NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM591200 Query DataSets for GSM591200
Status Public on Dec 22, 2010
Title GIS2_delta vs. wt (1)
Sample type RNA
 
Channel 1
Source name BY4741 total RNA (WT)
Organism Saccharomyces cerevisiae
Characteristics cell line/genotype: BY4741 (WT)
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name delta Gis2 total RNA
Organism Saccharomyces cerevisiae
Characteristics cell line/genotype: delta Gis2
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/2010-01/86208.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)
GSE24004 Gis2 mutant versus wild-type 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 1145 938 48 63 1097 875 1273 1023 50 65 1225 960 0 0 485 407 17 20 100 100 99 99 1972 2185 1.254 .798 .784 .806 .793 1.356 156 1140 .803 .98 70 2130 6715 184 198 147 161 0 1235 83 1152 1.05 1347 1264 .952 1.032 .07 .045
2 152 140 45 61 107 79 153 137 47 64 108 76 0 0 40 41 13 22 100 93 99 80 186 184 1.354 .738 .704 .696 .718 1.755 120 820 .793 .76 60 2350 6710 184 196 192 204 0 184 80 104 .972 180 100 1.029 .926 -.041 -.11
3 746 591 47 63 699 528 779 624 50 66 732 561 0 0 257 194 19 24 100 100 100 99 1227 1293 1.324 .755 .766 .756 .748 1.332 156 1140 .75 .97 70 2570 6710 183 197 235 249 0 778 83 695 .994 821 738 1.006 1.009 -.008 .013
4 75 85 46 61 29 24 79 83 48 63 33 22 0 0 22 25 16 19 70 55 50 24 53 55 1.208 .828 .667 1.03 .955 3.25 120 820 1.292 .3 60 2790 6715 185 197 280 292 0 112 80 32 1.089 109 29 .918 .878 .124 -.188
5 78 84 44 59 34 25 77 83 46 62 33 24 0 0 20 22 13 18 83 57 68 27 59 57 1.36 .735 .727 .794 .734 3.29 80 656 .947 .35 55 3005 6705 183 194 323 334 0 111 78 33 .968 109 32 1.033 .957 -.047 -.063
6 66 78 45 62 21 16 61 71 47 65 16 9 0 0 30 34 14 19 51 32 29 12 37 25 1.313 .762 .563 .75 .9 3.989 120 820 1.277 .34 60 3210 6695 181 193 364 376 0 103 82 21 1.003 93 12 .997 .74 .004 -.433
7 347 321 46 61 301 260 357 335 48 63 311 274 0 0 97 96 16 18 100 100 100 97 561 585 1.158 .864 .881 .826 .861 1.397 120 820 .88 .94 60 3455 6710 184 196 413 425 0 423 80 342 1.137 441 361 .879 1.16 .185 .214
8 115 116 45 60 70 56 110 114 47 63 65 54 0 0 34 30 13 19 96 87 90 70 126 119 1.25 .8 .831 .784 .855 1.913 120 820 .856 .68 60 3670 6710 184 196 456 468 0 153 79 74 1.053 150 71 .95 1.094 .075 .129
9 108 102 46 62 62 40 106 101 48 63 60 39 0 0 28 24 14 17 98 85 88 57 102 99 1.55 .645 .65 .634 .674 2.146 120 940 .722 .59 65 3895 6715 184 197 500 513 0 134 82 53 .849 133 51 1.177 .856 -.236 -.225
10 124 106 46 62 78 44 124 103 49 64 78 41 0 0 33 28 27 20 92 78 76 50 122 119 1.773 .564 .526 .497 .523 2.209 120 820 .342 .45 60 4110 6715 185 197 544 556 0 140 82 58 .743 136 54 1.347 .692 -.429 -.531
11 2782 2203 49 63 2733 2140 3415 2800 51 65 3366 2737 0 0 1442 1142 19 20 100 100 100 100 4873 6103 1.277 .783 .813 .79 .794 1.265 156 1140 .783 .99 70 4335 6710 183 197 588 602 0 2900 83 2817 1.031 3686 3603 .97 1.07 .044 .098
12 80 96 45 62 35 34 78 93 47 64 33 31 0 0 22 26 14 19 84 69 58 41 69 64 1.029 .971 .939 .951 1.073 2.933 156 1140 1.454 .41 70 4555 6710 183 197 632 646 0 126 82 45 1.279 122 41 .782 1.237 .355 .306
13 90 88 47 62 43 26 87 88 48 64 40 26 0 0 28 23 14 23 86 53 65 15 69 66 1.654 .605 .65 .612 .665 3.023 208 1512 1.401 .32 80 4775 6715 183 199 675 691 0 116 82 34 .796 116 34 1.256 .856 -.329 -.225
14 162 141 46 61 116 80 154 137 47 63 108 76 0 0 53 43 14 17 99 95 99 84 196 184 1.45 .69 .704 .645 .68 2 208 1512 .694 .81 80 5000 6715 183 199 720 736 0 186 80 105 .908 180 100 1.101 .926 -.139 -.11
15 111 112 46 61 65 51 110 110 48 63 64 49 0 0 31 30 21 24 94 82 73 50 116 113 1.275 .785 .766 .766 .788 1.96 208 1660 .942 .72 85 5220 6720 183 200 763 780 0 147 80 67 1.033 145 65 .968 1.008 .047 .011
16 536 369 46 61 490 308 573 378 48 63 527 317 0 0 203 140 15 17 100 99 100 98 798 844 1.591 .629 .602 .615 .624 1.369 208 1512 .636 .97 80 5440 6715 183 199 808 824 0 486 80 405 .827 498 417 1.209 .792 -.273 -.337
17 124 117 45 60 79 57 123 114 48 62 78 54 0 0 36 37 14 17 98 86 93 68 136 132 1.386 .722 .692 .656 .691 1.98 208 1512 .79 .75 80 5665 6715 183 199 853 869 0 154 79 75 .95 150 71 1.053 .911 -.074 -.134
18 98 94 45 60 53 34 96 92 47 62 51 32 0 0 28 27 14 16 91 73 80 49 87 83 1.559 .642 .627 .658 .682 2.482 208 1512 .744 .56 80 5885 6715 183 199 897 913 0 124 79 45 .844 121 42 1.184 .826 -.244 -.276
19 123 117 46 60 77 57 122 117 48 62 76 57 0 0 39 34 18 20 94 85 83 71 134 133 1.351 .74 .75 .736 .754 2.297 156 1140 .784 .64 70 6110 6715 184 198 943 957 0 154 79 75 .974 154 75 1.026 .987 -.037 -.018
20 56 67 46 62 10 5 53 66 48 64 7 4 0 0 18 19 15 19 33 18 14 5 15 11 2 .5 .571 .97 1.125 4.124 316 2384 2.898 .18 100 2120 6930 224 244 142 162 -50 88 82 7 .658 87 5 1.519 .752 -.603 -.411

Total number of rows: 10944

Table truncated, full table size 2269 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap