rbbt-marq 1.0.0

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  1. data/LICENSE +20 -0
  2. data/R/CustomDS.R +80 -0
  3. data/R/GEO.R +249 -0
  4. data/R/MA.R +359 -0
  5. data/README.rdoc +58 -0
  6. data/bin/marq_config +209 -0
  7. data/install_scripts/CustomDS/Rakefile +223 -0
  8. data/install_scripts/GEO/Rakefile +272 -0
  9. data/install_scripts/GEO/platforms/GPL100.yaml +7 -0
  10. data/install_scripts/GEO/platforms/GPL1002.yaml +7 -0
  11. data/install_scripts/GEO/platforms/GPL1007.yaml +7 -0
  12. data/install_scripts/GEO/platforms/GPL101.yaml +7 -0
  13. data/install_scripts/GEO/platforms/GPL1010.yaml +7 -0
  14. data/install_scripts/GEO/platforms/GPL1073.yaml +7 -0
  15. data/install_scripts/GEO/platforms/GPL1074.yaml +4 -0
  16. data/install_scripts/GEO/platforms/GPL1090.yaml +7 -0
  17. data/install_scripts/GEO/platforms/GPL1104.yaml +7 -0
  18. data/install_scripts/GEO/platforms/GPL118.yaml +7 -0
  19. data/install_scripts/GEO/platforms/GPL1205.yaml +4 -0
  20. data/install_scripts/GEO/platforms/GPL1211.yaml +7 -0
  21. data/install_scripts/GEO/platforms/GPL1213.yaml +7 -0
  22. data/install_scripts/GEO/platforms/GPL1219.yaml +4 -0
  23. data/install_scripts/GEO/platforms/GPL1223.yaml +7 -0
  24. data/install_scripts/GEO/platforms/GPL1226.yaml +7 -0
  25. data/install_scripts/GEO/platforms/GPL1229.yaml +7 -0
  26. data/install_scripts/GEO/platforms/GPL1230.yaml +7 -0
  27. data/install_scripts/GEO/platforms/GPL1231.yaml +7 -0
  28. data/install_scripts/GEO/platforms/GPL1232.yaml +7 -0
  29. data/install_scripts/GEO/platforms/GPL1260.yaml +4 -0
  30. data/install_scripts/GEO/platforms/GPL1261.yaml +4 -0
  31. data/install_scripts/GEO/platforms/GPL127.yaml +4 -0
  32. data/install_scripts/GEO/platforms/GPL128.yaml +7 -0
  33. data/install_scripts/GEO/platforms/GPL1290.yaml +7 -0
  34. data/install_scripts/GEO/platforms/GPL1292.yaml +7 -0
  35. data/install_scripts/GEO/platforms/GPL1293.yaml +7 -0
  36. data/install_scripts/GEO/platforms/GPL1294.yaml +7 -0
  37. data/install_scripts/GEO/platforms/GPL1295.yaml +7 -0
  38. data/install_scripts/GEO/platforms/GPL13.yaml +4 -0
  39. data/install_scripts/GEO/platforms/GPL1310.yaml +7 -0
  40. data/install_scripts/GEO/platforms/GPL1313.yaml +7 -0
  41. data/install_scripts/GEO/platforms/GPL1323.yaml +7 -0
  42. data/install_scripts/GEO/platforms/GPL1331.yaml +7 -0
  43. data/install_scripts/GEO/platforms/GPL1352.yaml +4 -0
  44. data/install_scripts/GEO/platforms/GPL1355.yaml +4 -0
  45. data/install_scripts/GEO/platforms/GPL1382.yaml +7 -0
  46. data/install_scripts/GEO/platforms/GPL1387.yaml +7 -0
  47. data/install_scripts/GEO/platforms/GPL1397.yaml +4 -0
  48. data/install_scripts/GEO/platforms/GPL14.yaml +7 -0
  49. data/install_scripts/GEO/platforms/GPL1412.yaml +7 -0
  50. data/install_scripts/GEO/platforms/GPL1415.yaml +7 -0
  51. data/install_scripts/GEO/platforms/GPL1420.yaml +7 -0
  52. data/install_scripts/GEO/platforms/GPL144.yaml +7 -0
  53. data/install_scripts/GEO/platforms/GPL1449.yaml +7 -0
  54. data/install_scripts/GEO/platforms/GPL1458.yaml +7 -0
  55. data/install_scripts/GEO/platforms/GPL1523.yaml +7 -0
  56. data/install_scripts/GEO/platforms/GPL1524.yaml +7 -0
  57. data/install_scripts/GEO/platforms/GPL1528.yaml +7 -0
  58. data/install_scripts/GEO/platforms/GPL153.yaml +7 -0
  59. data/install_scripts/GEO/platforms/GPL1530.yaml +7 -0
  60. data/install_scripts/GEO/platforms/GPL1535.yaml +4 -0
  61. data/install_scripts/GEO/platforms/GPL155.yaml +7 -0
  62. data/install_scripts/GEO/platforms/GPL163.yaml +7 -0
  63. data/install_scripts/GEO/platforms/GPL168.yaml +7 -0
  64. data/install_scripts/GEO/platforms/GPL169.yaml +7 -0
  65. data/install_scripts/GEO/platforms/GPL1704.yaml +4 -0
  66. data/install_scripts/GEO/platforms/GPL1708.yaml +7 -0
  67. data/install_scripts/GEO/platforms/GPL1739.yaml +7 -0
  68. data/install_scripts/GEO/platforms/GPL1740.yaml +4 -0
  69. data/install_scripts/GEO/platforms/GPL1749.yaml +7 -0
  70. data/install_scripts/GEO/platforms/GPL177.yaml +7 -0
  71. data/install_scripts/GEO/platforms/GPL1790.yaml +7 -0
  72. data/install_scripts/GEO/platforms/GPL1792.yaml +7 -0
  73. data/install_scripts/GEO/platforms/GPL181.yaml +7 -0
  74. data/install_scripts/GEO/platforms/GPL1818.yaml +7 -0
  75. data/install_scripts/GEO/platforms/GPL1820.yaml +4 -0
  76. data/install_scripts/GEO/platforms/GPL1823.yaml +7 -0
  77. data/install_scripts/GEO/platforms/GPL1826.yaml +7 -0
  78. data/install_scripts/GEO/platforms/GPL183.yaml +7 -0
  79. data/install_scripts/GEO/platforms/GPL1831.yaml +7 -0
  80. data/install_scripts/GEO/platforms/GPL1833.yaml +7 -0
  81. data/install_scripts/GEO/platforms/GPL1872.yaml +4 -0
  82. data/install_scripts/GEO/platforms/GPL1911.yaml +7 -0
  83. data/install_scripts/GEO/platforms/GPL1914.yaml +4 -0
  84. data/install_scripts/GEO/platforms/GPL1928.yaml +7 -0
  85. data/install_scripts/GEO/platforms/GPL1942.yaml +7 -0
  86. data/install_scripts/GEO/platforms/GPL1945.yaml +7 -0
  87. data/install_scripts/GEO/platforms/GPL1964.yaml +7 -0
  88. data/install_scripts/GEO/platforms/GPL198.yaml +4 -0
  89. data/install_scripts/GEO/platforms/GPL1981.yaml +4 -0
  90. data/install_scripts/GEO/platforms/GPL200.yaml +7 -0
  91. data/install_scripts/GEO/platforms/GPL2006.yaml +7 -0
  92. data/install_scripts/GEO/platforms/GPL201.yaml +4 -0
  93. data/install_scripts/GEO/platforms/GPL2011.yaml +7 -0
  94. data/install_scripts/GEO/platforms/GPL2026.yaml +7 -0
  95. data/install_scripts/GEO/platforms/GPL205.yaml +7 -0
  96. data/install_scripts/GEO/platforms/GPL207.yaml +7 -0
  97. data/install_scripts/GEO/platforms/GPL2136.yaml +7 -0
  98. data/install_scripts/GEO/platforms/GPL220.yaml +7 -0
  99. data/install_scripts/GEO/platforms/GPL226.yaml +7 -0
  100. data/install_scripts/GEO/platforms/GPL24.yaml +4 -0
  101. data/install_scripts/GEO/platforms/GPL246.yaml +4 -0
  102. data/install_scripts/GEO/platforms/GPL247.yaml +7 -0
  103. data/install_scripts/GEO/platforms/GPL2507.yaml +4 -0
  104. data/install_scripts/GEO/platforms/GPL2529.yaml +4 -0
  105. data/install_scripts/GEO/platforms/GPL2531.yaml +7 -0
  106. data/install_scripts/GEO/platforms/GPL254.yaml +7 -0
  107. data/install_scripts/GEO/platforms/GPL2569.yaml +7 -0
  108. data/install_scripts/GEO/platforms/GPL257.yaml +7 -0
  109. data/install_scripts/GEO/platforms/GPL2598.yaml +7 -0
  110. data/install_scripts/GEO/platforms/GPL260.yaml +7 -0
  111. data/install_scripts/GEO/platforms/GPL2614.yaml +4 -0
  112. data/install_scripts/GEO/platforms/GPL2622.yaml +7 -0
  113. data/install_scripts/GEO/platforms/GPL2623.yaml +7 -0
  114. data/install_scripts/GEO/platforms/GPL2660.yaml +7 -0
  115. data/install_scripts/GEO/platforms/GPL2670.yaml +7 -0
  116. data/install_scripts/GEO/platforms/GPL2677.yaml +7 -0
  117. data/install_scripts/GEO/platforms/GPL2700.yaml +4 -0
  118. data/install_scripts/GEO/platforms/GPL2721.yaml +7 -0
  119. data/install_scripts/GEO/platforms/GPL2727.yaml +7 -0
  120. data/install_scripts/GEO/platforms/GPL273.yaml +7 -0
  121. data/install_scripts/GEO/platforms/GPL2763.yaml +7 -0
  122. data/install_scripts/GEO/platforms/GPL2824.yaml +7 -0
  123. data/install_scripts/GEO/platforms/GPL284.yaml +7 -0
  124. data/install_scripts/GEO/platforms/GPL287.yaml +4 -0
  125. data/install_scripts/GEO/platforms/GPL2872.yaml +7 -0
  126. data/install_scripts/GEO/platforms/GPL288.yaml +4 -0
  127. data/install_scripts/GEO/platforms/GPL2883.yaml +7 -0
  128. data/install_scripts/GEO/platforms/GPL289.yaml +4 -0
  129. data/install_scripts/GEO/platforms/GPL2895.yaml +4 -0
  130. data/install_scripts/GEO/platforms/GPL2897.yaml +7 -0
  131. data/install_scripts/GEO/platforms/GPL2902.yaml +7 -0
  132. data/install_scripts/GEO/platforms/GPL2987.yaml +4 -0
  133. data/install_scripts/GEO/platforms/GPL2995.yaml +7 -0
  134. data/install_scripts/GEO/platforms/GPL3039.yaml +4 -0
  135. data/install_scripts/GEO/platforms/GPL3050.yaml +7 -0
  136. data/install_scripts/GEO/platforms/GPL3084.yaml +7 -0
  137. data/install_scripts/GEO/platforms/GPL3113.yaml +7 -0
  138. data/install_scripts/GEO/platforms/GPL317.yaml +7 -0
  139. data/install_scripts/GEO/platforms/GPL319.yaml +7 -0
  140. data/install_scripts/GEO/platforms/GPL32.yaml +4 -0
  141. data/install_scripts/GEO/platforms/GPL3222.yaml +7 -0
  142. data/install_scripts/GEO/platforms/GPL3295.yaml +7 -0
  143. data/install_scripts/GEO/platforms/GPL3305.yaml +4 -0
  144. data/install_scripts/GEO/platforms/GPL3306.yaml +7 -0
  145. data/install_scripts/GEO/platforms/GPL3307.yaml +7 -0
  146. data/install_scripts/GEO/platforms/GPL333.yaml +4 -0
  147. data/install_scripts/GEO/platforms/GPL3341.yaml +7 -0
  148. data/install_scripts/GEO/platforms/GPL3349.yaml +7 -0
  149. data/install_scripts/GEO/platforms/GPL339.yaml +4 -0
  150. data/install_scripts/GEO/platforms/GPL340.yaml +4 -0
  151. data/install_scripts/GEO/platforms/GPL3408.yaml +7 -0
  152. data/install_scripts/GEO/platforms/GPL341.yaml +4 -0
  153. data/install_scripts/GEO/platforms/GPL3415.yaml +4 -0
  154. data/install_scripts/GEO/platforms/GPL3423.yaml +7 -0
  155. data/install_scripts/GEO/platforms/GPL3440.yaml +7 -0
  156. data/install_scripts/GEO/platforms/GPL3457.yaml +4 -0
  157. data/install_scripts/GEO/platforms/GPL3504.yaml +4 -0
  158. data/install_scripts/GEO/platforms/GPL3506.yaml +4 -0
  159. data/install_scripts/GEO/platforms/GPL355.yaml +7 -0
  160. data/install_scripts/GEO/platforms/GPL3558.yaml +7 -0
  161. data/install_scripts/GEO/platforms/GPL3607.yaml +7 -0
  162. data/install_scripts/GEO/platforms/GPL368.yaml +4 -0
  163. data/install_scripts/GEO/platforms/GPL3695.yaml +7 -0
  164. data/install_scripts/GEO/platforms/GPL371.yaml +7 -0
  165. data/install_scripts/GEO/platforms/GPL3834.yaml +4 -0
  166. data/install_scripts/GEO/platforms/GPL4006.yaml +7 -0
  167. data/install_scripts/GEO/platforms/GPL4055.yaml +7 -0
  168. data/install_scripts/GEO/platforms/GPL409.yaml +7 -0
  169. data/install_scripts/GEO/platforms/GPL4191.yaml +7 -0
  170. data/install_scripts/GEO/platforms/GPL4226.yaml +7 -0
  171. data/install_scripts/GEO/platforms/GPL4371.yaml +7 -0
  172. data/install_scripts/GEO/platforms/GPL4567.yaml +4 -0
  173. data/install_scripts/GEO/platforms/GPL4685.yaml +4 -0
  174. data/install_scripts/GEO/platforms/GPL483.yaml +7 -0
  175. data/install_scripts/GEO/platforms/GPL49.yaml +7 -0
  176. data/install_scripts/GEO/platforms/GPL50.yaml +7 -0
  177. data/install_scripts/GEO/platforms/GPL500.yaml +7 -0
  178. data/install_scripts/GEO/platforms/GPL507.yaml +4 -0
  179. data/install_scripts/GEO/platforms/GPL51.yaml +7 -0
  180. data/install_scripts/GEO/platforms/GPL513.yaml +7 -0
  181. data/install_scripts/GEO/platforms/GPL519.yaml +7 -0
  182. data/install_scripts/GEO/platforms/GPL52.yaml +7 -0
  183. data/install_scripts/GEO/platforms/GPL529.yaml +7 -0
  184. data/install_scripts/GEO/platforms/GPL53.yaml +7 -0
  185. data/install_scripts/GEO/platforms/GPL5356.yaml +7 -0
  186. data/install_scripts/GEO/platforms/GPL538.yaml +7 -0
  187. data/install_scripts/GEO/platforms/GPL54.yaml +7 -0
  188. data/install_scripts/GEO/platforms/GPL543.yaml +7 -0
  189. data/install_scripts/GEO/platforms/GPL544.yaml +7 -0
  190. data/install_scripts/GEO/platforms/GPL545.yaml +7 -0
  191. data/install_scripts/GEO/platforms/GPL546.yaml +7 -0
  192. data/install_scripts/GEO/platforms/GPL547.yaml +7 -0
  193. data/install_scripts/GEO/platforms/GPL549.yaml +7 -0
  194. data/install_scripts/GEO/platforms/GPL550.yaml +4 -0
  195. data/install_scripts/GEO/platforms/GPL56.yaml +7 -0
  196. data/install_scripts/GEO/platforms/GPL560.yaml +4 -0
  197. data/install_scripts/GEO/platforms/GPL564.yaml +7 -0
  198. data/install_scripts/GEO/platforms/GPL57.yaml +7 -0
  199. data/install_scripts/GEO/platforms/GPL570.yaml +4 -0
  200. data/install_scripts/GEO/platforms/GPL571.yaml +4 -0
  201. data/install_scripts/GEO/platforms/GPL576.yaml +7 -0
  202. data/install_scripts/GEO/platforms/GPL58.yaml +7 -0
  203. data/install_scripts/GEO/platforms/GPL5823.yaml +4 -0
  204. data/install_scripts/GEO/platforms/GPL59.yaml +7 -0
  205. data/install_scripts/GEO/platforms/GPL5915.yaml +4 -0
  206. data/install_scripts/GEO/platforms/GPL5947.yaml +7 -0
  207. data/install_scripts/GEO/platforms/GPL61.yaml +7 -0
  208. data/install_scripts/GEO/platforms/GPL64.yaml +7 -0
  209. data/install_scripts/GEO/platforms/GPL6419.yaml +7 -0
  210. data/install_scripts/GEO/platforms/GPL6424.yaml +7 -0
  211. data/install_scripts/GEO/platforms/GPL65.yaml +7 -0
  212. data/install_scripts/GEO/platforms/GPL6574.yaml +4 -0
  213. data/install_scripts/GEO/platforms/GPL6649.yaml +4 -0
  214. data/install_scripts/GEO/platforms/GPL67.yaml +7 -0
  215. data/install_scripts/GEO/platforms/GPL6720.yaml +7 -0
  216. data/install_scripts/GEO/platforms/GPL7054.yaml +4 -0
  217. data/install_scripts/GEO/platforms/GPL737.yaml +7 -0
  218. data/install_scripts/GEO/platforms/GPL738.yaml +7 -0
  219. data/install_scripts/GEO/platforms/GPL74.yaml +4 -0
  220. data/install_scripts/GEO/platforms/GPL75.yaml +4 -0
  221. data/install_scripts/GEO/platforms/GPL76.yaml +4 -0
  222. data/install_scripts/GEO/platforms/GPL764.yaml +7 -0
  223. data/install_scripts/GEO/platforms/GPL772.yaml +7 -0
  224. data/install_scripts/GEO/platforms/GPL782.yaml +7 -0
  225. data/install_scripts/GEO/platforms/GPL783.yaml +7 -0
  226. data/install_scripts/GEO/platforms/GPL784.yaml +7 -0
  227. data/install_scripts/GEO/platforms/GPL80.yaml +4 -0
  228. data/install_scripts/GEO/platforms/GPL81.yaml +4 -0
  229. data/install_scripts/GEO/platforms/GPL82.yaml +4 -0
  230. data/install_scripts/GEO/platforms/GPL83.yaml +4 -0
  231. data/install_scripts/GEO/platforms/GPL85.yaml +4 -0
  232. data/install_scripts/GEO/platforms/GPL86.yaml +4 -0
  233. data/install_scripts/GEO/platforms/GPL87.yaml +4 -0
  234. data/install_scripts/GEO/platforms/GPL870.yaml +7 -0
  235. data/install_scripts/GEO/platforms/GPL875.yaml +7 -0
  236. data/install_scripts/GEO/platforms/GPL884.yaml +7 -0
  237. data/install_scripts/GEO/platforms/GPL887.yaml +7 -0
  238. data/install_scripts/GEO/platforms/GPL89.yaml +4 -0
  239. data/install_scripts/GEO/platforms/GPL890.yaml +7 -0
  240. data/install_scripts/GEO/platforms/GPL891.yaml +7 -0
  241. data/install_scripts/GEO/platforms/GPL90.yaml +7 -0
  242. data/install_scripts/GEO/platforms/GPL91.yaml +4 -0
  243. data/install_scripts/GEO/platforms/GPL92.yaml +4 -0
  244. data/install_scripts/GEO/platforms/GPL920.yaml +7 -0
  245. data/install_scripts/GEO/platforms/GPL922.yaml +7 -0
  246. data/install_scripts/GEO/platforms/GPL924.yaml +7 -0
  247. data/install_scripts/GEO/platforms/GPL93.yaml +4 -0
  248. data/install_scripts/GEO/platforms/GPL96.yaml +4 -0
  249. data/install_scripts/GEO/platforms/GPL968.yaml +4 -0
  250. data/install_scripts/GEO/platforms/GPL97.yaml +4 -0
  251. data/install_scripts/GEO/platforms/GPL98.yaml +7 -0
  252. data/install_scripts/GEO/platforms/GPL981.yaml +7 -0
  253. data/install_scripts/GEO/platforms/GPL99.yaml +7 -0
  254. data/install_scripts/GEO/platforms/GPL999.yaml +7 -0
  255. data/install_scripts/GEO/series/GSE10018.yaml +61 -0
  256. data/install_scripts/GEO/series/GSE1002.yaml +135 -0
  257. data/install_scripts/GEO/series/GSE10066.yaml +31 -0
  258. data/install_scripts/GEO/series/GSE10073.yaml +19 -0
  259. data/install_scripts/GEO/series/GSE10091.yaml +15 -0
  260. data/install_scripts/GEO/series/GSE101.yaml +17 -0
  261. data/install_scripts/GEO/series/GSE10100.yaml +15 -0
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  267. data/install_scripts/GEO/series/GSE103.yaml +19 -0
  268. data/install_scripts/GEO/series/GSE104.yaml +19 -0
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  270. data/install_scripts/GEO/series/GSE10521.yaml +56 -0
  271. data/install_scripts/GEO/series/GSE10554.yaml +19 -0
  272. data/install_scripts/GEO/series/GSE1073.yaml +127 -0
  273. data/install_scripts/GEO/series/GSE10860.yaml +25 -0
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  296. data/install_scripts/GEO/series/GSE11983.yaml +15 -0
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  298. data/install_scripts/GEO/series/GSE12055.yaml +109 -0
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  300. data/install_scripts/GEO/series/GSE12104.yaml +10 -0
  301. data/install_scripts/GEO/series/GSE12138.yaml +13 -0
  302. data/install_scripts/GEO/series/GSE12150.yaml +32 -0
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  305. data/install_scripts/GEO/series/GSE1365.yaml +14 -0
  306. data/install_scripts/GEO/series/GSE1404.yaml +596 -0
  307. data/install_scripts/GEO/series/GSE1492.yaml +15 -0
  308. data/install_scripts/GEO/series/GSE15222.yaml +731 -0
  309. data/install_scripts/GEO/series/GSE1553.yaml +23 -0
  310. data/install_scripts/GEO/series/GSE1617.yaml +39 -0
  311. data/install_scripts/GEO/series/GSE1688.yaml +36 -0
  312. data/install_scripts/GEO/series/GSE1693.yaml +60 -0
  313. data/install_scripts/GEO/series/GSE1752.yaml +32 -0
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  319. data/install_scripts/GEO/series/GSE1763.yaml +19 -0
  320. data/install_scripts/GEO/series/GSE1915.yaml +39 -0
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  322. data/install_scripts/GEO/series/GSE1941.yaml +23 -0
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  325. data/install_scripts/GEO/series/GSE1975.yaml +65 -0
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  328. data/install_scripts/GEO/series/GSE2159.yaml +31 -0
  329. data/install_scripts/GEO/series/GSE2246.yaml +157 -0
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  331. data/install_scripts/GEO/series/GSE2267.yaml +155 -0
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  474. data/lib/MARQ.rb +79 -0
  475. data/lib/MARQ/CustomDS.rb +99 -0
  476. data/lib/MARQ/GEO.rb +588 -0
  477. data/lib/MARQ/ID.rb +144 -0
  478. data/lib/MARQ/MADB.rb +238 -0
  479. data/lib/MARQ/annotations.rb +740 -0
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  484. data/tasks/install.rake +21 -0
  485. metadata +588 -0
@@ -0,0 +1,25 @@
1
+ ---
2
+ :description: |-
3
+ The role of the S. cerevisiae Yap4 transcription factor in the response to hyperosmolarity was investigated in two ways. Firstly, to assess the overall response of the yap4 deleted strain genome wide analysis upon a mild upshift in osmolarity was compared to the same response in the wt strain. Secondly, in order to identify genes whose osmo-expression is differentially regulated in the mutant strain (ie potential Yap4 target genes) the relative abundance of cDNAs of the wt and yap4 mutant strain obtained upon an osmotic upshift were directly compared by microarray analysis.
4
+ Keywords: Mutant Stress Response
5
+ :title: Role of Yap4 in Yeast Osmotic Stress Response
6
+ :arrays:
7
+ GSM114156:
8
+ condition: yap4 OsmoticStress
9
+ GSM114157:
10
+ condition: yap4 OsmoticStress
11
+ GSM114137:
12
+ condition: wt OsmoticStress
13
+ GSM114139:
14
+ condition: wt OsmoticStress
15
+ GSM114153:
16
+ condition: wt vs yap4 OsmoticStress
17
+ GSM114142:
18
+ condition: wt OsmoticStress
19
+ GSM114154:
20
+ condition: wt vs YAP4 wt vs yap4 OsmoticStress
21
+ GSM114143:
22
+ condition: wt vs YAP4 wt vs yap4 OsmoticStress
23
+ GSM114155:
24
+ condition: yap4 OsmoticStress
25
+ :platform: GPL537
@@ -0,0 +1,31 @@
1
+ ---
2
+ :description: |-
3
+ In Saccharomyces cerevisiae growth, size control and cell cycle progression are strictly coordinated and regulated according to the nutritional conditions. In particular, ribosome biogenesis appears a key event in this regulatory network. SFP1 encodes a zinc-finger protein promoting the transcription of a large cluster of genes involved in ribosome biogenesis. It has been suggested that Sfp1 is a cell size modulator acting at Start. To better study the regulatory role of Sfp1 and its putative involvement in cell size and cycle control, we analysed the behaviour of an sfp1 null mutant strain and of an isogenic reference strain growing in chemostat cultures. This approach allowed us to analyze both strains at the same specific growth rate, thus eliminating the secondary effects due to the slow growing phenotype that the sfp1 null mutant shows in shake flask. We studied glucose(anaerobic)- and ethanol(aerobic)-limited cultures, as paradigms of two different metabolic states. Major alterations of the transcriptional profile were observed during growth on glucose, while no significant differences were observed when comparing ethanol growing cultures. In particular, in the former growth condition, Sfp1 appears involved in the control of ribosome biogenesis but not of ribosomal protein gene expression.
4
+ Keywords: global transcriptional profile, genetic modification, ribosome biogenesis
5
+ :title: SFP1 dependent transcription
6
+ :arrays:
7
+ GSM118589:
8
+ treatment: sfp1 delta EtOH-lim
9
+ GSM118590:
10
+ treatment: sfp1 delta Glu-lim
11
+ GSM118591:
12
+ treatment: sfp1 delta Glu-lim
13
+ GSM118592:
14
+ treatment: sfp1 delta Glu-lim
15
+ GSM118581:
16
+ treatment: CENPK113.7D EtOH-lim
17
+ GSM118582:
18
+ treatment: CENPK113.7D EtOH-lim
19
+ GSM118583:
20
+ treatment: CENPK113.7D EtOH-lim
21
+ GSM118584:
22
+ treatment: CENPK113.7D Glu-lim
23
+ GSM118585:
24
+ treatment: CENPK113.7D Glu-lim
25
+ GSM118586:
26
+ treatment: CENPK113.7D Glu-lim
27
+ GSM118587:
28
+ treatment: sfp1 delta EtOH-lim
29
+ GSM118588:
30
+ treatment: sfp1 delta EtOH-lim
31
+ :platform: GPL90
@@ -0,0 +1,55 @@
1
+ ---
2
+ :description: |-
3
+ Tetracyclines are effective but slow-acting antimalarial drugs whose mechanism of action remains uncertain. To characterize the antimalarial mechanism of tetracyclines, we evaluated their stage-specific activities, impacts on parasite transcription, and effects on two predicted organelle targets, the apicoplast and the mitochondrion, in cultured Plasmodium falciparum. Antimalarial effects were much greater after two 48-h life cycles than after one cycle, even if the drugs were removed at the end of the first cycle. Doxycycline-treated parasites appeared morphologically normal until late in the second cycle of treatment but failed to develop into merozoites. Doxycycline specifically impaired the expression of apicoplast genes. Apicoplast morphology initially appeared normal in the presence of doxycycline. However, apicoplasts were abnormal in the progeny of doxycycline-treated parasites, as evidenced by a block in apicoplast genome replication, a lack of processing of an apicoplast-targeted protein, and failure to elongate and segregate during schizogeny. Replication of the nuclear and mitochondrial genomes and mitochondrial morphology appeared normal. Our results demonstrate that tetracyclines specifically block expression of the apicoplast genome, resulting in the distribution of nonfunctional apicoplasts into daughter merozoites. The loss of apicoplast function in the progeny of treated parasites leads to a slow but potent antimalarial effect.
4
+ Keywords: Plasmodium falciparum treated with Doxycycline
5
+ :title: Tetracyclines Specifically Target the Apicoplast of the Malaria Parasite Plasmodium falciparum
6
+ :arrays:
7
+ GSM119447:
8
+ condition: doxy 25h
9
+ GSM119436:
10
+ condition: control 30h
11
+ GSM119437:
12
+ condition: control 35h
13
+ GSM119448:
14
+ condition: doxy 30h
15
+ GSM119450:
16
+ condition: doxy 40h
17
+ GSM119438:
18
+ condition: control 40h
19
+ GSM119449:
20
+ condition: doxy 35h
21
+ GSM119440:
22
+ condition: control 50h
23
+ GSM119451:
24
+ condition: doxy 45h
25
+ GSM119439:
26
+ condition: control 45h
27
+ GSM119441:
28
+ condition: control 55h
29
+ GSM119430:
30
+ condition: control 0h
31
+ GSM119452:
32
+ condition: doxy 50h
33
+ GSM119431:
34
+ condition: control 5h
35
+ GSM119442:
36
+ condition: doxy 0h
37
+ GSM119453:
38
+ condition: doxy 55h
39
+ GSM119443:
40
+ condition: doxy 5h
41
+ GSM119432:
42
+ condition: control 10h
43
+ GSM119444:
44
+ condition: doxy 10h
45
+ GSM119433:
46
+ condition: control 15h
47
+ GSM119434:
48
+ condition: control 20h
49
+ GSM119445:
50
+ condition: doxy 15h
51
+ GSM119446:
52
+ condition: doxy 20h
53
+ GSM119435:
54
+ condition: control 25h
55
+ :platform: GPL3983
@@ -0,0 +1,492 @@
1
+ ---
2
+ :arrays:
3
+ GSM238874:
4
+ tissue: primary visual cortex
5
+ disease: "Alzheimer\xE2\x80\x99s disease"
6
+ GSM238817:
7
+ tissue: medial temporal gyrus
8
+ disease: "Alzheimer\xE2\x80\x99s disease"
9
+ GSM119639:
10
+ tissue: hippocampus
11
+ disease: control
12
+ GSM238845:
13
+ tissue: superior frontal gyrus
14
+ disease: "Alzheimer\xE2\x80\x99s disease"
15
+ GSM238846:
16
+ tissue: superior frontal gyrus
17
+ disease: "Alzheimer\xE2\x80\x99s disease"
18
+ GSM119668:
19
+ tissue: superior frontal gyrus
20
+ disease: control
21
+ GSM238818:
22
+ tissue: medial temporal gyrus
23
+ disease: "Alzheimer\xE2\x80\x99s disease"
24
+ GSM238847:
25
+ tissue: superior frontal gyrus
26
+ disease: "Alzheimer\xE2\x80\x99s disease"
27
+ GSM238790:
28
+ tissue: entorhinal cortex
29
+ disease: "Alzheimer\xE2\x80\x99s disease"
30
+ GSM119669:
31
+ tissue: superior frontal gyrus
32
+ disease: control
33
+ GSM238819:
34
+ tissue: medial temporal gyrus
35
+ disease: "Alzheimer\xE2\x80\x99s disease"
36
+ GSM238875:
37
+ tissue: primary visual cortex
38
+ disease: "Alzheimer\xE2\x80\x99s disease"
39
+ GSM238791:
40
+ tissue: entorhinal cortex
41
+ disease: "Alzheimer\xE2\x80\x99s disease"
42
+ GSM238848:
43
+ tissue: superior frontal gyrus
44
+ disease: "Alzheimer\xE2\x80\x99s disease"
45
+ GSM238763:
46
+ tissue: entorhinal cortex
47
+ disease: "Alzheimer\xE2\x80\x99s disease"
48
+ GSM119640:
49
+ tissue: hippocampus
50
+ disease: control
51
+ GSM238877:
52
+ tissue: primary visual cortex
53
+ disease: "Alzheimer\xE2\x80\x99s disease"
54
+ GSM238792:
55
+ tissue: entorhinal cortex
56
+ disease: "Alzheimer\xE2\x80\x99s disease"
57
+ GSM119641:
58
+ tissue: medial temporal gyrus
59
+ disease: control
60
+ GSM119670:
61
+ tissue: superior frontal gyrus
62
+ disease: control
63
+ GSM238793:
64
+ tissue: entorhinal cortex
65
+ disease: "Alzheimer\xE2\x80\x99s disease"
66
+ GSM119642:
67
+ tissue: medial temporal gyrus
68
+ disease: control
69
+ GSM238820:
70
+ tissue: medial temporal gyrus
71
+ disease: "Alzheimer\xE2\x80\x99s disease"
72
+ GSM238794:
73
+ tissue: entorhinal cortex
74
+ disease: "Alzheimer\xE2\x80\x99s disease"
75
+ GSM119671:
76
+ tissue: superior frontal gyrus
77
+ disease: control
78
+ GSM119643:
79
+ tissue: medial temporal gyrus
80
+ disease: control
81
+ GSM238963:
82
+ tissue: primary visual cortex
83
+ disease: "Alzheimer\xE2\x80\x99s disease"
84
+ GSM119672:
85
+ tissue: superior frontal gyrus
86
+ disease: control
87
+ GSM238821:
88
+ tissue: medial temporal gyrus
89
+ disease: "Alzheimer\xE2\x80\x99s disease"
90
+ GSM119644:
91
+ tissue: medial temporal gyrus
92
+ disease: control
93
+ GSM238795:
94
+ tissue: entorhinal cortex
95
+ disease: "Alzheimer\xE2\x80\x99s disease"
96
+ GSM119615:
97
+ tissue: entorhinal cortex
98
+ disease: control
99
+ GSM119616:
100
+ tissue: entorhinal cortex
101
+ disease: control
102
+ GSM238851:
103
+ tissue: superior frontal gyrus
104
+ disease: "Alzheimer\xE2\x80\x99s disease"
105
+ GSM119673:
106
+ tissue: superior frontal gyrus
107
+ disease: control
108
+ GSM238822:
109
+ tissue: medial temporal gyrus
110
+ disease: "Alzheimer\xE2\x80\x99s disease"
111
+ GSM119645:
112
+ tissue: medial temporal gyrus
113
+ disease: control
114
+ GSM238796:
115
+ tissue: entorhinal cortex
116
+ disease: "Alzheimer\xE2\x80\x99s disease"
117
+ GSM238797:
118
+ tissue: entorhinal cortex
119
+ disease: "Alzheimer\xE2\x80\x99s disease"
120
+ GSM119674:
121
+ tissue: superior frontal gyrus
122
+ disease: control
123
+ GSM238823:
124
+ tissue: medial temporal gyrus
125
+ disease: "Alzheimer\xE2\x80\x99s disease"
126
+ GSM119617:
127
+ tissue: entorhinal cortex
128
+ disease: control
129
+ GSM119675:
130
+ tissue: superior frontal gyrus
131
+ disease: control
132
+ GSM238824:
133
+ tissue: medial temporal gyrus
134
+ disease: "Alzheimer\xE2\x80\x99s disease"
135
+ GSM119646:
136
+ tissue: medial temporal gyrus
137
+ disease: control
138
+ GSM119618:
139
+ tissue: entorhinal cortex
140
+ disease: control
141
+ GSM119619:
142
+ tissue: entorhinal cortex
143
+ disease: control
144
+ GSM119676:
145
+ tissue: superior frontal gyrus
146
+ disease: control
147
+ GSM119647:
148
+ tissue: medial temporal gyrus
149
+ disease: control
150
+ GSM238825:
151
+ tissue: medial temporal gyrus
152
+ disease: "Alzheimer\xE2\x80\x99s disease"
153
+ GSM238798:
154
+ tissue: entorhinal cortex
155
+ disease: "Alzheimer\xE2\x80\x99s disease"
156
+ GSM238854:
157
+ tissue: superior frontal gyrus
158
+ disease: "Alzheimer\xE2\x80\x99s disease"
159
+ GSM238799:
160
+ tissue: hippocampus
161
+ disease: "Alzheimer\xE2\x80\x99s disease"
162
+ GSM119677:
163
+ tissue: primary visual cortex
164
+ disease: control
165
+ GSM238826:
166
+ tissue: posterior cingulate
167
+ disease: "Alzheimer\xE2\x80\x99s disease"
168
+ GSM119648:
169
+ tissue: medial temporal gyrus
170
+ disease: control
171
+ GSM119678:
172
+ tissue: primary visual cortex
173
+ disease: control
174
+ GSM238827:
175
+ tissue: posterior cingulate
176
+ disease: "Alzheimer\xE2\x80\x99s disease"
177
+ GSM119649:
178
+ tissue: medial temporal gyrus
179
+ disease: control
180
+ GSM238855:
181
+ tissue: superior frontal gyrus
182
+ disease: "Alzheimer\xE2\x80\x99s disease"
183
+ GSM238856:
184
+ tissue: superior frontal gyrus
185
+ disease: "Alzheimer\xE2\x80\x99s disease"
186
+ GSM119620:
187
+ tissue: entorhinal cortex
188
+ disease: control
189
+ GSM119679:
190
+ tissue: primary visual cortex
191
+ disease: control
192
+ GSM238857:
193
+ tissue: superior frontal gyrus
194
+ disease: "Alzheimer\xE2\x80\x99s disease"
195
+ GSM119621:
196
+ tissue: entorhinal cortex
197
+ disease: control
198
+ GSM119650:
199
+ tissue: medial temporal gyrus
200
+ disease: control
201
+ GSM238941:
202
+ tissue: primary visual cortex
203
+ disease: "Alzheimer\xE2\x80\x99s disease"
204
+ GSM238858:
205
+ tissue: superior frontal gyrus
206
+ disease: "Alzheimer\xE2\x80\x99s disease"
207
+ GSM119622:
208
+ tissue: entorhinal cortex
209
+ disease: control
210
+ GSM238800:
211
+ tissue: hippocampus
212
+ disease: "Alzheimer\xE2\x80\x99s disease"
213
+ GSM119651:
214
+ tissue: medial temporal gyrus
215
+ disease: control
216
+ GSM238942:
217
+ tissue: primary visual cortex
218
+ disease: "Alzheimer\xE2\x80\x99s disease"
219
+ GSM119623:
220
+ tissue: entorhinal cortex
221
+ disease: control
222
+ GSM238943:
223
+ tissue: primary visual cortex
224
+ disease: "Alzheimer\xE2\x80\x99s disease"
225
+ GSM119652:
226
+ tissue: medial temporal gyrus
227
+ disease: control
228
+ GSM238801:
229
+ tissue: hippocampus
230
+ disease: "Alzheimer\xE2\x80\x99s disease"
231
+ GSM119680:
232
+ tissue: primary visual cortex
233
+ disease: control
234
+ GSM119653:
235
+ tissue: posterior cingulate
236
+ disease: control
237
+ GSM238944:
238
+ tissue: primary visual cortex
239
+ disease: "Alzheimer\xE2\x80\x99s disease"
240
+ GSM238802:
241
+ tissue: hippocampus
242
+ disease: "Alzheimer\xE2\x80\x99s disease"
243
+ GSM119624:
244
+ tissue: entorhinal cortex
245
+ disease: control
246
+ GSM119681:
247
+ tissue: primary visual cortex
248
+ disease: control
249
+ GSM238860:
250
+ tissue: superior frontal gyrus
251
+ disease: "Alzheimer\xE2\x80\x99s disease"
252
+ GSM119654:
253
+ tissue: posterior cingulate
254
+ disease: control
255
+ GSM238945:
256
+ tissue: primary visual cortex
257
+ disease: "Alzheimer\xE2\x80\x99s disease"
258
+ GSM238803:
259
+ tissue: hippocampus
260
+ disease: "Alzheimer\xE2\x80\x99s disease"
261
+ GSM119625:
262
+ tissue: entorhinal cortex
263
+ disease: control
264
+ GSM119682:
265
+ tissue: primary visual cortex
266
+ disease: control
267
+ GSM238946:
268
+ tissue: primary visual cortex
269
+ disease: "Alzheimer\xE2\x80\x99s disease"
270
+ GSM119655:
271
+ tissue: posterior cingulate
272
+ disease: control
273
+ GSM238804:
274
+ tissue: hippocampus
275
+ disease: "Alzheimer\xE2\x80\x99s disease"
276
+ GSM119626:
277
+ tissue: entorhinal cortex
278
+ disease: control
279
+ GSM238861:
280
+ tissue: superior frontal gyrus
281
+ disease: "Alzheimer\xE2\x80\x99s disease"
282
+ GSM119683:
283
+ tissue: primary visual cortex
284
+ disease: control
285
+ GSM119627:
286
+ tissue: entorhinal cortex
287
+ disease: control
288
+ GSM119656:
289
+ tissue: posterior cingulate
290
+ disease: control
291
+ GSM238947:
292
+ tissue: primary visual cortex
293
+ disease: "Alzheimer\xE2\x80\x99s disease"
294
+ GSM238805:
295
+ tissue: hippocampus
296
+ disease: "Alzheimer\xE2\x80\x99s disease"
297
+ GSM238862:
298
+ tissue: superior frontal gyrus
299
+ disease: "Alzheimer\xE2\x80\x99s disease"
300
+ GSM119684:
301
+ tissue: primary visual cortex
302
+ disease: control
303
+ GSM238863:
304
+ tissue: superior frontal gyrus
305
+ disease: "Alzheimer\xE2\x80\x99s disease"
306
+ GSM238834:
307
+ tissue: posterior cingulate
308
+ disease: "Alzheimer\xE2\x80\x99s disease"
309
+ GSM238948:
310
+ tissue: primary visual cortex
311
+ disease: "Alzheimer\xE2\x80\x99s disease"
312
+ GSM238806:
313
+ tissue: hippocampus
314
+ disease: "Alzheimer\xE2\x80\x99s disease"
315
+ GSM119628:
316
+ tissue: hippocampus
317
+ disease: control
318
+ GSM119685:
319
+ tissue: primary visual cortex
320
+ disease: control
321
+ GSM238807:
322
+ tissue: hippocampus
323
+ disease: "Alzheimer\xE2\x80\x99s disease"
324
+ GSM119629:
325
+ tissue: hippocampus
326
+ disease: control
327
+ GSM119686:
328
+ tissue: primary visual cortex
329
+ disease: control
330
+ GSM238835:
331
+ tissue: posterior cingulate
332
+ disease: "Alzheimer\xE2\x80\x99s disease"
333
+ GSM238949:
334
+ tissue: primary visual cortex
335
+ disease: "Alzheimer\xE2\x80\x99s disease"
336
+ GSM119657:
337
+ tissue: posterior cingulate
338
+ disease: control
339
+ GSM238808:
340
+ tissue: hippocampus
341
+ disease: "Alzheimer\xE2\x80\x99s disease"
342
+ GSM238864:
343
+ tissue: superior frontal gyrus
344
+ disease: "Alzheimer\xE2\x80\x99s disease"
345
+ GSM119687:
346
+ tissue: primary visual cortex
347
+ disease: control
348
+ GSM119658:
349
+ tissue: posterior cingulate
350
+ disease: control
351
+ GSM119659:
352
+ tissue: posterior cingulate
353
+ disease: control
354
+ GSM238837:
355
+ tissue: posterior cingulate
356
+ disease: "Alzheimer\xE2\x80\x99s disease"
357
+ GSM238865:
358
+ tissue: superior frontal gyrus
359
+ disease: "Alzheimer\xE2\x80\x99s disease"
360
+ GSM119688:
361
+ tissue: primary visual cortex
362
+ disease: control
363
+ GSM238809:
364
+ tissue: medial temporal gyrus
365
+ disease: "Alzheimer\xE2\x80\x99s disease"
366
+ GSM119630:
367
+ tissue: hippocampus
368
+ disease: control
369
+ GSM238838:
370
+ tissue: posterior cingulate
371
+ disease: "Alzheimer\xE2\x80\x99s disease"
372
+ GSM238867:
373
+ tissue: superior frontal gyrus
374
+ disease: "Alzheimer\xE2\x80\x99s disease"
375
+ GSM119631:
376
+ tissue: hippocampus
377
+ disease: control
378
+ GSM238839:
379
+ tissue: posterior cingulate
380
+ disease: "Alzheimer\xE2\x80\x99s disease"
381
+ GSM238951:
382
+ tissue: primary visual cortex
383
+ disease: "Alzheimer\xE2\x80\x99s disease"
384
+ GSM119632:
385
+ tissue: hippocampus
386
+ disease: control
387
+ GSM238868:
388
+ tissue: superior frontal gyrus
389
+ disease: "Alzheimer\xE2\x80\x99s disease"
390
+ GSM119660:
391
+ tissue: posterior cingulate
392
+ disease: control
393
+ GSM119633:
394
+ tissue: hippocampus
395
+ disease: control
396
+ GSM119661:
397
+ tissue: posterior cingulate
398
+ disease: control
399
+ GSM238952:
400
+ tissue: primary visual cortex
401
+ disease: "Alzheimer\xE2\x80\x99s disease"
402
+ GSM238810:
403
+ tissue: medial temporal gyrus
404
+ disease: "Alzheimer\xE2\x80\x99s disease"
405
+ GSM238840:
406
+ tissue: posterior cingulate
407
+ disease: "Alzheimer\xE2\x80\x99s disease"
408
+ GSM238811:
409
+ tissue: medial temporal gyrus
410
+ disease: "Alzheimer\xE2\x80\x99s disease"
411
+ GSM119634:
412
+ tissue: hippocampus
413
+ disease: control
414
+ GSM238953:
415
+ tissue: primary visual cortex
416
+ disease: "Alzheimer\xE2\x80\x99s disease"
417
+ GSM119662:
418
+ tissue: posterior cingulate
419
+ disease: control
420
+ GSM238841:
421
+ tissue: posterior cingulate
422
+ disease: "Alzheimer\xE2\x80\x99s disease"
423
+ GSM119663:
424
+ tissue: posterior cingulate
425
+ disease: control
426
+ GSM238812:
427
+ tissue: medial temporal gyrus
428
+ disease: "Alzheimer\xE2\x80\x99s disease"
429
+ GSM119635:
430
+ tissue: hippocampus
431
+ disease: control
432
+ GSM238870:
433
+ tissue: superior frontal gyrus
434
+ disease: "Alzheimer\xE2\x80\x99s disease"
435
+ GSM238955:
436
+ tissue: primary visual cortex
437
+ disease: "Alzheimer\xE2\x80\x99s disease"
438
+ GSM119664:
439
+ tissue: posterior cingulate
440
+ disease: control
441
+ GSM238813:
442
+ tissue: medial temporal gyrus
443
+ disease: "Alzheimer\xE2\x80\x99s disease"
444
+ GSM238871:
445
+ tissue: superior frontal gyrus
446
+ disease: "Alzheimer\xE2\x80\x99s disease"
447
+ GSM119636:
448
+ tissue: hippocampus
449
+ disease: control
450
+ GSM238842:
451
+ tissue: superior frontal gyrus
452
+ disease: "Alzheimer\xE2\x80\x99s disease"
453
+ GSM119665:
454
+ tissue: posterior cingulate
455
+ disease: control
456
+ GSM238843:
457
+ tissue: superior frontal gyrus
458
+ disease: "Alzheimer\xE2\x80\x99s disease"
459
+ GSM238872:
460
+ tissue: primary visual cortex
461
+ disease: "Alzheimer\xE2\x80\x99s disease"
462
+ GSM119666:
463
+ tissue: superior frontal gyrus
464
+ disease: control
465
+ GSM238815:
466
+ tissue: medial temporal gyrus
467
+ disease: "Alzheimer\xE2\x80\x99s disease"
468
+ GSM119637:
469
+ tissue: hippocampus
470
+ disease: control
471
+ GSM119667:
472
+ tissue: superior frontal gyrus
473
+ disease: control
474
+ GSM238844:
475
+ tissue: superior frontal gyrus
476
+ disease: "Alzheimer\xE2\x80\x99s disease"
477
+ GSM238816:
478
+ tissue: medial temporal gyrus
479
+ disease: "Alzheimer\xE2\x80\x99s disease"
480
+ GSM119638:
481
+ tissue: hippocampus
482
+ disease: control
483
+ GSM238873:
484
+ tissue: primary visual cortex
485
+ disease: "Alzheimer\xE2\x80\x99s disease"
486
+ :description: "Information about the genes that are preferentially expressed during the course of Alzheimer\xE2\x80\x99s disease (AD) could improve our understanding of the molecular mechanisms involved in the pathogenesis of this common cause of cognitive impairment in older persons, provide new opportunities in the diagnosis, early detection, and tracking of this disorder, and provide novel targets for the discovery of interventions to treat and prevent this disorder. Information about the genes that are preferentially expressed in relationship to normal neurological aging could provide new information about the molecular mechanisms that are involved in normal age-related cognitive decline and a host of age-related neurological disorders, and they could provide novel targets for the discovery of interventions to mitigate some of these deleterious effects.\n\
487
+ Aim 1. Collect brain samples from three Alzheimer\xE2\x80\x99s Disease Centers (ADCs) for subsequent gene expression profiling. Individuals will be stratified with respect to diagnostic groups (using both clinical and neuropathological criteria), age groups, and APOE genotype. 150 individual brains will be sampled from the Arizona ADC, the Duke University ADC, and the Washington University ADC. Miniscule sample sizes (200 um of sectioned tissue) from six brain regions that are histopathologically or metabolically relevant to AD and aging will be collected, ensuring that this proposal does not deplete the national resource. Frozen and fixed samples will be sent to Phoenix, sectioned in a standardized fashion, and then returned. Aim 2. Tissue heterogeneity will be eliminated prior to expression profiling by performing laser capture microscopy on all brain regions. Aim 3. Expression profile LCM-captured cells on the Affymetrix U133 Plus 2.0 array (~55,000 transcripts), and quickly provide these data to the community at large. Aim 4. Identify pathogenic cascades related to each of the clinico-pathologic correlates using unsupervised and supervised analyses coupled with a hypothesis-driven approach. Aim 5. Validation of the expression correlates at the protein and functional levels.\n\
488
+ Scientific progress in the last few years has improved our understanding of AD and raised the hope of identifying treatments to halt the progression and prevent the onset of this disorder. For instance, researchers have begun to characterize the cascade of molecular events which lead to the major histopathological features of the disorder: neuritic plaques, which contain extra-cellular deposits of amyloid beta-peptides (Abeta); neurofibrillary tangles, which contain the hyperphosphorylated form of the intracellular, microtubule-associated protein, tau; and a loss of neurons and synapses. These molecular events provide targets for the development of promising new treatments. For example, A-beta has been postulated to trigger a cascade of events that are involved in the pathogenesis of AD. This proposal hopes to provide new information about the genes that are preferentially expressed in the development of AD histopathology, including the over-expression of APP, amyloid-induced neurotoxicity, and hyperphosphorylation of tau, as well as bring clarity to the metabolic abnormalities that seem to play a role in dementia and AD development and pathology.\n\
489
+ We will perform LCM on 6 brain regions with about 14 biological replicates per brain region. The brain regions are as follows: 1) entorhinal cortex 2) hippocampus 3) medial temporal gyrus 4) posterior cingulate 5) superior frontal gyrus and 6) primary visual cortex. We will collect layer III pyramidal cells from the white matter in each region, isolate total RNA from LCMed cell lysates, and perform double round amplification of each sample for array analysis.\n\
490
+ Keywords: other"
491
+ :title: Alzheimer's disease and the normal aged brain (steph-affy-human-433773)
492
+ :platform: GPL570