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Sample GSM94997 Query DataSets for GSM94997
Status Public on Feb 03, 2006
Title glucose pulse (2g/l) on galactose chemostat (t=5min)
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=5min
Organism Saccharomyces cerevisiae
Characteristics t=5min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58908.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 1706 1247 95 62 1611 1185 1408 959 96 65 1313 897 0 0 1062 908 19 24 100 100 100 100 2796 2210 1.359 .736 .683 .686 .704 1.328 52 388 .76 .957 90 1410 19900 57 66 24 33 0 1299 65 1234 .766 999 934 1.305 .712 -.384 -.491 -.491
2 11294 8824 96 62 11198 8762 11992 8980 98 66 11896 8918 0 0 3354 3105 21 26 100 100 100 100 19960 20814 1.278 .782 .75 .768 .788 1.143 52 407 .787 .981 90 1600 19890 56 65 43 52 0 9192 65 9128 .815 9355 9290 1.227 .781 -.295 -.357 -.357
3 24185 18029 97 66 24088 17963 25433 18310 99 68 25336 18244 0 0 6477 6606 20 22 100 100 100 100 42051 43580 1.341 .746 .72 .716 .73 1.173 52 401 .766 .978 90 1790 19890 56 65 62 71 0 18782 69 18713 .777 19074 19006 1.287 .75 -.364 -.415 -.415
4 1603 1062 97 69 1506 993 1095 683 98 71 998 614 0 0 1270 959 20 23 100 100 100 98 2499 1612 1.517 .659 .615 .594 .625 1.363 52 402 .696 .969 90 1970 19900 57 66 80 89 0 1106 72 1034 .687 712 640 1.456 .641 -.542 -.642 -.642
5 4462 3540 102 70 4360 3470 4706 3651 103 72 4604 3581 0 0 1139 927 20 24 100 100 100 100 7830 8185 1.256 .796 .778 .794 .794 1.111 52 396 .793 .985 90 2150 19890 56 65 98 107 0 3688 73 3615 .829 3803 3731 1.206 .81 -.27 -.304 -.304
6 21412 36218 104 72 21308 36146 22601 37685 106 75 22497 37613 0 0 4849 8920 22 31 100 100 100 100 57454 60110 .589 1.696 1.672 1.687 1.714 1.089 52 401 1.703 .989 90 2330 19890 56 65 116 125 0 37730 75 37655 1.767 39258 39183 .566 1.742 .821 .801 .801
7 3902 3857 100 67 3802 3790 4026 3969 101 70 3926 3902 0 0 635 683 20 23 100 100 100 100 7592 7828 1.003 .997 .994 .994 .996 1.114 52 420 1.004 .98 90 2520 19880 55 64 135 144 0 4018 70 3948 1.038 4135 4065 .963 1.035 .054 .05 .05
8 396 265 101 70 295 195 333 183 102 71 232 113 0 0 261 188 20 23 100 83 100 75 490 345 1.513 .661 .487 .664 .69 1.675 12 104 .7 .874 50 2710 19890 58 63 156 161 0 276 73 203 .689 191 118 1.452 .507 -.538 -.979 -.979
9 1244 829 102 70 1142 759 606 402 102 73 504 332 0 0 1764 1180 22 23 95 98 95 96 1901 836 1.505 .665 .659 .681 .635 1.728 80 524 .662 .961 100 2890 19890 56 66 172 182 0 864 73 791 .692 419 346 1.444 .686 -.53 -.543 -.543
10 277 204 106 75 171 129 161 130 105 77 55 55 0 0 273 179 23 27 78 68 62 50 300 110 1.326 .754 1 .983 .855 2.522 32 176 .667 .856 60 3090 19880 57 63 194 200 0 213 78 134 .786 135 57 1.272 1.042 -.348 .059 .059
11 2643 5521 103 72 2540 5449 2203 4800 104 75 2100 4728 0 0 1323 2706 21 28 100 100 100 100 7989 6828 .466 2.145 2.251 2.17 2.172 1.131 52 382 2.084 .983 90 3240 19860 53 62 207 216 0 5751 75 5676 2.235 5000 4925 .447 2.345 1.16 1.23 1.23
12 1017 799 101 73 916 726 645 508 103 75 544 435 0 0 859 721 20 24 100 100 98 98 1642 979 1.262 .793 .8 .79 .789 1.277 80 512 .816 .978 100 3430 19870 54 64 226 236 0 832 76 756 .826 529 453 1.211 .833 -.276 -.264 -.264
13 1072 1259 99 73 973 1186 879 1083 99 77 780 1010 0 0 696 885 19 26 100 100 100 100 2159 1790 .82 1.219 1.295 1.166 1.208 1.314 52 334 1.242 .952 80 3620 19880 56 64 246 254 0 1312 76 1236 1.27 1128 1052 .788 1.349 .345 .432 .432
14 2530 3121 103 75 2427 3046 770 965 104 78 667 890 0 0 2935 3637 19 27 100 100 100 100 5473 1557 .797 1.255 1.334 1.218 1.19 1.571 52 395 1.233 .958 90 3800 19860 53 62 263 272 0 3251 78 3173 1.307 1005 927 .765 1.39 .387 .475 .475
15 584 524 102 76 482 448 369 338 103 79 267 262 0 0 525 466 20 26 100 90 90 82 930 529 1.076 .929 .981 .902 .912 1.748 52 392 .894 .938 90 3970 19860 53 62 280 289 0 546 79 467 .968 352 273 1.033 1.022 -.047 .032 .032
16 423 311 103 76 320 235 251 209 102 79 148 133 0 0 353 246 20 24 100 94 100 90 555 281 1.362 .734 .899 .714 .658 1.876 52 414 .702 .89 90 4160 19860 53 62 299 308 0 324 79 245 .765 218 139 1.307 .936 -.386 -.095 -.095
17 516 351 103 77 413 274 393 270 104 79 290 193 0 0 346 247 20 26 100 93 90 87 687 483 1.507 .663 .666 .667 .674 1.655 32 236 .676 .924 70 4340 19860 54 61 318 325 0 366 80 285 .691 281 201 1.447 .693 -.533 -.528 -.528
18 3764 2881 97 73 3667 2808 3087 2244 99 76 2990 2171 0 0 2613 2096 18 24 100 100 100 100 6475 5161 1.306 .766 .726 .723 .758 1.204 52 331 .78 .992 80 4520 19840 52 60 336 344 0 3001 76 2925 .798 2338 2262 1.254 .756 -.326 -.403 -.403
19 562 635 99 76 463 559 274 275 101 78 175 199 0 0 716 866 19 24 100 94 98 90 1022 374 .828 1.207 1.137 1.125 1.129 1.703 52 334 1.212 .979 80 4700 19860 54 62 354 362 0 662 79 582 1.258 286 207 .795 1.185 .331 .244 .244
20 244 154 101 74 143 80 169 134 102 76 68 60 0 0 161 79 19 24 93 81 87 65 223 128 1.788 .559 .882 .744 .59 1.719 32 236 .506 .676 70 4890 19860 54 61 373 380 0 160 77 83 .583 140 63 1.716 .919 -.779 -.122 -.122

Total number of rows: 10752

Table truncated, full table size 2430 Kbytes.




Supplementary data files not provided

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