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Sample GSM95011 Query DataSets for GSM95011
Status Public on Feb 03, 2006
Title glucose pulse (0.2g/l) on galactose chemostat (t=15min)
Sample type RNA
 
Channel 1
Source name ref- t=0
Organism Saccharomyces cerevisiae
Characteristics ref- t=0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name t=15min
Organism Saccharomyces cerevisiae
Characteristics t=15min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58957.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 Feb 02, 2006
Last update date Jan 19, 2007
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 GPL3415
Series (1)
GSE4158 Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source

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 1867 802 93 162 1774 640 973 446 97 169 880 284 0 0 1907 788 43 54 100 98 96 84 2414 1164 2.772 .361 .323 .374 .439 2.441 52 334 .346 .707 80 1470 21170 57 65 47 55 0 1152 233 920 .518 641 408 1.929 .464 -.948 -1.109 -1.109
2 14814 21879 92 168 14722 21711 14565 21127 94 177 14473 20959 0 0 4074 6001 19 59 100 100 100 100 36433 35432 .678 1.475 1.448 1.465 1.57 1.391 52 414 1.479 .859 90 1650 21160 55 64 64 73 0 31436 241 31195 2.119 30356 30114 .472 2.081 1.083 1.057 1.057
3 15391 5985 93 167 15298 5818 14472 5553 94 171 14379 5386 0 0 9375 3750 18 49 100 100 100 100 21116 19765 2.629 .38 .375 .375 .429 2.238 52 414 .337 .751 90 1840 21160 55 64 83 92 0 8599 240 8359 .546 7979 7739 1.83 .538 -.872 -.894 -.894
4 3061 1569 91 160 2970 1409 2643 1339 93 164 2552 1179 0 0 1931 979 20 61 100 98 100 96 4379 3731 2.108 .474 .462 .438 .458 1.45 52 403 .469 .904 90 2020 21170 56 65 101 110 0 2254 230 2024 .682 1924 1694 1.467 .664 -.553 -.591 -.591
5 4456 3271 93 160 4363 3111 4201 3130 94 162 4108 2970 0 0 1337 914 21 51 100 100 100 100 7474 7078 1.402 .713 .723 .713 .709 1.234 52 401 .677 .895 90 2200 21160 55 64 119 128 0 4700 230 4470 1.025 4497 4267 .976 1.039 .035 .055 .055
6 16372 28172 88 158 16284 28014 17157 31817 94 165 17069 31659 0 0 7628 16901 69 77 100 100 100 100 44298 48728 .581 1.72 1.855 1.435 1.93 2.301 80 489 1.912 .882 100 2380 21150 54 64 137 147 0 40478 227 40251 2.472 45715 45488 .405 2.665 1.306 1.414 1.414
7 2455 1658 86 165 2369 1493 2407 1581 86 169 2321 1416 0 0 767 532 16 47 100 100 100 100 3862 3737 1.587 .63 .61 .613 .631 1.407 52 288 .604 .866 80 2570 21150 55 63 157 165 0 2382 237 2145 .906 2272 2035 1.104 .877 -.143 -.19 -.19
8 128 207 84 166 44 41 93 144 87 169 9 -22 0 0 212 256 19 49 33 17 15 8 85 -13 1.073 .932 null 4.036 4 4.116 80 450 .875 .432 100 2720 21150 54 64 171 181 -50 297 239 59 1.339 207 -32 .747 null .421 null
9 4421 636 84 159 4337 477 1290 367 86 164 1206 208 0 0 7750 811 19 48 100 65 100 59 4814 1414 9.092 .11 .172 .131 .141 2.988 52 377 .082 .603 90 2930 21160 55 64 192 201 0 914 228 685 .158 527 299 6.328 .248 -2.662 -2.013 -2.013
10 175 161 85 165 90 -4 91 161 91 196 6 -4 0 0 422 110 52 327 7 1 6 1 86 2 null null null 3.018 3.5 6.204 80 458 3.098 .072 100 3080 21150 54 64 207 217 -50 231 237 -6 null 231 -6 null null null null
11 3590 9772 89 172 3501 9600 3332 9422 93 176 3243 9250 0 0 1266 2911 38 46 100 100 100 100 13101 12493 .365 2.742 2.852 2.782 2.742 1.239 52 408 2.743 .899 90 3280 21150 54 63 227 236 0 14041 247 13793 3.94 13538 13291 .254 4.098 1.978 2.035 2.035
12 1492 589 95 175 1397 414 393 285 97 179 298 110 0 0 1885 670 27 48 100 63 100 55 1811 408 3.374 .296 .369 .282 .328 2.505 52 414 .302 .747 90 3460 21150 54 63 245 254 0 846 251 595 .426 409 158 2.349 .53 -1.232 -.915 -.915
13 1638 1136 96 168 1542 968 1494 907 99 172 1398 739 0 0 945 721 21 47 100 96 100 94 2510 2137 1.593 .628 .529 .543 .64 2.007 52 332 .626 .737 80 3650 21150 55 63 265 273 0 1632 241 1391 .902 1303 1062 1.109 .76 -.149 -.397 -.397
14 4640 4556 101 172 4539 4384 880 766 107 183 779 594 0 0 7285 6825 35 116 100 84 93 65 8923 1373 1.035 .966 .763 .899 .982 2.888 32 210 .944 .966 70 3850 21140 54 61 285 292 0 6546 247 6299 1.388 1101 853 .721 1.096 .473 .132 .132
15 446 377 99 179 347 198 136 192 108 227 37 13 0 0 746 494 130 865 26 10 17 3 545 50 1.753 .571 .351 .824 .763 3.654 80 477 .621 .788 100 3990 21140 53 63 298 308 -50 542 257 284 .82 276 19 1.22 .505 -.287 -.986
16 860 585 97 176 763 409 646 482 98 183 549 306 0 0 696 435 18 56 96 80 96 76 1172 855 1.866 .536 .557 .475 .507 2.647 52 320 .565 .851 80 4200 21140 54 62 320 328 0 841 253 588 .77 693 440 1.298 .801 -.377 -.32 -.32
17 706 479 98 184 608 295 419 357 103 185 321 173 0 0 631 434 46 57 93 62 90 56 903 494 2.061 .485 .539 .344 .389 3.019 32 236 .568 .797 70 4370 21150 55 62 337 344 0 688 264 424 .697 513 249 1.434 .774 -.52 -.369 -.369
18 8299 2548 97 155 8202 2393 7774 2223 139 158 7677 2068 0 0 4524 1554 196 52 100 100 100 100 10595 9745 3.427 .292 .269 .264 .292 1.362 32 225 .274 .891 70 4560 21130 53 60 356 363 0 3661 223 3438 .419 3194 2971 2.385 .387 -1.254 -1.369 -1.369
19 468 277 93 168 375 109 126 169 106 173 33 1 0 0 1069 364 106 49 20 27 17 15 484 34 3.44 .291 .03 .828 .722 3.772 80 488 .323 .857 100 4720 21140 53 63 371 381 -50 398 241 157 .418 243 1 2.394 .044 -1.26 -4.522
20 159 160 94 167 65 -7 106 143 108 182 12 -24 0 0 175 69 190 92 12 7 5 2 58 -12 null null null 1.661 1.838 6.127 80 507 .156 .317 100 4900 21140 53 63 389 399 -50 230 240 -10 null 205 -34 null null null null

Total number of rows: 10752

Table truncated, full table size 2463 Kbytes.




Supplementary data files not provided
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