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Sample GSM90647 Query DataSets for GSM90647
Status Public on Jan 06, 2006
Title PmrA-vsPmrAc 60' (2)
Sample type RNA
 
Channel 1
Source name PmrA- (H2O)
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics PmrA- (H2O)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PmrAc (H2O)
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics PmrAc (H2O)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27300.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 Jan 04, 2006
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 GPL3048
Series (1)
GSE3975 S. typhimurium Bile regulated genes

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 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
1 5015 3648 350 212 4665 3436 1429 1010 352 222 1079 798 0 0 6974 5310 52 64 98 100 97 93 8101 1877 1.358 .737 .74 .769 .728 1.682 80 530 .752 .99 100 1300 17830 58 68 57 67 0 9354 544 8810 1.889 2590 2046 .529 1.896 .917 .923
2 5543 3810 349 219 5194 3591 2036 1150 358 227 1687 931 0 0 7759 5683 76 86 100 100 100 91 8785 2618 1.446 .691 .552 .613 .611 1.421 120 883 .716 .97 130 1540 17820 55 68 79 92 0 9769 562 9208 1.773 2949 2387 .564 1.415 .826 .501
3 8693 4983 347 217 8346 4766 4320 2028 355 223 3973 1811 0 0 9263 5426 63 61 100 100 100 100 13112 5784 1.751 .571 .456 .567 .554 1.587 52 420 .572 .97 90 1770 17840 59 68 104 113 0 12777 556 12221 1.464 5200 4644 .683 1.169 .55 .225
4 7520 3864 354 217 7166 3647 4707 1925 369 226 4353 1708 0 0 6710 3690 86 63 100 100 100 100 10813 6061 1.965 .509 .392 .455 .482 1.586 80 560 .523 .97 100 2000 17840 59 69 127 137 0 9908 556 9351 1.305 4936 4379 .766 1.006 .384 .009
5 7351 3852 353 219 6998 3633 2853 1292 360 227 2500 1073 0 0 7395 4087 69 64 100 98 100 97 10631 3573 1.926 .519 .429 .489 .509 1.549 80 560 .533 .97 100 2230 17840 59 69 150 160 0 9877 562 9315 1.331 3313 2751 .751 1.101 .413 .138
6 11669 6648 358 236 11311 6412 4460 2613 366 237 4102 2377 0 0 12992 7467 66 60 100 100 100 100 17723 6479 1.764 .567 .579 .583 .556 1.421 52 420 .563 .97 90 2450 17840 59 68 172 181 0 17046 605 16441 1.454 6700 6095 .688 1.486 .54 .571
7 13711 6833 362 233 13349 6600 2422 1359 364 236 2060 1126 0 0 16379 8032 62 62 100 100 100 100 19949 3186 2.023 .494 .547 .546 .51 1.428 52 332 .489 .99 80 2670 17840 60 68 195 203 0 17521 597 16923 1.268 3485 2887 .789 1.402 .342 .487
8 13987 6715 354 232 13633 6483 11529 6172 360 236 11175 5940 0 0 10848 5126 67 58 100 100 100 100 20116 17115 2.103 .476 .532 .51 .517 1.506 32 170 .469 .99 60 2900 17840 61 67 219 225 0 17218 595 16623 1.219 15826 15231 .82 1.363 .286 .447
9 12382 5953 359 225 12023 5728 5038 2307 366 233 4679 2082 0 0 15980 7682 87 75 100 100 100 100 17751 6761 2.099 .476 .445 .488 .481 1.357 120 784 .475 .98 120 3130 17850 59 71 239 251 0 15264 577 14687 1.222 5915 5338 .819 1.141 .289 .19
10 8175 3930 351 226 7824 3704 3409 1241 381 327 3058 1015 0 0 8690 4348 409 1453 96 46 83 41 11528 4073 2.112 .473 .332 .454 .468 1.455 80 636 .48 .97 110 3350 17850 59 70 261 272 0 10077 579 9497 1.214 3182 2603 .824 .851 .28 -.233
11 8781 4540 364 233 8417 4307 2494 1216 907 776 2130 983 0 0 10471 5365 4698 4797 40 32 34 25 12724 3113 1.954 .512 .462 .562 .532 1.688 52 412 .505 .98 90 3570 17840 59 68 284 293 0 11641 597 11044 1.312 3118 2521 .762 1.183 .392 .243
12 10789 6213 375 222 10414 5991 8220 5549 383 233 7845 5327 0 0 7876 4599 81 95 100 100 100 100 16405 13172 1.738 .575 .679 .568 .545 1.391 80 648 .564 .95 110 3800 17840 58 69 306 317 0 15931 569 15362 1.475 14228 13659 .678 1.741 .561 .8
13 5965 4590 396 210 5569 4380 5922 4232 448 256 5526 4022 0 0 3010 2563 309 323 100 96 100 96 9949 9548 1.271 .786 .728 .743 .893 2.279 32 236 .78 .84 70 4030 17850 61 68 331 338 0 11769 538 11231 2.017 10851 10313 .496 1.866 1.012 .9
14 10876 3332 354 214 10522 3118 13100 3584 361 210 12746 3370 0 0 5224 2030 53 55 100 100 100 100 13640 16116 3.375 .296 .264 .271 .273 1.558 12 62 .303 .92 40 4250 17850 63 67 355 359 0 8544 549 7995 .76 9190 8641 1.316 .678 -.396 -.561
15 1427 364 434 231 993 133 1368 315 445 238 934 84 0 0 713 187 103 69 100 50 75 41 1126 1018 7.466 .134 .09 .171 .137 1.531 12 104 .18 .76 50 4460 17850 62 67 375 380 0 933 592 341 .343 808 215 2.912 .231 -1.542 -2.117
16 6515 2604 380 242 6135 2362 1527 677 385 241 1147 435 0 0 8342 3361 67 57 100 100 100 93 8497 1582 2.597 .385 .379 .343 .361 1.641 32 236 .389 .97 70 4690 17850 61 68 397 404 0 6677 621 6056 .987 1736 1115 1.013 .972 -.019 -.04
17 960 402 376 229 584 173 895 402 384 231 519 173 0 0 256 106 83 61 100 83 100 75 757 692 3.376 .296 .333 .306 .299 1.556 12 104 .326 .76 50 1330 18040 81 86 62 67 0 1031 587 444 .76 1031 444 1.317 .855 -.397 -.227
18 1309 711 369 227 940 484 1152 697 379 230 783 470 0 0 733 345 67 61 93 90 93 90 1424 1253 1.942 .515 .6 .508 .506 1.631 32 236 .481 .86 70 1550 18050 81 88 83 90 0 1823 582 1241 1.32 1787 1205 .757 1.539 .401 .622
19 547 302 364 220 183 82 381 241 386 239 17 21 0 0 561 214 163 135 12 16 11 11 265 38 2.232 .448 1.235 .808 .655 5.231 80 650 .485 .74 110 1760 18060 80 91 102 113 -50 774 564 210 1.149 618 54 .87 3.167 .2 1.663
20 8185 3096 370 208 7815 2888 5317 2311 363 210 4947 2103 0 0 7437 2740 52 64 100 83 100 75 10703 7050 2.706 .37 .425 .284 .374 3.663 12 104 .356 .93 50 2010 18070 84 89 130 135 0 7938 533 7405 .948 5926 5392 1.055 1.09 -.078 .124

Total number of rows: 7680

Table truncated, full table size 1778 Kbytes.




Supplementary data files not provided
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