Data Set Group2: GSE15222 Human Brain Normal Myers (Apr09)

Data Set: GSE15222 Human Brain All Cases Myers (Apr09) RankInv GN Accession: GN234 GEO Series: GSE15222 Title: Genetic control of human brain transcript expression in Alzheimer Organism: Human (Homo sapiens, hg19) Group: AD-cases-controls-Myers Tissue: Brain mRNA Dataset Status: Public Platforms: Illumina Sentrix HumanRef-8 Expression BeadChip v2 Rev0 (GPL2700) Normalization: RankInv

Contact Information Amanda Myers Miller School of Medicine, University of Miami 1580 NW 10th Ave, Batchelor Miami, FL 33136 USA Tel. 305-243-3522 amyers@med.miami.edu Website Download datasets and supplementary data files GN234_MeanDataAnnotated_rev081815.txt (N/A) GN234_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

Summary:

Myers and colleagues generated massive neocortical transcriptome data sets for a set of unrelated elderly neurologically and neuropathologically normal humans and from confirmed late onset Alzheimer's disease patients (LOAD, n = 187 normal and 176 LOAD cases, see DOI:10.1016/j.ajhg.2009.03.011 for detail). They used an Illumina Sentrix Bead array (HumanRef-8) that measures expression of approximately 19,730 curated RefSeq sequences (Human Build 34). Case identifiers: All case identifiers (IDs) in GeneNetwork begin with a capital C followed by a six digit GEO identifier, followed by the sex and age in years. Non-Alzheimer cases are labeled with the suffix letter N: C225652M85N. Alzheimer cases are labeled with the suffix letter A: C388217F97A. Data were initially downloaded from the NCBI GEO archive under the experiment ID GSE15222. All data were generated using the Illumina HumanRef-8 expression BeadChip (GPL2700) v2 Rev0. This data set in GeneNetwork includes data for 24,354 probes. We have realigned the 50-mer sequences by BLAT to the latest version of the human genome (Feb 2009, hg19) and reannotated the array (August 2009). The annotation in GN will differ from that provided in GEO for this platform. We were unable to obtain 50-mer sequences for several thousand probes (e.g., HTT), and these probes have therefore not been realigned to the human genome. The GEO data set was processed by Myers and colleagues using Illumina's Rank Invariant transform. We performed a series of QC and renormalization steps to the data to allow more facile comparison to other data sets in GeneNetwork. In brief, data is log2 transformed. We recentered each array to a mean expression of 8 units and a standard deviation of 2 units (2z + 8 transform). The values are therefore modified z scores and each unit represents roughly a two-fold difference in expression. Average expression across all 363 cases range from a low of 6 units (e.g., SYT15) to a high of 19 units for ARSK. APOE has an average expression of 15 units and APP has an average expression of 11.5 units.. The distribution is far from normal with a great excess of measurements of genes with low to moderate expression clustered between 6.5 and 8.5 units. A small number of arrays (n = 6, GSM226040, GSM226041, GSM226042, GSM226044, GSM226045, GSM226046) had a different distribution from the great majority of other arrays. This was probably due to a batch processing effect. Members of this minority group belonged to both normal and LOAD cases. This putative batch effect has been eliminated in the GeneNetwork rendition of the Myers data. To eliminate the putative batch effect, we simply computed a mean offset for each probe in the "minority set" relative to the remaining "majority set" and added or subtracted this offset to force the mean of each probe in the minority set to conform to mean of the same probe in the majority set.

About the cases used to generate this set of data:

Index GEO Series Organ Region Tissue Case ID Age Sex 1 GSM225652 Temporal Cortex Normal C225652M85N 85 M 2 GSM225662 Temporal Cortex Normal C225662M85N 85 M 3 GSM225664 Temporal Cortex Normal C225664F79N 79 F 4 GSM225665 Temporal Cortex Normal C225665F85N 85 F 5 GSM225666 Temporal Cortex Normal C225666F73N 73 F 6 GSM225667 Temporal Cortex Normal C225667M81N 81 M 7 GSM225668 Temporal Cortex Normal C225668M79N 79 M 8 GSM225669 Temporal Cortex Normal C225669M77N 77 M 9 GSM225670 Temporal Cortex Normal C225670M69N 69 M 10 GSM225671 Temporal Cortex Normal C225671M86N 86 M 11 GSM225672 Temporal Cortex Normal C225672F83N 83 F 12 GSM225673 Temporal Cortex Normal C225673M78N 78 M 13 GSM225674 Temporal Cortex Normal C225674M94N 94 M 14 GSM225675 Temporal Cortex Normal C225675F81N 81 F 15 GSM225676 Temporal Cortex Normal C225676M76N 76 M 16 GSM225677 Temporal Cortex Normal C225677M83N 83 M 17 GSM225678 Temporal Cortex Normal C225678M68N 68 M 18 GSM225679 Temporal Cortex Normal C225679F82N 82 F 19 GSM225680 Temporal Cortex Normal C225680F70N 70 F 20 GSM225681 Temporal Cortex Normal C225681M86N 86 M 21 GSM225682 Temporal Cortex Normal C225682M78N 78 M 22 GSM225683 Temporal Cortex Normal C225683M82N 82 M 23 GSM225684 Temporal Cortex Normal C225684F94N 94 F 24 GSM225685 Temporal Cortex Normal C225685F87N 87 F 25 GSM225686 Temporal Cortex Normal C225686M74N 74 M 26 GSM225687 Temporal Cortex Normal C225687M85N 85 M 27 GSM225688 Temporal Cortex Normal C225688M75N 75 M 28 GSM225689 Temporal Cortex Normal C225689F86N 86 F 29 GSM225690 Temporal Cortex Normal C225690M75N 75 M 30 GSM225691 Temporal Cortex Normal C225691M81N 81 M 31 GSM225692 Temporal Cortex Normal C225692F72N 72 F 32 GSM225693 Temporal Cortex Normal C225693F81N 81 F 33 GSM225695 Temporal Cortex Normal C225695M81N 81 M 34 GSM225696 Temporal Cortex Normal C225696M81N 81 M 35 GSM225697 Temporal Cortex Normal C225697M91N 91 M 36 GSM225698 Temporal Cortex Normal C225698M84N 84 M 37 GSM225699 Temporal Cortex Normal C225699M96N 96 M 38 GSM225700 Temporal Cortex Normal C225700F97N 97 F 39 GSM225701 Temporal Cortex Normal C225701M90N 90 M 40 GSM225702 Temporal Cortex Normal C225702F67N 67 F 41 GSM225703 Temporal Cortex Normal C225703F83N 83 F 42 GSM225704 Temporal Cortex Normal C225704F82N 82 F 43 GSM225705 Temporal Cortex Normal C225705F66N 66 F 44 GSM225706 Temporal Cortex Normal C225706F72N 72 F 45 GSM225707 Temporal Cortex Normal C225707F65N 65 F 46 GSM225708 Temporal Cortex Normal C225708F75N 75 F 47 GSM225709 Temporal Cortex Normal C225709F74N 74 F 48 GSM225711 Temporal Cortex Normal C225711M68N 68 M 49 GSM225713 Temporal Cortex Normal C225713F80N 80 F 50 GSM225714 Temporal Cortex Normal C225714M80N 80 M 51 GSM225715 Temporal Cortex Normal C225715M66N 66 M 52 GSM225717 Temporal Cortex Normal C225717M88N 88 M 53 GSM225718 Temporal Cortex Normal C225718F91N 91 F 54 GSM225719 Temporal Cortex Normal C225719M73N 73 M 55 GSM225720 Temporal Cortex Normal C225720M76N 76 M 56 GSM225721 Temporal Cortex Normal C225721M75N 75 M 57 GSM225722 Temporal Cortex Normal C225722F86N 86 F 58 GSM225723 Temporal Cortex Normal C225723F72N 72 F 59 GSM225724 Temporal Cortex Normal C225724M97N 97 M 60 GSM225725 Temporal Cortex Normal C225725M86N 86 M 61 GSM225726 Temporal Cortex Normal C225726M82N 82 M 62 GSM225727 Temporal Cortex Normal C225727F95N 95 F 63 GSM225728 Temporal Cortex Normal C225728F76N 76 F 64 GSM225729 Temporal Cortex Normal C225729M76N 76 M 65 GSM225730 Temporal Cortex Normal C225730M69N 69 M 66 GSM225731 Temporal Cortex Normal C225731F80N 80 F 67 GSM225732 Temporal Cortex Normal C225732F99N 99 F 68 GSM225733 Temporal Cortex Normal C225733M68N 68 M 69 GSM225734 Temporal Cortex Normal C225734M70N 70 M 70 GSM225735 Temporal Cortex Normal C225735F87N 87 F 71 GSM225736 Temporal Cortex Normal C225736F99N 99 F 72 GSM225737 Temporal Cortex Normal C225737F88N 88 F 73 GSM225739 Temporal Cortex Normal C225739M65N 65 M 74 GSM225741 Temporal Cortex Normal C225741M82N 82 M 75 GSM225742 Temporal Cortex Normal C225742F78N 78 F 76 GSM225743 Temporal Cortex Normal C225743F85N 85 F 77 GSM225744 Temporal Cortex Normal C225744F100N 100 F 78 GSM225745 Temporal Cortex Normal C225745F87N 87 F 79 GSM225746 Temporal Cortex Normal C225746F85N 85 F 80 GSM225747 Temporal Cortex Normal C225747F97N 97 F 81 GSM225748 Temporal Cortex Normal C225748M65N 65 M 82 GSM225749 Temporal Cortex Normal C225749M65N 65 M 83 GSM225751 Temporal Cortex Normal C225751F87N 87 F 84 GSM225752 Temporal Cortex Normal C225752F85N 85 F 85 GSM225753 Temporal Cortex Normal C225753M68N 68 M 86 GSM225754 Temporal Cortex Normal C225754M71N 71 M 87 GSM225755 Temporal Cortex Normal C225755F83N 83 F 88 GSM225756 Temporal Cortex Normal C225756M76N 76 M 89 GSM225757 Temporal Cortex Normal C225757M67N 67 M 90 GSM225758 Temporal Cortex Normal C225758F100N 100 F 91 GSM225759 Temporal Cortex Normal C225759M79N 79 M 92 GSM225760 Temporal Cortex Normal C225760M74N 74 M 93 GSM225761 Temporal Cortex Normal C225761F88N 88 F 94 GSM225762 Temporal Cortex Normal C225762M70N 70 M 95 GSM225763 Temporal Cortex Normal C225763F97N 97 F 96 GSM225764 Temporal Cortex Normal C225764M69N 69 M 97 GSM225915 Temporal Cortex Normal C225915F99N 99 F 98 GSM225916 Temporal Cortex Normal C225916M81N 81 M 99 GSM225917 Temporal Cortex Normal C225917F85N 85 F 100 GSM225918 Temporal Cortex Normal C225918F82N 82 F 101 GSM225919 Temporal Cortex Normal C225919M70N 70 M 102 GSM225920 Temporal Cortex Normal C225920M73N 73 M 103 GSM225921 Temporal Cortex Normal C225921M83N 83 M 104 GSM225922 Temporal Cortex Normal C225922M74N 74 M 105 GSM225923 Temporal Cortex Normal C225923M77N 77 M 106 GSM225924 Temporal Cortex Normal C225924M81N 81 M 107 GSM225925 Temporal Cortex Normal C225925M65N 65 M 108 GSM225926 Temporal Cortex Normal C225926F73N 73 F 109 GSM225927 Temporal Cortex Normal C225927F85N 85 F 110 GSM225928 Temporal Cortex Normal C225928M69N 69 M 111 GSM225929 Temporal Cortex Normal C225929M72N 72 M 112 GSM225930 Temporal Cortex Normal C225930F76N 76 F 113 GSM225931 Temporal Cortex Normal C225931M73N 73 M 114 GSM225932 Temporal Cortex Normal C225932M66N 66 M 115 GSM225933 Temporal Cortex Normal C225933F85N 85 F 116 GSM225934 Temporal Cortex Normal C225934M87N 87 M 117 GSM225935 Temporal Cortex Normal C225935F86N 86 F 118 GSM225936 Temporal Cortex Normal C225936F73N 73 F 119 GSM225937 Temporal Cortex Normal C225937M86N 86 M 120 GSM225938 Temporal Cortex Normal C225938M72N 72 M 121 GSM225939 Temporal Cortex Normal C225939F69N 69 F 122 GSM225940 Temporal Cortex Normal C225940F88N 88 F 123 GSM225941 Temporal Cortex Normal C225941M77N 77 M 124 GSM225942 Temporal Cortex Normal C225942M96N 96 M 125 GSM225943 Temporal Cortex Normal C225943F78N 78 F 126 GSM225944 Temporal Cortex Normal C225944M77N 77 M 127 GSM225945 Temporal Cortex Normal C225945F99N 99 F 128 GSM225946 Temporal Cortex Normal C225946M78N 78 M 129 GSM225947 Temporal Cortex Normal C225947F76N 76 F 130 GSM225948 Temporal Cortex Normal C225948M78N 78 M 131 GSM225949 Temporal Cortex Normal C225949F97N 97 F 132 GSM225950 Temporal Cortex Normal C225950F86N 86 F 133 GSM225951 Temporal Cortex Normal C225951M77N 77 M 134 GSM225952 Temporal Cortex Normal C225952M87N 87 M 135 GSM225953 Temporal Cortex Normal C225953F72N 72 F 136 GSM225954 Temporal Cortex Normal C225954F91N 91 F 137 GSM225955 Temporal Cortex Normal C225955F85N 85 F 138 GSM225956 Temporal Cortex Normal C225956M88N 88 M 139 GSM225957 Temporal Cortex Normal C225957F86N 86 F 140 GSM225958 Temporal Cortex Normal C225958F93N 93 F 141 GSM225959 Temporal Cortex Normal C225959M82N 82 M 142 GSM225961 Temporal Cortex Normal C225961F72N 72 F 143 GSM225962 Temporal Cortex Normal C225962F85N 85 F 144 GSM225963 Temporal Cortex Normal C225963M70N 70 M 145 GSM225964 Temporal Cortex Normal C225964F67N 67 F 146 GSM225965 Temporal Cortex Normal C225965F74N 74 F 147 GSM226034 Temporal Cortex Normal C226034M69N 69 M 148 GSM226035 Temporal Cortex Normal C226035M85N 85 M 149 GSM226037 Temporal Cortex Normal C226037M89N 89 M 150 GSM226038 Temporal Cortex Normal C226038M86N 86 M 151 GSM226039 Temporal Cortex Normal C226039M90N 90 M 152 GSM226040 Temporal Cortex Normal C226040F94N 94 F 153 GSM226041 Temporal Cortex Normal C226041F91N 91 F 154 GSM226042 Temporal Cortex Normal C226042F91N 91 F 155 GSM226044 Temporal Cortex Normal C226044F95N 95 F 156 GSM226045 Temporal Cortex Normal C226045F95N 95 F 157 GSM226046 Temporal Cortex Normal C226046F91N 91 F 158 GSM226047 Temporal Cortex Normal C226047M80N 80 M 159 GSM226048 Temporal Cortex Normal C226048M83N 83 M 160 GSM226049 Temporal Cortex Normal C226049M67N 67 M 161 GSM226050 Temporal Cortex Normal C226050M76N 76 M 162 GSM226051 Temporal Cortex Normal C226051F86N 86 F 163 GSM226052 Temporal Cortex Normal C226052F86N 86 F 164 GSM226053 Temporal Cortex Normal C226053M83N 83 M 165 GSM226055 Temporal Cortex Normal C226055M84N 84 M 166 GSM226056 Temporal Cortex Normal C226056M80N 80 M 167 GSM226082 Temporal Cortex Normal C226082M72N 72 M 168 GSM226145 Temporal Cortex Normal C226145M67N 67 M 169 GSM226146 Temporal Cortex Normal C226146F96N 96 F 170 GSM226147 Temporal Cortex Normal C226147F75N 75 F 171 GSM226148 Temporal Cortex Normal C226148F89N 89 F 172 GSM226149 Temporal Cortex Normal C226149F86N 86 F 173 GSM226150 Temporal Cortex Normal C226150M67N 67 M 174 GSM226151 Temporal Cortex Normal C226151M77N 77 M 175 GSM226154 Temporal Cortex Normal C226154M65N 65 M 176 GSM226155 Temporal Cortex Normal C226155M69N 69 M 177 GSM226156 Temporal Cortex Normal C226156M84N 84 M 178 GSM226157 Temporal Cortex Normal C226157F85N 85 F 179 GSM226158 Temporal Cortex Normal C226158M94N 94 M 180 GSM226159 Temporal Cortex Normal C226159F89N 89 F 181 GSM226160 Temporal Cortex Normal C226160M87N 87 M 182 GSM226162 Temporal Cortex Normal C226162M90N 90 M 183 GSM226163 Temporal Cortex Normal C226163F88N 88 F 184 GSM226164 Temporal Cortex Normal C226164M94N 94 M 185 GSM226165 Temporal Cortex Normal C226165F86N 86 F 186 GSM226167 Temporal Cortex Normal C226167F93N 93 F 187 GSM226168 Temporal Cortex Normal C226168M91N 91 M 188 GSM388217 Cortical Tissue Alzheimer's C388217F97A 97 F 189 GSM388218 Cortical Tissue Alzheimer's C388218F101A 101 F 190 GSM388219 Cortical Tissue Alzheimer's C388219M84A 84 M 191 GSM388220 Cortical Tissue Alzheimer's C388220F95A 95 F 192 GSM388221 Cortical Tissue Alzheimer's C388221F97A 97 F 193 GSM388222 Cortical Tissue Alzheimer's C388222F102A 102 F 194 GSM388223 Cortical Tissue Alzheimer's C388223M87A 87 M 195 GSM388224 Cortical Tissue Alzheimer's C388224F77A 77 F 196 GSM388225 Cortical Tissue Alzheimer's C388225M87A 87 M 197 GSM388226 Cortical Tissue Alzheimer's C388226M84A 84 M 198 GSM388228 Cortical Tissue Alzheimer's C388228F92A 92 F 199 GSM388229 Cortical Tissue Alzheimer's C388229M93A 93 M 200 GSM388230 Cortical Tissue Alzheimer's C388230F93A 93 F 201 GSM388231 Cortical Tissue Alzheimer's C388231F87A 87 F 202 GSM388232 Cortical Tissue Alzheimer's C388232F90A 90 F 203 GSM388233 Cortical Tissue Alzheimer's C388233M75A 75 M 204 GSM388234 Cortical Tissue Alzheimer's C388234M92A 92 M 205 GSM388235 Cortical Tissue Alzheimer's C388235M83A 83 M 206 GSM388236 Cortical Tissue Alzheimer's C388236M88A 88 M 207 GSM388237 Cortical Tissue Alzheimer's C388237M89A 89 M 208 GSM388238 Cortical Tissue Alzheimer's C388238F74A 74 F 209 GSM388239 Cortical Tissue Alzheimer's C388239F79A 79 F 210 GSM388240 Cortical Tissue Alzheimer's C388240M80A 80 M 211 GSM388241 Cortical Tissue Alzheimer's C388241F97A 97 F 212 GSM388242 Cortical Tissue Alzheimer's C388242M87A 87 M 213 GSM388243 Cortical Tissue Alzheimer's C388243F89A 89 F 214 GSM388244 Cortical Tissue Alzheimer's C388244F90A 90 F 215 GSM388245 Cortical Tissue Alzheimer's C388245M90A 90 M 216 GSM388246 Cortical Tissue Alzheimer's C388246M78A 78 M 217 GSM388247 Cortical Tissue Alzheimer's C388247F80A 80 F 218 GSM388248 Cortical Tissue Alzheimer's C388248F79A 79 F 219 GSM388249 Cortical Tissue Alzheimer's C388249F87A 87 F 220 GSM388250 Cortical Tissue Alzheimer's C388250F88A 88 F 221 GSM388251 Cortical Tissue Alzheimer's C388251M86A 86 M 222 GSM388252 Cortical Tissue Alzheimer's C388252F74A 74 F 223 GSM388253 Cortical Tissue Alzheimer's C388253F72A 72 F 224 GSM388254 Cortical Tissue Alzheimer's C388254M81A 81 M 225 GSM388255 Cortical Tissue Alzheimer's C388255F68A 68 F 226 GSM388256 Cortical Tissue Alzheimer's C388256F81A 81 F 227 GSM388257 Cortical Tissue Alzheimer's C388257F82A 82 F 228 GSM388258 Cortical Tissue Alzheimer's C388258M78A 78 M 229 GSM388259 Cortical Tissue Alzheimer's C388259M74A 74 M 230 GSM388260 Cortical Tissue Alzheimer's C388260M88A 88 M 231 GSM388261 Cortical Tissue Alzheimer's C388261F78A 78 F 232 GSM388262 Cortical Tissue Alzheimer's C388262M83A 83 M 233 GSM388263 Cortical Tissue Alzheimer's C388263M83A 83 M 234 GSM388264 Cortical Tissue Alzheimer's C388264M80A 80 M 235 GSM388265 Cortical Tissue Alzheimer's C388265M84A 84 M 236 GSM388266 Cortical Tissue Alzheimer's C388266F79A 79 F 237 GSM388267 Cortical Tissue Alzheimer's C388267F86A 86 F 238 GSM388268 Cortical Tissue Alzheimer's C388268M92A 92 M 239 GSM388269 Cortical Tissue Alzheimer's C388269F81A 81 F 240 GSM388270 Cortical Tissue Alzheimer's C388270F79A 79 F 241 GSM388271 Cortical Tissue Alzheimer's C388271M74A 74 M 242 GSM388272 Cortical Tissue Alzheimer's C388272F73A 73 F 243 GSM388273 Cortical Tissue Alzheimer's C388273M87A 87 M 244 GSM388274 Cortical Tissue Alzheimer's C388274F86A 86 F 245 GSM388275 Cortical Tissue Alzheimer's C388275F86A 86 F 246 GSM388276 Cortical Tissue Alzheimer's C388276F87A 87 F 247 GSM388277 Cortical Tissue Alzheimer's C388277F92A 92 F 248 GSM388278 Cortical Tissue Alzheimer's C388278F78A 78 F 249 GSM388279 Cortical Tissue Alzheimer's C388279F94A 94 F 250 GSM388281 Cortical Tissue Alzheimer's C388281F94A 94 F 251 GSM388282 Cortical Tissue Alzheimer's C388282M76A 76 M 252 GSM388284 Cortical Tissue Alzheimer's C388284M91A 91 M 253 GSM388285 Cortical Tissue Alzheimer's C388285M86A 86 M 254 GSM388286 Cortical Tissue Alzheimer's C388286M77A 77 M 255 GSM388287 Cortical Tissue Alzheimer's C388287M82A 82 M 256 GSM388288 Cortical Tissue Alzheimer's C388288M78A 78 M 257 GSM388289 Cortical Tissue Alzheimer's C388289M79A 79 M 258 GSM388290 Cortical Tissue Alzheimer's C388290F84A 84 F 259 GSM388291 Cortical Tissue Alzheimer's C388291F87A 87 F 260 GSM388292 Cortical Tissue Alzheimer's C388292F86A 86 F 261 GSM388294 Cortical Tissue Alzheimer's C388294M83A 83 M 262 GSM388295 Cortical Tissue Alzheimer's C388295M83A 83 M 263 GSM388296 Cortical Tissue Alzheimer's C388296M81A 81 M 264 GSM388297 Cortical Tissue Alzheimer's C388297F93A 93 F 265 GSM388298 Cortical Tissue Alzheimer's C388298M71A 71 M 266 GSM388299 Cortical Tissue Alzheimer's C388299M78A 78 M 267 GSM388300 Cortical Tissue Alzheimer's C388300F75A 75 F 268 GSM388301 Cortical Tissue Alzheimer's C388301F84A 84 F 269 GSM388302 Cortical Tissue Alzheimer's C388302M73A 73 M 270 GSM388303 Cortical Tissue Alzheimer's C388303F89A 89 F 271 GSM388304 Cortical Tissue Alzheimer's C388304FNAA NA F 272 GSM388305 Cortical Tissue Alzheimer's C388305M69A 69 M 273 GSM388306 Cortical Tissue Alzheimer's C388306M83A 83 M 274 GSM388307 Cortical Tissue Alzheimer's C388307M71A 71 M 275 GSM388308 Cortical Tissue Alzheimer's C388308F86A 86 F 276 GSM388309 Cortical Tissue Alzheimer's C388309M82A 82 M 277 GSM388310 Cortical Tissue Alzheimer's C388310FNAA NA F 278 GSM388311 Cortical Tissue Alzheimer's C388311M88A 88 M 279 GSM388312 Cortical Tissue Alzheimer's C388312M77A 77 M 280 GSM388313 Cortical Tissue Alzheimer's C388313M85A 85 M 281 GSM388314 Cortical Tissue Alzheimer's C388314F81A 81 F 282 GSM388315 Cortical Tissue Alzheimer's C388315F86A 86 F 283 GSM388316 Cortical Tissue Alzheimer's C388316M89A 89 M 284 GSM388317 Cortical Tissue Alzheimer's C388317F73A 73 F 285 GSM388318 Cortical Tissue Alzheimer's C388318F96A 96 F 286 GSM388319 Cortical Tissue Alzheimer's C388319M73A 73 M 287 GSM388320 Cortical Tissue Alzheimer's C388320M81A 81 M 288 GSM388321 Cortical Tissue Alzheimer's C388321F84A 84 F 289 GSM388322 Cortical Tissue Alzheimer's C388322F93A 93 F 290 GSM388323 Cortical Tissue Alzheimer's C388323F82A 82 F 291 GSM388324 Cortical Tissue Alzheimer's C388324M76A 76 M 292 GSM388325 Cortical Tissue Alzheimer's C388325M77A 77 M 293 GSM388326 Cortical Tissue Alzheimer's C388326F86A 86 F 294 GSM388327 Cortical Tissue Alzheimer's C388327F85A 85 F 295 GSM388328 Cortical Tissue Alzheimer's C388328M83A 83 M 296 GSM388329 Cortical Tissue Alzheimer's C388329M76A 76 M 297 GSM388330 Cortical Tissue Alzheimer's C388330M81A 81 M 298 GSM388331 Cortical Tissue Alzheimer's C388331M79A 79 M 299 GSM388332 Cortical Tissue Alzheimer's C388332M81A 81 M 300 GSM388333 Cortical Tissue Alzheimer's C388333F78A 78 F 301 GSM388334 Cortical Tissue Alzheimer's C388334M80A 80 M 302 GSM388335 Cortical Tissue Alzheimer's C388335M84A 84 M 303 GSM388336 Cortical Tissue Alzheimer's C388336F85A 85 F 304 GSM388337 Cortical Tissue Alzheimer's C388337M75A 75 M 305 GSM388338 Cortical Tissue Alzheimer's C388338F80A 80 F 306 GSM388339 Cortical Tissue Alzheimer's C388339F97A 97 F 307 GSM388340 Cortical Tissue Alzheimer's C388340F82A 82 F 308 GSM388341 Cortical Tissue Alzheimer's C388341M82A 82 M 309 GSM388342 Cortical Tissue Alzheimer's C388342M77A 77 M 310 GSM388343 Cortical Tissue Alzheimer's C388343M81A 81 M 311 GSM388345 Cortical Tissue Alzheimer's C388345F96A 96 F 312 GSM388346 Cortical Tissue Alzheimer's C388346F90A 90 F 313 GSM388347 Cortical Tissue Alzheimer's C388347M86A 86 M 314 GSM388348 Cortical Tissue Alzheimer's C388348M88A 88 M 315 GSM388349 Cortical Tissue Alzheimer's C388349F90A 90 F 316 GSM388350 Cortical Tissue Alzheimer's C388350F90A 90 F 317 GSM388351 Cortical Tissue Alzheimer's C388351F84A 84 F 318 GSM388352 Cortical Tissue Alzheimer's C388352M84A 84 M 319 GSM388353 Cortical Tissue Alzheimer's C388353F91A 91 F 320 GSM388354 Cortical Tissue Alzheimer's C388354F81A 81 F 321 GSM388355 Cortical Tissue Alzheimer's C388355F84A 84 F 322 GSM388356 Cortical Tissue Alzheimer's C388356M80A 80 M 323 GSM388357 Cortical Tissue Alzheimer's C388357M81A 81 M 324 GSM388358 Cortical Tissue Alzheimer's C388358F87A 87 F 325 GSM388359 Cortical Tissue Alzheimer's C388359M85A 85 M 326 GSM388360 Cortical Tissue Alzheimer's C388360F90A 90 F 327 GSM388361 Cortical Tissue Alzheimer's C388361M79A 79 M 328 GSM388362 Cortical Tissue Alzheimer's C388362F87A 87 F 329 GSM388363 Cortical Tissue Alzheimer's C388363M75A 75 M 330 GSM388364 Cortical Tissue Alzheimer's C388364F92A 92 F 331 GSM388365 Cortical Tissue Alzheimer's C388365F84A 84 F 332 GSM388366 Cortical Tissue Alzheimer's C388366M75A 75 M 333 GSM388367 Cortical Tissue Alzheimer's C388367F76A 76 F 334 GSM388368 Cortical Tissue Alzheimer's C388368F86A 86 F 335 GSM388369 Cortical Tissue Alzheimer's C388369M82A 82 M 336 GSM388370 Cortical Tissue Alzheimer's C388370M76A 76 M 337 GSM388371 Cortical Tissue Alzheimer's C388371F81A 81 F 338 GSM388372 Cortical Tissue Alzheimer's C388372F80A 80 F 339 GSM388373 Cortical Tissue Alzheimer's C388373M83A 83 M 340 GSM388374 Cortical Tissue Alzheimer's C388374F83A 83 F 341 GSM388375 Cortical Tissue Alzheimer's C388375F84A 84 F 342 GSM388376 Cortical Tissue Alzheimer's C388376M93A 93 M 343 GSM388377 Cortical Tissue Alzheimer's C388377F92A 92 F 344 GSM388378 Cortical Tissue Alzheimer's C388378M78A 78 M 345 GSM388379 Cortical Tissue Alzheimer's C388379M90A 90 M 346 GSM388380 Cortical Tissue Alzheimer's C388380M83A 83 M 347 GSM388381 Cortical Tissue Alzheimer's C388381M79A 79 M 348 GSM388382 Cortical Tissue Alzheimer's C388382M84A 84 M 349 GSM388383 Cortical Tissue Alzheimer's C388383F90A 90 F 350 GSM388384 Cortical Tissue Alzheimer's C388384F88A 88 F 351 GSM388385 Cortical Tissue Alzheimer's C388385M77A 77 M 352 GSM388386 Cortical Tissue Alzheimer's C388386F80A 80 F 353 GSM388387 Cortical Tissue Alzheimer's C388387M87A 87 M 354 GSM388388 Cortical Tissue Alzheimer's C388388M86A 86 M 355 GSM388389 Cortical Tissue Alzheimer's C388389M74A 74 M 356 GSM388390 Cortical Tissue Alzheimer's C388390F86A 86 F 357 GSM388391 Cortical Tissue Alzheimer's C388391F81A 81 F 358 GSM388392 Cortical Tissue Alzheimer's C388392F73A 73 F 359 GSM388393 Cortical Tissue Alzheimer's C388393M83A 83 M 360 GSM388394 Cortical Tissue Alzheimer's C388394M86A 86 M 361 GSM388395 Cortical Tissue Alzheimer's C388395F86A 86 F 362 GSM388396 Cortical Tissue Alzheimer's C388396M78A 78 M 363 GSM388397 Cortical Tissue Alzheimer's C388397M83A 83 M

About the tissue used to generate this set of data:

About the array platform:

Illumina Human 50 mer probes. Total of 24357 probes according to Myers et al. A total of 24354 probes included in this GeneNetwork file. From the Methods section of the paper: Genotyping and Expression Profiling DNA was hybridized to the Affymetrix GeneChip Human Mapping 500K Array Set (502,627 SNPs) as previously described.11,12 Genotypes were extracted with the use of both SNiPer-HD13 and BRLMM (Affymetrix, Santa Clara, CA) algorithms. Genotypes that exhibited less than 98% concordance between calls were excluded. SNPs with call rates less than 90% were excluded from the analysis. HardyWeinberg equilibrium (HWE) was assessed with exact tests and the PLINK analysis toolset.14 SNPs with HWE exact-test p values less than 0.05, as well as SNPs with minor-allele frequencies less than 1%, were excluded. Allele calls had a mean of 97% and a range of 90%–99%. cRNA was hybridized to Illumina Human Refseq-8 Expression BeadChip (24,357 transcripts) via standard protocols. Expression profiles were extracted and rank invariant normalized15–17 with the use of the BeadStudio software available from Illumina, with the Illumina custom error model used. Rankinvariant-normalized expression data were log10 transformed, and missing data were encoded as missing, rather than as a zero level of expression.

About data values and data processing:

Notes:

Access to the original data from Dr. Myers' laboratory or GEO GSE15222 PMI = Post Mortem Interval Cannot find this record in the GEO website: WGACON-120 This data is based on May 2004 (NCBI35/hg17).

Experiment Type:

Expression profiling by array We recently surveyed the relationship between the human brain transcriptome and genome in a series of neuropathologically normal postmortem samples. We now have analyzed additional samples with a confirmed pathologic diagnosis of late onset Alzheimer's disease (LOAD, final n=187 controls, 176 cases). Nine percent of the cortical transcripts we analyzed had expression profiles correlated with their genotypes in the combined cohort and approximately 5% of transcripts had SNP-transcript relationships that could distinguish LOAD samples. Two of these transcripts have been previously implicated in LOAD candidate gene SNP-expression screens. This study shows how the relationship between common inherited genetic variants and brain transcript expression can be used in the study of human brain disorders. We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power to find risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease. see DOI:10.1016/j.ajhg.2009.03.011 for further details and complete author list. Expression quantitative trait loci study using human brain from 363 cortical samples. Affymetrix 500K chip for genotyping, Illumina Sentrix Human-ref 8 bead array chip for expression. Genotyping data will be available at dbGAP.

Contributor:

Webster J, Gibbs R, Myers A

Citation:

Data source acknowledgment:

http://labs.med.miami.edu/myers

Study Id:

78

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)