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Sample GSM591193 Query DataSets for GSM591193
Status Public on Dec 22, 2010
Title Gis2 Overexpression (3b)
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/2009-01/82576.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 1000 578 122 91 878 487 987 569 124 91 865 478 0 0 174 96 43 20 100 100 100 100 1365 1343 1.803 .555 .553 .555 .534 1.241 32 236 .545 .95 70 2300 6670 87 94 78 85 0 1537 242 1295 1.475 1513 1271 .678 1.47 .561 .556
2 231 213 110 89 121 124 223 138 116 90 113 49 0 0 85 276 41 20 84 78 62 53 245 162 .976 1.025 .434 .545 .501 3.169 32 236 3.003 .49 70 2530 6660 86 93 101 108 0 566 237 330 2.726 367 130 .367 1.153 1.447 .206
3 445 214 118 90 327 124 441 209 121 91 323 119 0 0 93 34 40 18 100 100 100 100 451 442 2.637 .379 .368 .381 .392 1.371 32 236 .366 .85 70 2750 6670 87 94 123 130 0 569 239 330 1.009 556 316 .992 .98 .012 -.029
4 163 128 123 91 40 37 165 138 124 94 42 47 0 0 50 25 40 21 50 58 16 58 77 89 1.081 .925 1.119 .589 .68 2.685 12 68 .04 .05 40 2970 6690 91 95 147 151 0 340 242 98 2.46 367 125 .406 2.976 1.299 1.573
5 208 128 104 94 104 34 201 133 115 95 97 39 0 0 53 20 40 21 91 75 66 33 138 136 3.059 .327 .402 .275 .324 2.967 12 68 .172 .37 40 3190 6670 89 93 169 173 0 340 250 90 .869 354 104 1.15 1.069 -.202 .097
6 176 97 116 88 60 9 136 95 120 91 20 7 0 0 224 25 38 20 37 33 18 11 69 27 6.667 .15 .35 .51 .528 3.98 80 560 .034 .18 100 3390 6670 86 96 186 196 -50 258 234 24 .399 253 19 2.507 .931 -1.326 -.103
7 355 235 117 92 238 143 326 231 120 93 209 139 0 0 94 37 42 19 100 100 100 100 381 348 1.664 .601 .665 .621 .668 1.552 32 176 .503 .79 60 3620 6680 89 95 211 217 0 625 245 380 1.598 614 370 .626 1.769 .676 .823
8 1723 864 121 92 1602 772 1763 888 120 95 1642 796 0 0 307 143 37 20 100 100 100 100 2374 2438 2.075 .482 .485 .483 .474 1.185 32 236 .477 .98 70 3840 6670 87 94 232 239 0 2298 245 2053 1.282 2362 2117 .78 1.289 .358 .367
9 257 138 114 89 143 49 261 131 118 90 147 42 0 0 62 29 40 19 96 90 87 59 192 189 2.918 .343 .286 .317 .341 2.207 32 236 .269 .58 70 4060 6680 88 95 254 261 0 367 237 130 .911 348 112 1.097 .76 -.134 -.396
10 222 121 121 92 101 29 230 122 123 91 109 30 0 0 66 27 38 21 81 62 62 34 130 139 3.483 .287 .275 .344 .296 2.657 32 176 .201 .43 60 4270 6680 89 95 276 282 0 322 245 77 .764 324 80 1.31 .732 -.389 -.45
11 1841 803 113 88 1728 715 1888 814 119 89 1775 726 0 0 452 190 38 19 100 100 100 100 2443 2501 2.417 .414 .409 .41 .408 1.244 32 236 .408 .98 70 4490 6680 88 95 297 304 0 2136 234 1902 1.1 2165 1931 .909 1.088 .138 .121
12 541 396 117 90 424 306 528 403 121 92 411 313 0 0 111 72 38 20 100 100 100 100 730 724 1.386 .722 .762 .726 .786 1.385 32 236 .694 .92 70 4710 6680 88 95 319 326 0 1053 239 814 1.919 1072 832 .521 2.025 .941 1.018
13 221 141 114 91 107 50 223 136 119 91 109 45 0 0 61 36 41 20 86 76 69 53 157 154 2.14 .467 .413 .407 .476 2.516 52 420 .293 .49 90 4920 6690 88 97 339 348 0 375 242 133 1.243 362 120 .805 1.098 .314 .135
14 321 181 113 87 208 94 314 178 118 88 201 91 0 0 99 45 39 20 96 94 92 88 302 292 2.213 .452 .453 .424 .472 2.481 52 420 .373 .75 90 5150 6690 88 97 362 371 0 481 231 250 1.202 473 242 .832 1.204 .265 .268
15 261 150 120 86 141 64 260 145 122 89 140 59 0 0 74 36 39 20 90 90 80 75 205 199 2.203 .454 .421 .442 .419 2.425 52 340 .297 .53 80 5370 6690 89 97 385 393 0 399 229 170 1.207 386 157 .828 1.121 .272 .165
16 1113 548 120 90 993 458 1135 573 122 91 1015 483 0 0 358 193 37 19 100 100 100 100 1451 1498 2.168 .461 .476 .437 .45 1.381 52 340 .466 .96 80 5590 6690 89 97 407 415 0 1457 239 1218 1.227 1524 1285 .815 1.266 .295 .34
17 334 221 112 90 222 131 315 221 118 90 203 131 0 0 100 54 40 20 100 100 96 96 353 334 1.695 .59 .645 .593 .635 1.603 52 340 .547 .85 80 5810 6690 89 97 429 437 0 588 239 348 1.569 588 348 .637 1.716 .65 .779
18 263 134 118 87 145 47 263 128 122 88 145 41 0 0 72 29 41 21 92 80 76 46 192 186 3.085 .324 .283 .293 .322 2.351 52 340 .229 .52 80 6030 6690 89 97 451 459 0 356 231 125 .862 340 109 1.16 .752 -.214 -.411
19 320 183 115 84 205 99 306 185 119 87 191 101 0 0 72 34 40 19 100 96 96 96 304 292 2.071 .483 .529 .479 .522 1.464 32 236 .389 .72 70 6250 6690 89 96 473 480 0 487 223 263 1.284 492 269 .779 1.406 .361 .492
20 155 98 118 91 37 7 143 99 122 93 25 8 0 0 90 25 41 21 35 16 18 3 44 33 5.286 .189 .32 .49 .387 3.863 80 560 .109 .29 100 2300 6890 108 118 77 87 -50 261 242 19 .503 263 21 1.987 .851 -.991 -.233

Total number of rows: 10944

Table truncated, full table size 2366 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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