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Sample GSM93632 Query DataSets for GSM93632
Status Public on Jan 25, 2006
Title Prostate - MDA-2A
Sample type RNA
 
Channel 1
Source name MDA-2A control
Organism Homo sapiens
Characteristics MDA-2A control
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MDA-2A 1uM 5-aza-dC 5 days
Organism Homo sapiens
Characteristics MDA-2A 1uM 5-aza-dC 5 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, methylation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27550.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 24, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3295
Series (1)
GSE4089 DNA methyltransferase inhibitor 5-aza-dC-treated prostate cancer cell lines

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 703 605 184 218 519 387 710 603 205 236 526 385 0 0 148 176 79 111 100 93 100 84 906 911 1.341 .746 .732 .736 .796 1.496 32 167 2.279 .51 60 1900 8210 26 32 15 21 0 582 210 372 .717 580 370 1.395 .704 -.48 -.507 -.507
2 513 357 191 226 322 131 503 332 205 235 312 106 0 0 137 123 72 102 96 50 93 25 453 418 2.458 .407 .34 .377 .419 2.648 32 222 .598 .42 70 2030 8210 25 32 27 34 0 343 217 126 .391 319 102 2.556 .327 -1.354 -1.614 -1.614
3 1351 1302 189 227 1162 1075 1426 1386 206 236 1237 1159 0 0 464 502 78 107 100 98 100 98 2237 2396 1.081 .925 .937 .874 .989 1.645 52 289 .985 .9 80 2190 8200 24 32 43 51 0 1252 218 1034 .89 1333 1114 1.124 .901 -.169 -.151 -.151
4 9731 15194 195 223 9536 14971 1783 3235 212 244 1588 3012 0 0 11607 18747 77 144 92 100 90 86 24507 4600 .637 1.57 1.897 1.473 1.495 3.282 52 248 1.674 .91 80 2320 8210 25 33 56 64 0 14610 214 14395 1.51 3111 2896 .662 1.824 .594 .867 .867
5 326 334 190 218 136 116 235 264 206 229 45 46 0 0 194 214 74 99 46 38 36 26 252 91 1.172 .853 1.022 1.408 1.172 3.361 52 278 1.21 .54 80 2460 8200 24 32 70 78 -50 321 210 112 .82 254 44 1.219 .983 -.286 -.025
6 440 525 189 236 251 289 440 357 212 286 251 121 0 0 173 599 88 295 81 18 59 12 540 372 .869 1.151 .482 .566 .587 3.879 32 176 12.676 .18 60 2620 8210 26 32 87 93 0 505 227 278 1.107 343 116 .903 .464 .147 -1.109 -1.109
7 518 412 188 216 330 196 493 369 204 261 305 153 0 0 116 141 77 248 100 31 100 3 526 458 1.684 .594 .502 .526 .596 2.285 32 224 .744 .41 70 2770 8200 24 31 101 108 0 396 208 188 .571 355 147 1.751 .482 -.808 -1.052 -1.052
8 20056 23809 189 220 19867 23589 21269 24912 202 251 21080 24692 0 0 7357 9626 70 125 100 100 100 100 43456 45772 .842 1.187 1.171 1.17 1.235 1.444 52 331 1.238 .95 90 2910 8200 23 32 114 123 0 22893 212 22682 1.142 23954 23742 .876 1.126 .191 .172 .172
9 928 1165 189 249 739 916 890 1193 195 265 701 944 0 0 194 482 53 120 100 91 100 83 1655 1645 .807 1.24 1.347 1.261 1.255 1.956 12 104 1.729 .74 50 3050 8200 25 30 130 135 0 1120 239 881 1.192 1147 908 .839 1.295 .253 .373 .373
10 470 353 198 218 272 135 507 336 207 250 309 118 0 0 173 166 62 120 87 50 75 25 407 427 2.015 .496 .382 .529 .446 3.047 32 166 .642 .35 60 3210 8210 26 32 146 152 0 339 210 130 .477 323 113 2.095 .367 -1.067 -1.445 -1.445
11 3917 4897 194 221 3723 4676 4139 5207 209 244 3945 4986 0 0 1312 1613 70 110 100 100 98 98 8399 8931 .796 1.256 1.264 1.254 1.252 1.757 80 410 1.253 .91 100 3360 8200 23 33 159 169 0 4709 213 4496 1.208 5007 4794 .828 1.215 .272 .281 .281
12 2403 2649 193 246 2210 2403 2376 2921 202 260 2183 2675 0 0 1009 1058 80 106 100 100 96 100 4613 4858 .92 1.087 1.225 1.152 1.009 2.217 32 195 1.062 .84 70 3510 8210 25 32 175 182 0 2547 237 2311 1.046 2809 2572 .956 1.178 .064 .237 .237
13 1080 1504 187 225 893 1279 1022 1346 205 257 835 1121 0 0 545 736 87 116 94 100 92 100 2172 1956 .698 1.432 1.343 1.464 1.437 2.068 52 224 1.459 .83 80 3650 8210 25 33 189 197 0 1446 216 1230 1.377 1294 1078 .726 1.291 .462 .368 .368
14 334 316 185 250 149 66 281 290 200 270 96 40 0 0 171 149 78 126 55 28 42 13 215 136 2.258 .443 .417 .891 .809 3.413 52 262 .887 .33 80 3770 8190 23 31 201 209 -50 304 240 63 .426 279 38 2.348 .401 -1.231 -1.32
15 14698 16260 192 247 14506 16013 16754 17149 214 273 16562 16902 0 0 6191 6503 145 134 100 100 100 100 30519 33464 .906 1.104 1.021 1.14 1.131 1.507 52 323 1.109 .94 90 3930 8200 23 32 216 225 0 15635 238 15397 1.061 16489 16252 .942 .981 .086 -.027 -.027
16 4444 6179 187 240 4257 5939 4379 5919 201 272 4192 5679 0 0 1662 2604 76 132 100 100 100 100 10196 9871 .717 1.395 1.355 1.386 1.454 1.572 52 243 1.474 .94 80 4080 8200 24 32 232 240 0 5941 231 5711 1.341 5691 5461 .745 1.303 .424 .381 .381
17 372 243 192 234 180 9 359 228 207 254 167 -6 0 0 191 122 77 116 73 11 55 3 189 161 20 .05 null .765 .651 5.152 52 254 -1 -1 80 4210 8190 23 31 245 253 -50 234 225 9 .048 219 null 20.8 null -4.379 null
18 359 273 183 235 176 38 369 255 202 258 186 20 0 0 109 120 75 112 78 21 63 9 214 206 4.632 .216 .108 .612 .676 3.641 52 256 1.787 .08 80 4360 8190 23 31 260 268 -50 263 226 37 .208 245 19 4.817 .103 -2.268 -3.274
19 3095 3406 190 249 2905 3157 3220 3678 206 269 3030 3429 0 0 913 1142 72 124 100 100 98 100 6062 6459 .92 1.087 1.132 1.116 1.151 1.629 80 384 1.119 .92 100 4510 8200 23 33 274 284 0 3275 239 3036 1.045 3537 3297 .957 1.088 .063 .122 .122
20 428 335 195 247 233 88 422 308 210 265 227 61 0 0 148 141 73 109 82 38 73 17 321 288 2.648 .378 .269 .596 .581 3.741 52 255 .468 .21 80 4650 8190 23 31 289 297 -50 322 238 85 .363 296 59 2.754 .258 -1.461 -1.952

Total number of rows: 43008

Table truncated, full table size 9606 Kbytes.




Supplementary data files not provided
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