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Sample GSM591191 Query DataSets for GSM591191
Status Public on Dec 22, 2010
Title Gis2 Overexpression (2a)
Sample type RNA
 
Channel 1
Source name BY4741 pBG1805 empty vector
Organism Saccharomyces cerevisiae
Characteristics cell line: BY4741
transfection: pBG1805 empty vector
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name BY4741 pBG1805-Gis2p
Organism Saccharomyces cerevisiae
Characteristics cell line: BY4741
transfection: pBG1805-Gis2p
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol GenePix 4200A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2008-11/82095.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 Sep 07, 2010
Last update date Dec 22, 2010
Contact name Andre Gerber
E-mail(s) [email protected]
Phone +41 44 6337378
Fax +41 44 6337364
Organization name Swiss Federal Institute of Technology
Department Institute of Pharmaceutical Science
Street address Wolfgang Pauli Str. 10, HCI H396
City ETH Hoenggerberg, Zuerich
ZIP/Postal code ZH
Country Switzerland
 
Platform ID GPL8546
Series (2)
GSE24002 Gis2 overexpression versus control cells
GSE24005 Gis2 studies

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 1190 463 36 29 1154 434 1222 471 37 29 1186 442 0 0 415 150 9 4 100 100 100 100 1588 1628 2.659 .376 .373 .38 .375 1.16 32 236 .368 .99 70 2230 7010 53 60 63 70 0 1653 104 1550 1.343 1682 1578 .745 1.331 .425 .412
2 166 67 34 29 132 38 166 66 35 29 132 37 0 0 38 13 6 4 100 100 100 100 170 169 3.474 .288 .28 .279 .272 1.433 32 236 .272 .9 70 2460 7000 52 59 86 93 0 239 104 136 1.028 236 132 .973 1.001 .04 .001
3 391 148 35 29 356 119 393 153 36 29 358 124 0 0 74 31 6 4 100 100 100 100 475 482 2.992 .334 .346 .324 .345 1.249 32 236 .342 .97 70 2680 7000 52 59 108 115 0 528 104 425 1.193 546 443 .838 1.237 .255 .306
4 69 39 35 29 34 10 67 39 41 29 32 10 0 0 12 7 60 6 0 68 0 43 44 42 3.4 .294 .313 .278 .259 1.989 32 236 .208 .62 70 2900 7000 52 59 130 137 0 139 104 36 1.05 139 36 .952 1.116 .071 .158
5 106 45 35 30 71 15 76 41 36 29 41 11 0 0 149 14 9 4 100 87 100 68 86 52 4.733 .211 .268 .264 .271 1.995 32 236 .085 .7 70 3120 7010 53 60 152 159 0 161 107 54 .754 146 39 1.326 .958 -.407 -.062
6 67 38 36 30 31 8 66 38 36 30 30 8 0 0 15 7 6 4 90 71 87 46 39 38 3.875 .258 .267 .374 .367 2.565 32 176 .242 .57 60 3340 7010 54 60 175 181 0 136 107 29 .921 136 29 1.085 .952 -.118 -.071
7 332 131 36 29 296 102 357 137 37 29 321 108 0 0 92 27 7 4 100 100 100 100 398 429 2.902 .345 .336 .353 .349 1.3 32 176 .331 .97 60 3560 7010 54 60 197 203 0 468 104 364 1.23 489 386 .813 1.201 .299 .265
8 1800 609 37 30 1763 579 1922 663 39 30 1885 633 0 0 389 178 10 4 100 100 100 100 2342 2518 3.045 .328 .336 .317 .332 1.223 32 236 .339 .98 70 3780 7010 53 60 218 225 0 2174 107 2067 1.173 2367 2260 .853 1.199 .23 .262
9 198 69 36 29 162 40 201 67 37 29 165 38 0 0 39 15 7 4 100 100 100 96 202 203 4.05 .247 .23 .235 .245 1.548 32 236 .24 .91 70 4000 7010 53 60 240 247 0 246 104 143 .882 239 136 1.134 .822 -.182 -.282
10 138 70 36 29 102 41 141 70 37 29 105 41 0 0 33 15 6 4 100 100 100 96 143 146 2.488 .402 .39 .393 .391 1.641 32 176 .386 .91 60 4220 7020 55 61 263 269 0 250 104 146 1.435 250 146 .697 1.394 .521 .479
11 1630 638 39 30 1591 608 1802 698 41 30 1763 668 0 0 452 234 9 4 100 100 100 100 2199 2431 2.617 .382 .379 .354 .389 1.348 32 236 .394 .98 70 4440 7010 53 60 284 291 0 2278 107 2171 1.364 2492 2385 .733 1.353 .448 .436
12 420 256 40 31 380 225 429 271 41 30 389 240 0 0 73 46 9 4 100 100 100 100 605 629 1.689 .592 .617 .587 .602 1.208 32 176 .598 .97 60 4660 7020 55 61 307 313 0 914 111 803 2.114 968 857 .473 2.203 1.08 1.139
13 174 81 40 30 134 51 182 80 42 30 142 50 0 0 65 29 9 4 100 96 96 92 185 192 2.627 .381 .352 .349 .368 1.518 52 340 .384 .94 80 4880 7020 54 62 328 336 0 289 107 182 1.359 286 179 .736 1.257 .442 .33
14 241 106 40 30 201 76 264 110 43 30 224 80 0 0 84 29 11 4 96 98 96 98 277 304 2.645 .378 .357 .407 .359 1.559 52 340 .366 .96 80 5100 7020 54 62 350 358 0 378 107 271 1.35 393 286 .741 1.275 .433 .351
15 174 67 37 30 137 37 173 66 38 30 136 36 0 0 44 15 7 4 100 100 100 100 174 172 3.703 .27 .265 .261 .262 1.543 52 340 .259 .88 80 5320 7020 54 62 372 380 0 239 107 132 .964 236 129 1.037 .945 -.052 -.081
16 1252 430 38 30 1214 400 1320 438 41 30 1282 408 0 0 228 104 12 4 100 100 100 100 1614 1690 3.035 .329 .318 .324 .329 1.199 32 236 .325 .98 70 5540 7020 54 61 394 401 0 1535 107 1428 1.176 1564 1457 .85 1.136 .234 .184
17 279 92 39 30 240 62 312 100 41 30 273 70 0 0 90 28 11 4 100 96 100 96 302 343 3.871 .258 .256 .244 .256 1.377 32 236 .262 .96 70 5760 7020 54 61 416 423 0 328 107 221 .922 357 250 1.084 .915 -.117 -.127
18 184 67 37 30 147 37 184 66 38 30 147 36 0 0 54 14 8 4 100 98 100 96 184 183 3.973 .252 .245 .249 .261 1.638 52 340 .234 .9 80 5980 7020 54 62 438 446 0 239 107 132 .899 236 129 1.113 .874 -.154 -.194
19 145 62 36 30 109 32 145 59 36 30 109 29 0 0 27 11 6 4 100 100 100 100 141 138 3.406 .294 .266 .293 .29 1.332 32 236 .315 .91 70 6200 7020 54 61 460 467 0 221 107 114 1.048 211 104 .954 .95 .068 -.074
20 65 34 37 30 28 4 64 34 38 30 27 4 0 0 13 5 9 4 96 46 76 13 32 31 7 .143 .148 .179 .179 2.061 52 340 .121 .34 80 2240 7230 75 83 64 72 0 121 107 14 .51 121 14 1.961 .529 -.971 -.919

Total number of rows: 10944

Table truncated, full table size 2249 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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