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Sample GSM95000 Query DataSets for GSM95000
Status Public on Feb 03, 2006
Title glucose pulse (2g/l) on galactose chemostat (t=180min)
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=180min
Organism Saccharomyces cerevisiae
Characteristics t=180min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58918.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 1319 1384 112 60 1207 1324 768 780 112 62 656 720 0 0 1207 1291 18 17 100 100 100 100 2531 1376 .912 1.097 1.098 1.108 1.064 1.336 52 320 1.086 .973 90 1470 19780 45 54 30 39 0 1594 69 1525 1.263 898 829 .792 1.264 .337 .338 .338
2 13030 10876 108 61 12922 10815 12881 10846 109 62 12773 10785 0 0 2377 2041 18 16 100 100 100 100 23737 23558 1.195 .837 .844 .837 .834 1.067 52 403 .837 .993 90 1660 19790 46 55 49 58 0 12525 70 12454 .964 12490 12420 1.038 .972 -.053 -.04 -.04
3 10462 20392 109 64 10353 20328 10487 20097 112 66 10378 20033 0 0 3590 7574 18 19 100 100 100 100 30681 30411 .509 1.963 1.93 1.964 1.966 1.108 52 420 1.959 .99 90 1850 19780 45 54 68 77 0 23483 74 23409 2.261 23143 23070 .442 2.223 1.177 1.152 1.152
4 903 1042 109 64 794 978 675 721 110 65 566 657 0 0 1007 1302 17 17 82 87 78 81 1772 1223 .812 1.232 1.161 1.149 1.198 1.554 80 502 1.266 .987 100 2060 19780 45 55 89 99 0 1200 74 1126 1.418 830 757 .705 1.337 .504 .419 .419
5 3644 3759 108 64 3536 3695 3660 3870 110 65 3552 3806 0 0 695 663 18 16 100 100 100 100 7231 7358 .957 1.045 1.072 1.049 1.058 1.103 52 382 1.032 .987 90 2220 19780 45 54 105 114 0 4329 74 4255 1.203 4457 4383 .831 1.234 .267 .303 .303
6 19391 23748 107 63 19284 23685 23648 27849 108 65 23541 27786 0 0 9816 12276 17 17 100 100 100 100 42969 51327 .814 1.228 1.18 1.252 1.248 1.187 80 511 1.234 .995 100 2410 19780 45 55 124 134 0 27348 73 27275 1.414 32070 31998 .707 1.359 .5 .443 .443
7 3466 3188 106 62 3360 3126 3518 3230 107 63 3412 3168 0 0 404 488 17 16 100 100 100 100 6486 6580 1.075 .93 .928 .925 .929 1.09 52 408 .934 .988 90 2600 19780 45 54 143 152 0 3671 71 3600 1.071 3720 3648 .933 1.069 .099 .097 .097
8 227 159 105 63 122 96 163 105 106 64 58 42 0 0 196 155 17 17 92 73 76 57 218 100 1.271 .787 .724 .719 .715 3.228 52 335 .777 .895 80 2780 19780 46 54 162 170 0 183 73 111 .906 121 48 1.104 .834 -.142 -.262 -.262
9 1382 1043 104 60 1278 983 624 448 105 62 520 388 0 0 1821 1338 18 17 100 100 100 100 2261 908 1.3 .769 .746 .796 .804 1.333 52 414 .741 .977 90 2960 19780 45 54 179 188 0 1201 69 1132 .886 516 447 1.129 .859 -.175 -.219 -.219
10 248 163 109 65 139 98 150 97 109 64 41 32 0 0 233 153 17 16 78 71 56 46 237 73 1.418 .705 .78 .847 .741 2.423 32 236 .663 .873 70 3170 19780 46 53 201 208 0 188 75 113 .812 112 37 1.232 .899 -.301 -.154 -.154
11 2702 1830 105 65 2597 1765 2429 1621 106 64 2324 1556 0 0 917 673 19 16 100 100 100 100 4362 3880 1.471 .68 .67 .673 .676 1.118 52 396 .684 .985 90 3330 19780 45 54 216 225 0 2107 75 2033 .783 1867 1792 1.278 .771 -.354 -.375 -.375
12 1038 1226 106 65 932 1161 900 964 106 66 794 899 0 0 533 697 18 16 100 100 100 100 2093 1693 .803 1.246 1.132 1.232 1.247 1.224 52 400 1.272 .975 90 3520 19770 44 53 235 244 0 1412 75 1337 1.435 1110 1035 .697 1.304 .521 .383 .383
13 776 717 104 65 672 652 527 469 105 66 423 404 0 0 723 673 18 16 100 100 100 100 1324 827 1.031 .97 .955 .971 .962 1.356 52 408 .948 .983 90 3700 19780 45 54 253 262 0 826 75 751 1.117 540 465 .895 1.1 .16 .137 .137
14 1432 1382 103 65 1329 1317 330 272 104 66 227 207 0 0 3023 2906 17 16 93 91 90 87 2646 434 1.009 .991 .912 .858 .894 1.671 80 495 .965 .987 100 3890 19770 44 54 272 282 0 1591 75 1517 1.141 313 238 .876 1.05 .191 .071 .071
15 430 336 106 63 324 273 230 187 106 66 124 124 0 0 393 333 18 19 92 90 88 82 597 248 1.187 .843 1 .823 .837 1.88 52 318 .84 .93 80 4060 19770 45 53 290 298 0 387 73 314 .97 215 143 1.031 1.152 -.043 .204 .204
16 415 303 106 64 309 239 260 183 106 65 154 119 0 0 332 254 19 17 94 100 88 88 548 273 1.293 .773 .773 .869 .778 1.948 52 326 .765 .946 80 4260 19770 45 53 310 318 0 349 74 275 .891 211 137 1.123 .89 -.167 -.168 -.168
17 328 237 104 63 224 174 185 113 106 65 81 50 0 0 393 310 17 17 94 80 84 65 398 131 1.287 .777 .617 .718 .766 1.791 52 334 .785 .968 80 4430 19780 46 54 327 335 0 273 73 200 .895 130 58 1.118 .711 -.161 -.492 -.492
18 2425 2940 108 66 2317 2874 2051 2386 109 68 1943 2320 0 0 1781 2218 20 17 100 100 100 100 5191 4263 .806 1.24 1.194 1.28 1.242 1.184 52 334 1.244 .993 80 4620 19780 46 54 346 354 0 3386 76 3310 1.428 2748 2672 .7 1.375 .514 .459 .459
19 681 407 104 62 577 345 339 190 105 64 235 128 0 0 839 498 18 18 96 84 93 81 922 363 1.672 .598 .545 .571 .594 1.572 32 236 .591 .974 70 4800 19780 46 53 364 371 0 469 71 397 .689 219 147 1.452 .627 -.538 -.673 -.673
20 308 162 107 61 201 101 289 172 108 63 182 111 0 0 153 58 19 19 100 91 91 83 302 293 1.99 .502 .61 .518 .555 1.941 12 98 .433 .737 50 4980 19770 46 51 383 388 0 187 70 116 .579 198 128 1.728 .702 -.789 -.51 -.51

Total number of rows: 10752

Table truncated, full table size 2430 Kbytes.




Supplementary data files not provided
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