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Sample GSM78352 Query DataSets for GSM78352
Status Public on Oct 15, 2005
Title Na+FK 30min
Sample type RNA
 
Channel 1
Source name 0.8M NaCl +FK506 0min
Organism Saccharomyces cerevisiae
Characteristics 0.8M NaCl +FK506 0min
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 0.8M NaCl + FK506 30min
Organism Saccharomyces cerevisiae
Characteristics 0.8M NaCl + FK506 30min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: salt treatment, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7763.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 14, 2005
Last update date Sep 22, 2006
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 GPL2658
Series (1)
GSE3456 Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 3005 2632 410 268 2595 2364 null null 420 289 null null null null null null null null 100 96 null null null null 1.098 .911 null null .855 null 80 602 .958 .93 null null null 88 99 113 124 0 2860 291 2569 .99 null null 1.01 null -.015 null
2 2300 2183 402 262 1898 1921 null null 402 264 null null null null null null null null 75 81 null null null null .988 1.012 null null 1.191 null 32 164 .886 .87 null null null 94 100 133 139 0 2372 284 2088 1.1 null null .909 null .138 null
3 3746 3579 417 287 3329 3292 null null 431 317 null null null null null null null null 100 95 null null null null 1.011 .989 null null .892 null 80 548 .993 .93 null null null 88 99 148 159 0 3890 311 3579 1.075 null null .93 null .104 null
4 5512 6679 436 292 5076 6387 null null 441 311 null null null null null null null null 100 100 null null null null .795 1.258 null null 1.298 null 32 224 .979 .86 null null null 90 97 167 174 0 7259 317 6942 1.368 null null .731 null .452 null
5 2461 2370 436 301 2025 2069 null null 459 323 null null null null null null null null 88 90 null null null null .979 1.022 null null .99 null 80 478 .956 .92 null null null 90 100 181 191 0 2576 327 2249 1.111 null null .9 null .151 null
6 2784 2303 450 298 2334 2005 null null 453 303 null null null null null null null null 81 84 null null null null 1.164 .859 null null .81 null 32 176 .756 .86 null null null 92 98 203 209 0 2503 323 2180 .934 null null 1.071 null -.098 null
7 2828 2493 436 279 2392 2214 null null 597 524 null null null null null null null null 77 65 null null null null 1.08 .926 null null .994 null 80 522 .857 .92 null null null 89 100 218 229 0 2709 303 2406 1.006 null null .994 null .008 null
8 405 266 420 267 -15 -1 null null 607 565 null null null null null null null null 0 0 null null null null null null null null .956 null 80 444 .558 .83 null null null 89 99 236 246 -100 289 290 -1 null null null null null null null
9 395 276 406 259 -11 17 null null 412 268 null null null null null null null null 7 21 null null null null null null null null .943 null 80 452 .132 .11 null null null 90 100 254 264 -100 300 281 19 null null null null null null null
10 400 281 406 275 -6 6 null null 418 281 null null null null null null null null 11 13 null null null null null null null null 1.124 null 80 440 .018 0 null null null 90 100 272 282 -100 305 298 7 null null null null null null null
11 422 305 437 327 -15 -22 null null 447 345 null null null null null null null null 11 5 null null null null null null null null 1.537 null 80 440 .289 .22 null null null 90 100 289 299 -100 331 355 -24 null null null null null null null
12 484 426 483 414 1 12 null null 491 419 null null null null null null null null 13 16 null null null null .083 12 null null 1.227 null 80 452 .108 .08 null null null 90 100 307 317 -100 463 450 13 13 null null .077 null 3.7 null
13 508 435 494 419 14 16 null null 500 431 null null null null null null null null 21 16 null null null null .875 1.143 null null 1.016 null 80 444 .336 .2 null null null 90 100 324 334 -100 472 455 17 1.214 null null .824 null .28 null
14 492 408 479 387 13 21 null null 485 402 null null null null null null null null 17 15 null null null null .619 1.615 null null 1.009 null 80 444 .162 .11 null null null 90 100 342 352 -100 443 420 23 1.769 null null .565 null .823 null
15 485 399 477 367 8 32 null null 485 381 null null null null null null null null 13 13 null null null null .25 4 null null 1.679 null 80 444 .191 .12 null null null 90 100 359 369 -100 433 398 35 4.375 null null .229 null 2.129 null
16 433 296 449 312 -16 -16 null null 460 329 null null null null null null null null 7 0 null null null null null null null null .87 null 80 452 .418 .28 null null null 91 101 377 387 -100 321 339 -18 null null null null null null null
17 421 283 428 272 -7 11 null null 440 288 null null null null null null null null 7 10 null null null null null null null null 1.119 null 80 452 .254 .21 null null null 91 101 395 405 -100 307 295 12 null null null null null null null
18 425 286 436 294 -11 -8 null null 446 311 null null null null null null null null 7 5 null null null null null null null null 1.285 null 80 452 .261 .22 null null null 91 101 412 422 -100 310 319 -9 null null null null null null null
19 619 526 451 319 168 207 null null 460 338 null null null null null null null null 21 13 null null null null .812 1.232 null null .858 null 80 435 .824 .9 null null null 91 101 430 440 -100 571 346 225 1.339 null null .747 null .421 null
20 438 301 444 304 -6 -3 null null 451 321 null null null null null null null null 6 8 null null null null null null null null 1.326 null 80 452 .568 .45 null null null 91 101 447 457 -100 327 330 -3 null null null null null null null

Total number of rows: 8064

Table truncated, full table size 1979 Kbytes.




Supplementary data files not provided

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