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Sample GSM95005 Query DataSets for GSM95005
Status Public on Feb 03, 2006
Title glucose pulse (0.2g/l) on galactose chemostat (t=4min)
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=4min
Organism Saccharomyces cerevisiae
Characteristics t=4min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58953.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) 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 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 1651 1446 104 103 1547 1343 1520 1298 106 103 1416 1195 0 0 797 708 18 24 100 100 100 100 2890 2611 1.152 .868 .844 .876 .867 1.216 52 408 .868 .964 90 1700 20560 43 52 53 62 0 1648 117 1530 .989 1479 1362 1.011 .962 -.016 -.056 -.056
2 11661 13763 105 105 11556 13658 11459 13419 107 106 11354 13314 0 0 2918 3078 20 28 100 100 100 100 25214 24668 .846 1.182 1.173 1.192 1.204 1.082 52 414 1.156 .977 90 1880 20560 43 52 71 80 0 15682 120 15563 1.347 15290 15171 .743 1.336 .429 .418 .418
3 9169 10215 104 108 9065 10107 9010 9897 105 111 8906 9789 0 0 3547 3694 19 38 100 100 100 100 19172 18695 .897 1.115 1.099 1.134 1.136 1.13 52 408 1.09 .979 90 2070 20560 43 52 90 99 0 11640 123 11516 1.27 11277 11154 .787 1.252 .345 .325 .325
4 2202 2135 104 111 2098 2024 2075 1963 115 116 1971 1852 0 0 1199 1191 115 52 100 100 100 100 4122 3823 1.037 .965 .94 .962 .968 1.146 52 402 .97 .979 90 2250 20570 44 53 108 117 0 2433 126 2306 1.099 2237 2110 .91 1.071 .137 .099 .099
5 2817 3078 103 112 2714 2966 2796 3121 113 118 2693 3009 0 0 582 645 115 52 100 100 100 100 5680 5702 .915 1.093 1.117 1.091 1.099 1.096 52 400 1.073 .975 90 2430 20560 43 52 126 135 0 3507 128 3380 1.245 3556 3429 .803 1.273 .316 .348 .348
6 13447 17186 99 109 13348 17077 14722 18643 99 111 14623 18534 0 0 5616 7293 16 28 100 100 100 100 30425 33157 .782 1.279 1.267 1.294 1.274 1.196 80 484 1.284 .989 100 2610 20560 43 53 144 154 0 19583 124 19459 1.458 21243 21119 .686 1.444 .544 .53 .53
7 1766 1784 99 109 1667 1675 1726 1762 101 121 1627 1653 0 0 552 602 19 122 100 100 100 100 3342 3280 .995 1.005 1.016 .989 .982 1.139 52 377 .998 .979 90 2790 20550 42 51 162 171 0 2033 124 1909 1.145 2008 1884 .873 1.158 .195 .211 .211
8 152 139 98 108 54 31 108 112 100 116 10 4 0 0 139 98 19 104 33 11 21 5 85 14 1.742 .574 .4 1.159 1.067 3.387 80 490 .706 .693 100 2960 20560 43 53 179 189 0 158 123 35 .654 128 5 1.529 .456 -.612 -1.134 -1.134
9 2689 3635 97 110 2592 3525 2000 2605 99 111 1903 2495 0 0 2527 3318 21 29 100 100 100 100 6117 4398 .735 1.36 1.311 1.434 1.427 1.291 52 393 1.338 .974 90 3160 20570 44 53 199 208 0 4142 125 4017 1.55 2968 2843 .645 1.494 .632 .579 .579
10 180 163 95 109 85 54 112 106 97 112 17 -3 0 0 214 173 20 27 45 23 22 18 139 14 1.574 .635 null 1.025 1.004 3.053 80 511 .796 .868 100 3330 20560 43 53 216 226 0 186 124 62 .724 121 -3 1.381 null -.466 null null
11 2578 4310 98 115 2480 4195 2411 3876 99 118 2313 3761 0 0 1355 2391 17 28 100 100 100 100 6675 6074 .591 1.692 1.626 1.673 1.666 1.117 52 400 1.67 .979 90 3520 20550 42 51 235 244 0 4911 131 4780 1.927 4417 4286 .519 1.853 .947 .89 .89
12 1808 1418 101 132 1707 1286 1783 1456 103 136 1682 1324 0 0 766 675 24 41 100 100 100 100 2993 3006 1.327 .753 .787 .727 .71 1.224 32 236 .777 .953 70 3700 20560 44 51 254 261 0 1616 150 1465 .858 1659 1509 1.165 .897 -.22 -.157 -.157
13 1162 1023 98 125 1064 898 1056 956 98 128 958 831 0 0 712 562 16 32 100 100 100 100 1962 1789 1.185 .844 .867 .844 .874 1.263 52 340 .819 .955 80 3900 20560 44 52 274 282 0 1166 142 1023 .962 1089 947 1.04 .988 -.056 -.017 -.017
14 3209 2927 100 135 3109 2792 1130 1157 100 134 1030 1022 0 0 4022 3541 17 33 100 93 100 93 5901 2052 1.114 .898 .992 .901 .878 1.47 32 176 .885 .971 60 4090 20570 46 52 294 300 0 3335 154 3181 1.023 1318 1165 .977 1.131 .033 .177 .177
15 986 724 114 140 872 584 937 661 133 142 823 521 0 0 284 303 63 38 100 100 100 100 1456 1344 1.493 .67 .633 .618 .66 1.339 12 90 .731 .929 50 4240 20540 43 48 309 314 0 825 160 665 .763 753 594 1.31 .721 -.39 -.471 -.471
16 585 402 100 131 485 271 462 322 101 134 362 191 0 0 308 232 16 36 100 100 100 92 756 553 1.79 .559 .528 .489 .512 1.526 52 340 .621 .875 80 4450 20560 44 52 329 337 0 458 149 309 .637 367 218 1.571 .601 -.651 -.734 -.734
17 978 808 108 136 870 672 969 891 111 138 861 755 0 0 510 412 23 34 100 100 100 100 1542 1616 1.295 .772 .877 .756 .81 1.279 12 104 .781 .925 50 4620 20570 46 51 347 352 0 921 155 766 .88 1015 860 1.136 .999 -.184 -.001 -.001
18 6139 6421 101 128 6038 6293 6944 6798 123 142 6843 6670 0 0 2096 2336 119 89 100 100 100 100 12331 13513 .959 1.042 .975 1.038 1.058 1.097 32 230 1.048 .984 70 4810 20550 43 50 365 372 0 7316 146 7171 1.188 7746 7600 .842 1.111 .248 .151 .151
19 384 268 98 132 286 136 146 139 101 136 48 7 0 0 582 339 38 43 56 37 38 25 422 55 2.103 .476 .146 .694 .571 2.849 80 494 .564 .946 100 4980 20550 42 52 381 391 0 305 150 155 .542 158 8 1.846 .166 -.884 -2.589 -2.589
20 157 129 96 131 61 -2 113 114 97 134 17 -17 0 0 120 54 15 33 51 15 36 7 59 0 null null null 1.092 .732 5.559 80 500 .345 .155 100 5160 20550 42 52 399 409 0 147 149 -2 null 130 -19 null null null null null

Total number of rows: 10752

Table truncated, full table size 2447 Kbytes.




Supplementary data files not provided

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