2467 4069 0 0 671 1486 24 30 100 100 100 100 6508 6536 .582 1.718 1.649 1.666 1.72 1.366 96 200 1.807 .97 100 4090 5940 69 79 336 346 0 4672 99 4573 1.91 4622 4523 .524 1.833 .934 .874 .874
18 1833 557 107 88 1726 469 1864 560 106 91 1757 472 0 0 373 168 29 32 100 100 100 100 2195 2229 3.68 .272 .269 .262 .263 1.433 114 276 .272 .93 120 4230 5940 68 80 349 361 0 619 98 521 .302 622 525 3.311 .299 -1.727 -1.744 -1.744
19 3026 3794 112 96 2914 3698 3156 3871 114 102 3044 3775 0 0 1060 1345 43 47 99 100 99 100 6612 6819 .788 1.269 1.24 1.313 1.288 1.855 113 323 1.271 .95 130 4370 5940 67 80 362 375 0 4217 107 4110 1.411 4303 4196 .709 1.378 .496 .463 .463
20 3132 3749 106 93 3026 3656 3476 3950 112 102 3370 3857 0 0 1183 1501 43 49 97 100 97 100 6682 7227 .828 1.208 1.145 1.191 1.19 1.615 103 341 1.222 .96 120 4520 5940 68 80 378 390 0 4167 103 4064 1.343 4390 4287 .745 1.272 .425 .347 .347

Total number of rows: 41472

Table truncated, full table size 9194 Kbytes.




Supplementary data files not provided
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