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Sample GSM94998 Query DataSets for GSM94998
Status Public on Feb 03, 2006
Title glucose pulse (2g/l) on galactose chemostat (t=150min)
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=150min
Organism Saccharomyces cerevisiae
Characteristics t=150min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58917.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 1199 1377 107 96 1092 1281 995 1142 109 97 888 1046 0 0 671 834 32 28 100 100 100 100 2373 1934 .852 1.173 1.178 1.151 1.148 1.192 52 388 1.19 .98 90 1420 20000 39 48 33 42 0 1391 97 1294 1.185 1153 1056 .844 1.19 .245 .251 .251
2 11412 16327 109 94 11303 16233 11241 15982 108 96 11132 15888 0 0 2638 4145 18 27 100 100 100 100 27536 27020 .696 1.436 1.427 1.43 1.411 1.076 52 398 1.439 .992 90 1610 20000 39 48 52 61 0 16490 95 16395 1.45 16141 16046 .689 1.441 .537 .528 .528
3 25570 38077 106 94 25464 37983 26854 39279 106 98 26748 39185 0 0 7346 12981 17 26 100 100 100 100 63447 65933 .67 1.492 1.465 1.459 1.494 1.095 52 401 1.509 .994 90 1800 20000 39 48 71 80 0 38456 95 38361 1.506 39670 39575 .664 1.48 .591 .565 .565
4 1142 1197 102 97 1040 1100 768 762 104 100 666 665 0 0 1017 1155 19 27 100 100 100 100 2140 1331 .945 1.058 .998 1.019 1.066 1.259 52 401 1.101 .982 90 1980 20010 40 49 89 98 -100 1209 98 1111 1.068 770 672 .936 1.008 .095 .012
5 4087 5246 105 106 3982 5140 4137 5369 134 205 4032 5263 0 0 1011 1616 326 1091 100 100 100 96 9122 9295 .775 1.291 1.305 1.265 1.235 1.147 52 327 1.305 .977 80 2170 19990 39 47 109 117 0 5298 107 5191 1.304 5422 5315 .767 1.318 .383 .399 .399
6 18710 27781 103 101 18607 27680 22382 32236 124 173 22279 32135 0 0 8311 13442 273 909 100 100 98 98 46287 54414 .672 1.488 1.442 1.488 1.489 1.174 80 473 1.52 .985 100 2350 20010 40 50 126 136 0 28058 102 27956 1.502 32557 32455 .666 1.457 .587 .543 .543
7 3343 3090 97 97 3246 2993 3394 3231 98 98 3297 3134 0 0 573 597 16 25 100 100 100 100 6239 6431 1.085 .922 .951 .917 .925 1.102 52 407 .919 .988 90 2530 20000 39 48 144 153 0 3121 98 3023 .931 3263 3165 1.074 .96 -.103 -.059 -.059
8 233 190 96 94 137 96 151 137 98 96 55 43 0 0 202 147 17 24 78 68 68 46 233 98 1.427 .701 .782 .858 .786 2.807 32 170 .728 .884 60 2730 19990 40 46 166 172 0 192 95 97 .708 138 43 1.413 .79 -.499 -.341 -.341
9 1558 843 99 101 1459 742 1197 568 100 102 1098 467 0 0 1256 715 17 24 100 100 100 100 2201 1565 1.966 .509 .425 .48 .482 1.379 52 397 .518 .937 90 2900 20000 39 48 181 190 0 851 102 749 .514 574 472 1.947 .43 -.961 -1.219 -1.219
10 149 121 97 98 52 23 114 109 98 102 17 11 0 0 121 55 16 35 50 26 30 8 75 28 2.261 .442 .647 .829 .6 4.615 80 508 .438 .443 100 3080 19990 38 48 199 209 0 122 99 23 .447 110 11 2.239 .654 -1.163 -.614 -.614
11 2511 2847 94 101 2417 2746 2398 2573 97 103 2304 2472 0 0 972 1089 17 26 100 100 100 100 5163 4776 .88 1.136 1.073 1.146 1.121 1.144 52 400 1.131 .986 90 3260 19990 38 47 217 226 0 2875 102 2773 1.147 2599 2497 .872 1.084 .198 .116 .116
12 894 697 94 105 800 592 758 561 96 107 664 456 0 0 461 398 17 27 100 100 100 100 1392 1120 1.351 .74 .687 .69 .74 1.287 52 408 .773 .961 90 3440 20000 39 48 235 244 0 704 106 598 .747 567 461 1.338 .694 -.42 -.528 -.528
13 761 895 94 101 667 794 591 739 96 103 497 638 0 0 431 502 17 26 100 100 100 100 1461 1135 .84 1.19 1.284 1.181 1.203 1.261 52 334 1.183 .971 80 3630 20010 41 49 255 263 0 904 102 802 1.202 746 644 .832 1.296 .266 .375 .375
14 1631 1649 96 98 1535 1551 487 476 97 101 391 378 0 0 2767 2901 16 26 100 100 100 100 3086 769 .99 1.01 .967 .941 .961 1.451 52 403 1.04 .993 90 3810 19990 38 47 272 281 -100 1665 99 1566 1.02 481 382 .98 .976 .029 -.034
15 407 433 100 102 307 331 310 345 101 104 210 243 0 0 269 299 18 26 100 92 94 92 638 453 .927 1.078 1.157 1.099 1.124 1.689 52 402 1.096 .878 90 3990 19990 38 47 290 299 0 437 103 334 1.089 348 245 .918 1.169 .123 .225 .225
16 249 248 100 101 149 147 160 158 101 104 60 57 0 0 235 252 17 27 81 76 72 52 296 117 1.014 .987 .95 .997 .906 2.471 80 503 1.055 .909 100 4180 19990 38 48 309 319 0 250 102 148 .996 160 58 1.004 .959 -.005 -.06 -.06
17 325 300 100 104 225 196 190 204 100 106 90 100 0 0 301 262 16 26 96 76 88 63 421 190 1.148 .871 1.111 .717 .894 2.92 52 393 .869 .928 90 4360 20000 39 48 327 336 0 303 105 198 .88 206 101 1.137 1.122 -.185 .166 .166
18 2820 2611 100 104 2720 2507 2448 2247 101 106 2348 2143 0 0 2083 2011 17 27 100 100 100 100 5227 4491 1.085 .922 .913 .925 .943 1.345 52 326 .942 .987 80 4550 19990 39 47 347 355 0 2637 105 2532 .931 2269 2164 1.074 .922 -.103 -.118 -.118
19 542 366 98 103 444 263 283 218 100 105 185 115 0 0 661 379 16 28 98 88 98 78 707 300 1.688 .592 .622 .648 .653 1.985 52 328 .57 .948 80 4720 20000 40 48 364 372 0 370 104 266 .598 220 116 1.672 .628 -.741 -.672 -.672
20 142 126 98 103 44 23 121 117 99 105 23 14 0 0 79 48 16 27 57 33 36 18 67 37 1.913 .523 .609 .872 .781 2.917 80 486 .581 .33 100 4900 19990 38 48 381 391 0 127 104 23 .528 118 14 1.894 .615 -.922 -.702 -.702

Total number of rows: 10752

Table truncated, full table size 2424 Kbytes.




Supplementary data files not provided
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