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Sample GSM94989 Query DataSets for GSM94989
Status Public on Feb 03, 2006
Title glucose pulse (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/2005-01/58911.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 2132 1692 105 151 2027 1541 1825 1440 106 157 1720 1289 0 0 1228 952 21 47 100 100 100 100 3568 3009 1.315 .76 .749 .755 .755 1.185 52 399 .755 .976 90 1430 19880 55 64 26 35 0 2075 185 1890 .932 1766 1581 1.072 .919 -.101 -.122 -.122
2 12881 22142 108 158 12773 21984 12516 21988 110 163 12408 21830 0 0 2350 4139 21 45 100 100 100 100 34757 34238 .581 1.721 1.759 1.719 1.722 1.081 52 407 1.706 .992 90 1620 19870 54 63 45 54 0 27159 194 26965 2.111 26970 26776 .474 2.158 1.078 1.11 1.11
3 34705 16387 111 167 34594 16220 36591 17011 114 174 36480 16844 0 0 8613 4576 25 65 100 100 100 100 50814 53324 2.133 .469 .462 .465 .47 1.076 52 401 .469 .993 90 1810 19870 54 63 64 73 0 20100 205 19895 .575 20865 20660 1.739 .566 -.798 -.82 -.82
4 2350 1531 114 171 2236 1360 1681 1125 117 180 1567 954 0 0 1746 1061 36 88 100 100 100 100 3596 2521 1.644 .608 .609 .595 .621 1.208 52 396 .594 .97 90 1980 19880 55 64 81 90 0 1878 210 1668 .746 1380 1170 1.34 .747 -.423 -.421 -.421
5 3229 2782 115 158 3114 2624 3282 2823 116 163 3167 2665 0 0 790 728 21 44 100 100 100 100 5738 5832 1.187 .843 .841 .839 .843 1.106 52 404 .834 .981 90 2160 19860 53 62 99 108 0 3412 194 3219 1.034 3463 3269 .968 1.032 .048 .046 .046
6 18932 34209 111 164 18821 34045 19607 35219 113 170 19496 35055 0 0 3850 6477 23 55 100 100 100 100 52866 54551 .553 1.809 1.798 1.817 1.82 1.056 52 401 1.793 .994 90 2340 19870 54 63 117 126 0 41960 201 41759 2.219 43199 42998 .451 2.205 1.15 1.141 1.141
7 3137 2810 107 158 3030 2652 3141 2806 109 167 3034 2648 0 0 401 441 22 57 100 100 100 100 5682 5682 1.143 .875 .873 .871 .877 1.11 52 407 .867 .981 90 2530 19860 53 62 136 145 0 3447 194 3253 1.074 3442 3248 .931 1.071 .102 .098 .098
8 166 205 107 161 59 44 126 170 107 165 19 9 0 0 170 134 20 47 48 27 21 15 103 28 1.341 .746 .474 1.268 1.146 3.54 80 508 .843 .566 100 2710 19850 52 62 154 164 0 251 197 54 .915 209 11 1.093 .581 -.129 -.783 -.783
9 2313 999 110 177 2203 822 1110 500 112 184 1000 323 0 0 2933 1204 24 60 100 100 100 92 3025 1323 2.68 .373 .323 .355 .371 1.43 52 377 .391 .959 90 2910 19870 54 63 174 183 0 1225 217 1008 .458 613 396 2.185 .396 -1.128 -1.336 -1.336
10 170 188 108 166 62 22 117 164 109 173 9 -2 0 0 193 115 22 55 32 18 18 7 84 7 2.818 .355 null 1.834 1.356 4.919 80 482 .66 .457 100 3070 19850 52 62 190 200 0 231 204 27 .435 201 -2 2.298 null -1.2 null null
11 1633 8575 108 178 1525 8397 1743 8762 111 183 1635 8584 0 0 783 4241 21 51 100 100 100 100 9922 10219 .182 5.506 5.25 5.732 5.608 1.222 80 476 5.514 .987 100 3260 19850 52 62 209 219 0 10518 218 10300 6.754 10747 10529 .148 6.44 2.756 2.687 2.687
12 1468 1076 111 176 1357 900 1251 918 112 182 1140 742 0 0 861 619 21 53 100 100 100 98 2257 1882 1.508 .663 .651 .631 .665 1.237 52 400 .673 .968 90 3440 19850 52 61 227 236 0 1320 216 1104 .813 1126 910 1.229 .798 -.298 -.325 -.325
13 1240 1459 111 182 1129 1277 920 1135 113 190 809 953 0 0 883 967 25 61 100 100 100 100 2406 1762 .884 1.131 1.178 1.122 1.111 1.298 52 334 1.102 .969 80 3630 19860 54 62 247 255 0 1790 223 1566 1.387 1392 1169 .721 1.445 .472 .531 .531
14 2546 4412 110 173 2436 4239 780 1331 111 179 670 1158 0 0 4168 7302 23 58 100 100 100 100 6675 1828 .575 1.74 1.728 1.667 1.65 1.311 52 393 1.751 .995 90 3830 19840 51 60 266 275 0 5412 212 5199 2.134 1633 1420 .469 2.12 1.094 1.084 1.084
15 503 627 108 173 395 454 321 494 109 183 213 321 0 0 485 496 20 91 80 75 75 62 849 534 .87 1.149 1.507 1.564 1.196 2.824 80 479 5.47 .762 100 4000 19830 50 60 283 293 0 769 212 557 1.41 606 394 .709 1.849 .495 .886 .886
16 520 611 109 180 411 431 302 394 110 184 193 214 0 0 526 550 20 49 96 86 94 75 842 407 .954 1.049 1.109 1.053 1.021 1.809 52 401 1.048 .951 90 4190 19830 50 59 302 311 0 749 221 529 1.286 483 262 .777 1.36 .363 .444 .444
17 372 452 112 175 260 277 178 267 112 180 66 92 0 0 498 550 20 43 86 57 65 51 537 158 .939 1.065 1.394 1.006 1.062 3.247 52 381 1.104 .95 90 4370 19850 52 61 320 329 0 554 215 340 1.307 327 113 .765 1.71 .386 .774 .774
18 4353 1628 109 177 4244 1451 3837 1333 110 179 3728 1156 0 0 3053 1041 19 40 100 100 100 100 5695 4884 2.925 .342 .31 .349 .338 1.266 52 327 .337 .981 80 4540 19830 51 59 338 346 0 1997 217 1780 .419 1635 1418 2.385 .38 -1.254 -1.395 -1.395
19 999 807 107 178 892 629 464 518 109 186 357 340 0 0 1087 709 24 45 100 90 100 87 1521 697 1.418 .705 .952 .67 .701 1.709 32 176 .664 .954 60 4720 19840 53 59 357 363 0 990 218 772 .865 635 417 1.156 1.168 -.209 .224 .224
20 176 230 113 192 63 38 140 208 114 195 27 16 0 0 129 92 20 47 55 37 35 15 101 43 1.658 .603 .593 1.152 1.048 4.277 80 501 .792 .372 100 4900 19820 49 59 373 383 0 282 236 47 .74 255 20 1.352 .727 -.435 -.46 -.46

Total number of rows: 10752

Table truncated, full table size 2479 Kbytes.




Supplementary data files not provided
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