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
  321. data/install_scripts/GEO/series/GSE1927.yaml +14 -0
  322. data/install_scripts/GEO/series/GSE1941.yaml +23 -0
  323. data/install_scripts/GEO/series/GSE1942.yaml +31 -0
  324. data/install_scripts/GEO/series/GSE1944.yaml +58 -0
  325. data/install_scripts/GEO/series/GSE1975.yaml +65 -0
  326. data/install_scripts/GEO/series/GSE20.yaml +24 -0
  327. data/install_scripts/GEO/series/GSE2107.yaml +14 -0
  328. data/install_scripts/GEO/series/GSE2159.yaml +31 -0
  329. data/install_scripts/GEO/series/GSE2246.yaml +157 -0
  330. data/install_scripts/GEO/series/GSE2263.yaml +57 -0
  331. data/install_scripts/GEO/series/GSE2267.yaml +155 -0
  332. data/install_scripts/GEO/series/GSE23.yaml +58 -0
  333. data/install_scripts/GEO/series/GSE2329.yaml +43 -0
  334. data/install_scripts/GEO/series/GSE2330.yaml +55 -0
  335. data/install_scripts/GEO/series/GSE2349.yaml +19 -0
  336. data/install_scripts/GEO/series/GSE2412.yaml +58 -0
  337. data/install_scripts/GEO/series/GSE2419.yaml +27 -0
  338. data/install_scripts/GEO/series/GSE2420.yaml +29 -0
  339. data/install_scripts/GEO/series/GSE2434.yaml +37 -0
  340. data/install_scripts/GEO/series/GSE2526.yaml +23 -0
  341. data/install_scripts/GEO/series/GSE2579.yaml +19 -0
  342. data/install_scripts/GEO/series/GSE2806.yaml +11 -0
  343. data/install_scripts/GEO/series/GSE2831.yaml +35 -0
  344. data/install_scripts/GEO/series/GSE2832.yaml +17 -0
  345. data/install_scripts/GEO/series/GSE29.yaml +16 -0
  346. data/install_scripts/GEO/series/GSE3006.yaml +35 -0
  347. data/install_scripts/GEO/series/GSE3043.yaml +18 -0
  348. data/install_scripts/GEO/series/GSE3122.yaml +12 -0
  349. data/install_scripts/GEO/series/GSE3130.yaml +12 -0
  350. data/install_scripts/GEO/series/GSE3151.yaml +118 -0
  351. data/install_scripts/GEO/series/GSE3160.yaml +31 -0
  352. data/install_scripts/GEO/series/GSE3190.yaml +14 -0
  353. data/install_scripts/GEO/series/GSE3205.yaml +36 -0
  354. data/install_scripts/GEO/series/GSE3206.yaml +23 -0
  355. data/install_scripts/GEO/series/GSE3315.yaml +13 -0
  356. data/install_scripts/GEO/series/GSE3335.yaml +15 -0
  357. data/install_scripts/GEO/series/GSE34.yaml +31 -0
  358. data/install_scripts/GEO/series/GSE3470.yaml +15 -0
  359. data/install_scripts/GEO/series/GSE35.yaml +80 -0
  360. data/install_scripts/GEO/series/GSE3503.yaml +19 -0
  361. data/install_scripts/GEO/series/GSE3683.yaml +83 -0
  362. data/install_scripts/GEO/series/GSE3684.yaml +19 -0
  363. data/install_scripts/GEO/series/GSE3685.yaml +31 -0
  364. data/install_scripts/GEO/series/GSE3686.yaml +63 -0
  365. data/install_scripts/GEO/series/GSE3687.yaml +83 -0
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  370. data/install_scripts/GEO/series/GSE3813.yaml +9 -0
  371. data/install_scripts/GEO/series/GSE3814.yaml +71 -0
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  376. data/install_scripts/GEO/series/GSE3820.yaml +61 -0
  377. data/install_scripts/GEO/series/GSE3821.yaml +55 -0
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  383. data/install_scripts/GEO/series/GSE4144.yaml +9 -0
  384. data/install_scripts/GEO/series/GSE4261.yaml +59 -0
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  386. data/install_scripts/GEO/series/GSE4398.yaml +50 -0
  387. data/install_scripts/GEO/series/GSE4719.yaml +76 -0
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  390. data/install_scripts/GEO/series/GSE4807.yaml +67 -0
  391. data/install_scripts/GEO/series/GSE4826.yaml +39 -0
  392. data/install_scripts/GEO/series/GSE4934.yaml +23 -0
  393. data/install_scripts/GEO/series/GSE5027.yaml +31 -0
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  400. data/install_scripts/GEO/series/GSE5575.yaml +13 -0
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  402. data/install_scripts/GEO/series/GSE5836.yaml +37 -0
  403. data/install_scripts/GEO/series/GSE5837.yaml +37 -0
  404. data/install_scripts/GEO/series/GSE5938.yaml +187 -0
  405. data/install_scripts/GEO/series/GSE600.yaml +29 -0
  406. data/install_scripts/GEO/series/GSE6018.yaml +55 -0
  407. data/install_scripts/GEO/series/GSE6066.yaml +20 -0
  408. data/install_scripts/GEO/series/GSE6067.yaml +31 -0
  409. data/install_scripts/GEO/series/GSE6068.yaml +55 -0
  410. data/install_scripts/GEO/series/GSE6070.yaml +31 -0
  411. data/install_scripts/GEO/series/GSE6071.yaml +30 -0
  412. data/install_scripts/GEO/series/GSE6072.yaml +37 -0
  413. data/install_scripts/GEO/series/GSE6101.yaml +26 -0
  414. data/install_scripts/GEO/series/GSE6111.yaml +20 -0
  415. data/install_scripts/GEO/series/GSE6190.yaml +30 -0
  416. data/install_scripts/GEO/series/GSE6277.yaml +19 -0
  417. data/install_scripts/GEO/series/GSE6331.yaml +51 -0
  418. data/install_scripts/GEO/series/GSE6346.yaml +49 -0
  419. data/install_scripts/GEO/series/GSE6358.yaml +22 -0
  420. data/install_scripts/GEO/series/GSE6405.yaml +36 -0
  421. data/install_scripts/GEO/series/GSE6450.yaml +51 -0
  422. data/install_scripts/GEO/series/GSE6687.yaml +15 -0
  423. data/install_scripts/GEO/series/GSE6705.yaml +19 -0
  424. data/install_scripts/GEO/series/GSE6801.yaml +27 -0
  425. data/install_scripts/GEO/series/GSE6847.yaml +18 -0
  426. data/install_scripts/GEO/series/GSE6870.yaml +23 -0
  427. data/install_scripts/GEO/series/GSE7103.yaml +28 -0
  428. data/install_scripts/GEO/series/GSE7140.yaml +19 -0
  429. data/install_scripts/GEO/series/GSE7188.yaml +23 -0
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  431. data/install_scripts/GEO/series/GSE7337.yaml +19 -0
  432. data/install_scripts/GEO/series/GSE7338.yaml +19 -0
  433. data/install_scripts/GEO/series/GSE7362.yaml +123 -0
  434. data/install_scripts/GEO/series/GSE7369.yaml +15 -0
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  436. data/install_scripts/GEO/series/GSE7537.yaml +27 -0
  437. data/install_scripts/GEO/series/GSE7645.yaml +152 -0
  438. data/install_scripts/GEO/series/GSE7660.yaml +41 -0
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  440. data/install_scripts/GEO/series/GSE79.yaml +32 -0
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  442. data/install_scripts/GEO/series/GSE8088.yaml +13 -0
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  447. data/install_scripts/GEO/series/GSE8399.yaml +13 -0
  448. data/install_scripts/GEO/series/GSE850.yaml +15 -0
  449. data/install_scripts/GEO/series/GSE8506.yaml +32 -0
  450. data/install_scripts/GEO/series/GSE8542.yaml +47 -0
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  463. data/install_scripts/GEO/series/GSE8900.yaml +43 -0
  464. data/install_scripts/GEO/series/GSE8982.yaml +106 -0
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  466. data/install_scripts/GEO/series/GSE960.yaml +10 -0
  467. data/install_scripts/GEO/series/GSE961.yaml +14 -0
  468. data/install_scripts/GEO/series/GSE962.yaml +20 -0
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  470. data/install_scripts/GEO/series/GSE964.yaml +14 -0
  471. data/install_scripts/GEO/series/GSE965.yaml +14 -0
  472. data/install_scripts/GEO/series/GSE966.yaml +14 -0
  473. data/install_scripts/GEO/series/GSE993.yaml +9 -0
  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
  480. data/lib/MARQ/fdr.rb +177 -0
  481. data/lib/MARQ/main.rb +227 -0
  482. data/lib/MARQ/rankproduct.rb +146 -0
  483. data/lib/MARQ/score.rb +395 -0
  484. data/tasks/install.rake +21 -0
  485. metadata +588 -0
@@ -0,0 +1,55 @@
1
+ ---
2
+ :description: |-
3
+ Wt S. cerevisiae cells from a W303 background were exposed to multiple doses of MMS and Gamma Radiation and their global transcriptional response was measured
4
+ Keywords: dose response
5
+ :title: Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to MMS and IR
6
+ :arrays:
7
+ GSM139754:
8
+ condition: IR 1
9
+ GSM139743:
10
+ condition: MMS 0.01
11
+ GSM139755:
12
+ condition: IR 10
13
+ GSM139744:
14
+ condition: MMS 0.1
15
+ GSM139733:
16
+ condition: MMS 0
17
+ GSM139756:
18
+ condition: IR 100
19
+ GSM139745:
20
+ condition: IR 0
21
+ GSM139734:
22
+ condition: MMS 0.001
23
+ GSM139746:
24
+ condition: IR 1
25
+ GSM139735:
26
+ condition: MMS 0.01
27
+ GSM139747:
28
+ condition: IR 10
29
+ GSM139736:
30
+ condition: MMS 0.1
31
+ GSM139748:
32
+ condition: IR 100
33
+ GSM139737:
34
+ condition: MMS 0
35
+ GSM139750:
36
+ condition: IR 1
37
+ GSM139749:
38
+ condition: IR 0
39
+ GSM139738:
40
+ condition: MMS 0.001
41
+ GSM139751:
42
+ condition: IR 10
43
+ GSM139740:
44
+ condition: MMS 0.1
45
+ GSM139739:
46
+ condition: MMS 0.01
47
+ GSM139752:
48
+ condition: IR 100
49
+ GSM139741:
50
+ condition: MMS 0
51
+ GSM139753:
52
+ condition: IR 0
53
+ GSM139742:
54
+ condition: MMS 0.001
55
+ :platform: GPL4416
@@ -0,0 +1,20 @@
1
+ ---
2
+ :description: |-
3
+ Arsenic is ubiquitously present in nature and various mechanisms have evolved enabling cells to evade toxicity and acquire tolerance. Herein, we explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and sulfur metabolite profiling. Arsenite exposure affected transcription of genes encoding functions related to protein biosynthesis, arsenic detoxification, oxidative stress defense, redox maintenance and
4
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation and glutathione biosynthesis were induced at both gene and protein levels. Kinetic metabolic profiling evidenced a significant increase in the pools of sulfur metabolites as well as elevated glutathione levels. Moreover, the flux in the sulfur assimilation pathway as well as the glutathione synthesis rate strongly increased with a concomitant reduction of sulfur incorporation into proteins. By combining comparative genomics and molecular analyses, we pin-pointed transcription factors that mediate thecore of the transcriptional response to arsenite. Taken together, our data reveals that arsenite-exposed cells channel a large part of assimilated sulfur into glutathione biosynthesis and we provide evidence that the transcriptional regulators Yap1p and Met4p control this response in concert.
5
+ Keywords: stress
6
+ :arrays:
7
+ GSM140765:
8
+ treatment: As stress
9
+ GSM140767:
10
+ treatment: As stress
11
+ GSM140768:
12
+ treatment: As stress
13
+ GSM140769:
14
+ treatment: As stress
15
+ GSM140770:
16
+ treatment: As stress
17
+ GSM140762:
18
+ treatment: As stress
19
+ :title: 1.0 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour
20
+ :platform: GPL4462
@@ -0,0 +1,31 @@
1
+ ---
2
+ :description: |-
3
+ Arsenic is ubiquitously present in nature and various mechanisms have
4
+ evolved enabling cells to evade toxicity and acquire tolerance. Herein, we
5
+ explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent
6
+ arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and
7
+ sulfur metabolite profiling. Arsenite exposure affected transcription of
8
+ genes encoding functions related to protein biosynthesis, arsenic
9
+ detoxification, oxidative stress defense, redox maintenance and
10
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation
11
+ and glutathione biosynthesis were induced at both gene and protein levels.
12
+ Kinetic metabolic profiling evidenced a significant increase in the pools of
13
+ sulfur metabolites as well as elevated glutathione levels. Moreover, the
14
+ flux in the sulfur assimilation pathway as well as the glutathione synthesis
15
+ rate strongly increased with a concomitant reduction of sulfur incorporation
16
+ into proteins. By combining comparative genomics and molecular analyses, we
17
+ pin-pointed transcription factors that mediate thecore of the
18
+ transcriptional response to arsenite. Taken together, our data reveals that
19
+ arsenite-exposed cells channel a large part of assimilated sulfur into
20
+ glutathione biosynthesis and we provide evidence that the transcriptional
21
+ regulators Yap1p and Met4p control this response in concert.
22
+ Keywords: stress
23
+ :arrays:
24
+ GSM140771:
25
+ treatment: AS Stress 0.2mM
26
+ GSM140772:
27
+ treatment: AS Stress 0.2mM
28
+ GSM140773:
29
+ treatment: AS Stress 0.2mM
30
+ :title: 0.2 mM As(III) stressed wild-type vs (non-stressed) wild-type after 1 hour
31
+ :platform: GPL4462
@@ -0,0 +1,55 @@
1
+ ---
2
+ :description: |-
3
+ Arsenic is ubiquitously present in nature and various mechanisms have
4
+ evolved enabling cells to evade toxicity and acquire tolerance. Herein, we
5
+ explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent
6
+ arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and
7
+ sulfur metabolite profiling. Arsenite exposure affected transcription of
8
+ genes encoding functions related to protein biosynthesis, arsenic
9
+ detoxification, oxidative stress defense, redox maintenance and
10
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation
11
+ and glutathione biosynthesis were induced at both gene and protein levels.
12
+ Kinetic metabolic profiling evidenced a significant increase in the pools of
13
+ sulfur metabolites as well as elevated glutathione levels. Moreover, the
14
+ flux in the sulfur assimilation pathway as well as the glutathione synthesis
15
+ rate strongly increased with a concomitant reduction of sulfur incorporation
16
+ into proteins. By combining comparative genomics and molecular analyses, we
17
+ pin-pointed transcription factors that mediate thecore of the
18
+ transcriptional response to arsenite. Taken together, our data reveals that
19
+ arsenite-exposed cells channel a large part of assimilated sulfur into
20
+ glutathione biosynthesis and we provide evidence that the transcriptional
21
+ regulators Yap1p and Met4p control this response in concert.
22
+ Keywords: stress, time course
23
+ :arrays:
24
+ GSM140775:
25
+ condition: 1.0 mM As(III) stressed 15min
26
+ GSM140776:
27
+ condition: 1.0 mM As(III) stressed 15min
28
+ GSM140765:
29
+ condition: 1.0 mM As(III) stressed 1h
30
+ GSM140777:
31
+ condition: 1.0 mM As(III) stressed 30min
32
+ GSM140778:
33
+ condition: 1.0 mM As(III) stressed 30min
34
+ GSM140767:
35
+ condition: 1.0 mM As(III) stressed 1h
36
+ GSM140779:
37
+ condition: 1.0 mM As(III) stressed 30min
38
+ GSM140768:
39
+ condition: 1.0 mM As(III) stressed 1h
40
+ GSM140780:
41
+ condition: 1.0 mM As(III) stressed 18h
42
+ GSM140769:
43
+ condition: 1.0 mM As(III) stressed 1h
44
+ GSM140781:
45
+ condition: 1.0 mM As(III) stressed 18h
46
+ GSM140770:
47
+ condition: 1.0 mM As(III) stressed 1h
48
+ GSM140782:
49
+ condition: 1.0 mM As(III) stressed 18h
50
+ GSM140762:
51
+ condition: 1.0 mM As(III) stressed 1h
52
+ GSM140774:
53
+ condition: 1.0 mM As(III) stressed 15min
54
+ :title: Time Course 1.0 mM As(III)
55
+ :platform: GPL4462
@@ -0,0 +1,31 @@
1
+ ---
2
+ :title: 0.2 mM As(III) stressed yap1 deletion mutant vs 0.2 mM As(III) stressed wild-type after 1 hour
3
+ :platform: GPL4462
4
+ :arrays:
5
+ GSM140783:
6
+ condition: 0.2 mM As(III) stressed YAP1
7
+ GSM140784:
8
+ condition: 0.2 mM As(III) stressed YAP1
9
+ GSM140785:
10
+ condition: 0.2 mM As(III) stressed YAP1
11
+ :description: |-
12
+ Arsenic is ubiquitously present in nature and various mechanisms have
13
+ evolved enabling cells to evade toxicity and acquire tolerance. Herein, we
14
+ explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent
15
+ arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and
16
+ sulfur metabolite profiling. Arsenite exposure affected transcription of
17
+ genes encoding functions related to protein biosynthesis, arsenic
18
+ detoxification, oxidative stress defense, redox maintenance and
19
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation
20
+ and glutathione biosynthesis were induced at both gene and protein levels.
21
+ Kinetic metabolic profiling evidenced a significant increase in the pools of
22
+ sulfur metabolites as well as elevated glutathione levels. Moreover, the
23
+ flux in the sulfur assimilation pathway as well as the glutathione synthesis
24
+ rate strongly increased with a concomitant reduction of sulfur incorporation
25
+ into proteins. By combining comparative genomics and molecular analyses, we
26
+ pin-pointed transcription factors that mediate thecore of the
27
+ transcriptional response to arsenite. Taken together, our data reveals that
28
+ arsenite-exposed cells channel a large part of assimilated sulfur into
29
+ glutathione biosynthesis and we provide evidence that the transcriptional
30
+ regulators Yap1p and Met4p control this response in concert.
31
+ Keywords: stress
@@ -0,0 +1,30 @@
1
+ ---
2
+ :title: 1.0 mM As(III) stressed yap1 deletion mutant vs 1.0 mM As(III) stressed wild-type after 1 hour
3
+ :platform: GPL4462
4
+ :arrays:
5
+ GSM140787:
6
+ condition: 1.0 mM As(III) stressed YAP1
7
+ GSM140788:
8
+ condition: 1.0 mM As(III) stressed YAP1
9
+ GSM140789:
10
+ condition: 1.0 mM As(III) stressed YAP1
11
+ :description: |-
12
+ volved enabling cells to evade toxicity and acquire tolerance. Herein, we
13
+ explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent
14
+ arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and
15
+ sulfur metabolite profiling. Arsenite exposure affected transcription of
16
+ genes encoding functions related to protein biosynthesis, arsenic
17
+ detoxification, oxidative stress defense, redox maintenance and
18
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation
19
+ and glutathione biosynthesis were induced at both gene and protein levels.
20
+ Kinetic metabolic profiling evidenced a significant increase in the pools of
21
+ sulfur metabolites as well as elevated glutathione levels. Moreover, the
22
+ flux in the sulfur assimilation pathway as well as the glutathione synthesis
23
+ rate strongly increased with a concomitant reduction of sulfur incorporation
24
+ into proteins. By combining comparative genomics and molecular analyses, we
25
+ pin-pointed transcription factors that mediate thecore of the
26
+ transcriptional response to arsenite. Taken together, our data reveals that
27
+ arsenite-exposed cells channel a large part of assimilated sulfur into
28
+ glutathione biosynthesis and we provide evidence that the transcriptional
29
+ regulators Yap1p and Met4p control this response in concert.
30
+ Keywords: stress
@@ -0,0 +1,37 @@
1
+ ---
2
+ :title: 0.2 mM As(III) stressed met4 deletion mutant vs 0.2 mM As(III) stressed wild-type after 1 hour
3
+ :platform: GPL4462
4
+ :arrays:
5
+ GSM140790:
6
+ condition: 0.2 mM As(III) stressed MET4
7
+ GSM140791:
8
+ condition: 0.2 mM As(III) stressed MET4
9
+ GSM140793:
10
+ condition: 0.2 mM As(III) stressed MET4
11
+ GSM140794:
12
+ condition: 0.2 mM As(III) stressed MET4
13
+ GSM140795:
14
+ condition: 0.2 mM As(III) stressed MET4
15
+ GSM140796:
16
+ condition: 0.2 mM As(III) stressed MET4
17
+ :description: |-
18
+ Arsenic is ubiquitously present in nature and various mechanisms have
19
+ evolved enabling cells to evade toxicity and acquire tolerance. Herein, we
20
+ explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent
21
+ arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and
22
+ sulfur metabolite profiling. Arsenite exposure affected transcription of
23
+ genes encoding functions related to protein biosynthesis, arsenic
24
+ detoxification, oxidative stress defense, redox maintenance and
25
+ proteolytic activity. Importantly, enzymes involved in sulfate assimilation
26
+ and glutathione biosynthesis were induced at both gene and protein levels.
27
+ Kinetic metabolic profiling evidenced a significant increase in the pools of
28
+ sulfur metabolites as well as elevated glutathione levels. Moreover, the
29
+ flux in the sulfur assimilation pathway as well as the glutathione synthesis
30
+ rate strongly increased with a concomitant reduction of sulfur incorporation
31
+ into proteins. By combining comparative genomics and molecular analyses, we
32
+ pin-pointed transcription factors that mediate thecore of the
33
+ transcriptional response to arsenite. Taken together, our data reveals that
34
+ arsenite-exposed cells channel a large part of assimilated sulfur into
35
+ glutathione biosynthesis and we provide evidence that the transcriptional
36
+ regulators Yap1p and Met4p control this response in concert.
37
+ Keywords: stress
@@ -0,0 +1,26 @@
1
+ ---
2
+ :title: 300 ppm Citrinin treatment for 2 h (GPL4399)
3
+ :platform: GPL4399
4
+ :arrays:
5
+ GSM141466:
6
+ condition: citrinin treated for 2 h
7
+ GSM141455:
8
+ condition: citrinin treated for 2 h
9
+ GSM141467:
10
+ condition: citrinin treated for 2 h
11
+ GSM141456:
12
+ condition: citrinin treated for 2 h
13
+ GSM141468:
14
+ condition: citrinin treated for 2 h
15
+ GSM141457:
16
+ condition: citrinin treated for 2 h
17
+ GSM141469:
18
+ condition: citrinin treated for 2 h
19
+ GSM141470:
20
+ condition: citrinin treated for 2 h
21
+ GSM141471:
22
+ condition: citrinin treated for 2 h
23
+ :description: |-
24
+ The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited.
25
+ We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells.
26
+ Keywords: stress response
@@ -0,0 +1,20 @@
1
+ ---
2
+ :title: 300 ppm Citrinin treatment for 2 h (GPL1945)
3
+ :platform: GPL1945
4
+ :arrays:
5
+ GSM142075:
6
+ condition: citrinin treated for 2 h
7
+ GSM142076:
8
+ condition: citrinin treated for 2 h
9
+ GSM142077:
10
+ condition: citrinin treated for 2 h
11
+ GSM142078:
12
+ condition: citrinin treated for 2 h
13
+ GSM141513:
14
+ condition: citrinin treated for 2 h
15
+ GSM142080:
16
+ condition: citrinin treated for 2 h
17
+ :description: |-
18
+ The availability of yeast DNA microarrays provides the possibility of monitoring gene expression levels as a function to toxin exposure, and consequently as a means of determining mechanisms of toxicity. This system possesses the benefit of the essential volume of yeast cultures, the high reproducibility of expression profiles, and the massive functional information. Because small amount of biological sample cultures are required for this analysis, toxicity test for rare chemical such as mycotoxins which is a natural compound and difficult to be artificially synthesized. Citrinin [518-75-2], 4,6-dihydro-8-hydroxy-3,4,5-trimethyl-6-oxo-3H-2-benzopyran-7-crboxylic acid, is the one of the popular mycotoxicin produced by Penicillium and Aspergillus family possibly spread all over the world. This natural chemicals is one of the well characterized mycotoxin but the information especially mechanism of toxic action is limited.
19
+ We used two types of microarrays, one have ORF (Open reading Frame) fragment on the surface of the glass as probes and the other have probes as oligonucleotide probes on the microarray with 3 dimensions. We compared data properties and studied the toxicity of citrinin to yeast cells.
20
+ Keywords: stress response
@@ -0,0 +1,30 @@
1
+ ---
2
+ :arrays:
3
+ GSM143076:
4
+ condition: 12C Chemostat anaerobic C-lim 0.03h
5
+ GSM143088:
6
+ condition: 30C anaerobic N-lim chemostat 0.03h
7
+ GSM143077:
8
+ condition: 30C Anaerobic C-lim chemostat 0.03h
9
+ GSM143089:
10
+ condition: 30C anaerobic N-lim chemostat 0.03h
11
+ GSM143079:
12
+ condition: 30C Anaerobic C-lim chemostat 0.03h
13
+ GSM143081:
14
+ condition: 30C Anaerobic C-lim chemostat 0.03h
15
+ GSM143082:
16
+ condition: 12C anaerobic N-lim chemostat 0.03h
17
+ GSM143071:
18
+ condition: 12C Chemostat anaerobic C-lim 0.03h
19
+ GSM143083:
20
+ condition: 12C anaerobic N-lim chemostat 0.03h
21
+ GSM143084:
22
+ condition: 12C anaerobic N-lim chemostat 0.03h
23
+ GSM143073:
24
+ condition: 12C Chemostat anaerobic C-lim 0.03h
25
+ GSM143085:
26
+ condition: 30C anaerobic N-lim chemostat 0.03h
27
+ :description: "The global transcriptional response of Saccharomyces cerevisiae was investigated in low temperature chemostat cultures grown in carbon or nitrogen limitation. During steady state chemostats, the growth rates and in vivo fluxes were kept constant however the growth-limiting nutrient was significantly higher at 12oC than at 30oC and had significant effects on transcriptional responses. Growth at 12oC resulted in a rearrangement of transporters for the limiting nutrient, where hexose transporters (HXTs) and ammonium permeases (MEPs) were differentially expressed in cultures grown at 30oC in carbon and nitrogen limitations, respectively. In addition, we found repression of genes encoding proteins in reserve carbohydrates metabolism and metabolism of alternative carbon or nitrogen sources other than glucose or ammonia. However, there were also similar responses when the transcriptional response was evaluated regardless of the growth-limiting nutrient. In particular, induction of ribosome biogenesis genes emphasizes the significance of transcription and translational adaptation at low temperature. In contrast, genes encoding proteins during stress response were downregulated. This down-regulation of stress elements better known as environmental stress response (ESR) is in contradiction with previous low temperature transcriptome analyses. During continuous steady state low temperature cultivation, ESR no longer plays an integral role in S. cerevisiae\xE2\x80\x99s response to temperature change. Similarly, trehalose accumulation, consistent with its gene expression, was not indispensable for growth at 12oC. This response, however, does not exclude that ESR may be required for transition phase in low temperature growth when cells are transferred from one temperature to another.\n\
28
+ Keywords: chemostat temperature 12 degree celsuis 30 degree celsius"
29
+ :title: Temperature-dependent transcriptional response under anaerobic C and N limitations in Yeast
30
+ :platform: GPL90
@@ -0,0 +1,19 @@
1
+ ---
2
+ :arrays:
3
+ GSM144220:
4
+ condition: CEN.PK113-7D/pYX212 chemostat at Dcrit
5
+ GSM144221:
6
+ condition: CEN.PK113-7D/pYX212 chemostat at Dcrit
7
+ GSM144222:
8
+ condition: CEN.PK113-7D/pYX212-NOX chemostat at Dcrit
9
+ GSM144223:
10
+ condition: CEN.PK113-7D/pYX212-NOX chemostat at Dcrit
11
+ GSM144224:
12
+ condition: CEN.PK113-7D/pYX212-AOX chemostat at Dcrit
13
+ GSM144225:
14
+ condition: CEN.PK113-7D/pYX212-AOX chemostat at Dcrit
15
+ :description: |-
16
+ When the yeast Saccharomyces cerevisiae is subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from being purely respiratory to mixed respiratory and fermentative. This shift is characterized by ethanol production, a phenomenon known as the Crabtree effect due to its analogy with lactate overflow in cancer cells. It is well known that at high glycolytic fluxes there is glucose repression of respiratory pathways resulting in a decrease in the respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect (or overflow metabolism) is due to a limited respiratory capacity or caused by glucose-mediated repression of respiration. We addressed this issue by increasing respiration in S. cerevisiae by introducing a heterologous alternative oxidase, and observed reduced aerobic ethanol formation. In contrast, increasing non-respiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, while NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, while alternative oxidase is directed to the mitochondria. The onset of aerobic ethanol formation is demonstrated to be a consequence of an imbalance in mitochondrial redox balancing. In addition to answering fundamental physiological questions, our findings are relevant for all biomass derived applications of S. cerevisiae.
17
+ Keywords: Genetic Modification
18
+ :title: Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae
19
+ :platform: GPL2529
@@ -0,0 +1,51 @@
1
+ ---
2
+ :arrays:
3
+ GSM146328:
4
+ mutant: H39h
5
+ GSM146317:
6
+ mutant: wt0h
7
+ GSM146306:
8
+ mutant: H3
9
+ GSM146329:
10
+ mutant: H39h
11
+ GSM146318:
12
+ mutant: H30h
13
+ GSM146320:
14
+ mutant: wt6h
15
+ GSM146319:
16
+ mutant: H30h
17
+ GSM146321:
18
+ mutant: wt6h
19
+ GSM146322:
20
+ mutant: wt6h
21
+ GSM146323:
22
+ mutant: H36h
23
+ GSM146301:
24
+ mutant: wt
25
+ GSM146324:
26
+ mutant: H36h
27
+ GSM146302:
28
+ mutant: wt
29
+ GSM146325:
30
+ mutant: H36h
31
+ GSM146303:
32
+ mutant: wt
33
+ GSM146326:
34
+ mutant: wt9h
35
+ GSM146304:
36
+ mutant: H3
37
+ GSM146327:
38
+ mutant: wt9h
39
+ GSM146316:
40
+ mutant: wt0h
41
+ GSM146305:
42
+ mutant: H3
43
+ :description: |-
44
+ This SuperSeries is composed of the following subset Series:
45
+ GSE6319: Histone H3 K4,79R
46
+ GSE6326: Histone H3 K4,36,79R 0 hr
47
+ GSE6327: Histone H3 K4,36,79R 6 hr
48
+ GSE6328: Histone H3 K4,36,79R 9 hr
49
+ Keywords: SuperSeries
50
+ :title: Histone H3,K4,79R and H3,K4,36,79R (at 0, 6, and 9 hours) Mutations
51
+ :platform: GPL90
@@ -0,0 +1,49 @@
1
+ ---
2
+ :arrays:
3
+ GSM146692:
4
+ treatment: none
5
+ stimulation: Polyl C
6
+ GSM146693:
7
+ treatment: none
8
+ stimulation: Polyl C
9
+ GSM146682:
10
+ treatment: none
11
+ stimulation: LPS
12
+ GSM146694:
13
+ treatment: GW3965
14
+ stimulation: Polyl C
15
+ GSM146695:
16
+ treatment: GW3965
17
+ stimulation: Polyl C
18
+ GSM146684:
19
+ treatment: none
20
+ stimulation: LPS
21
+ GSM146696:
22
+ treatment: GW7845
23
+ stimulation: Polyl C
24
+ GSM146697:
25
+ treatment: GW7845
26
+ stimulation: Polyl C
27
+ GSM146686:
28
+ treatment: GW3965
29
+ stimulation: LPS
30
+ GSM146687:
31
+ treatment: GW3965
32
+ stimulation: LPS
33
+ GSM146688:
34
+ treatment: GW7845
35
+ stimulation: LPS
36
+ GSM146690:
37
+ treatment: none
38
+ stimulation: none
39
+ GSM146689:
40
+ treatment: GW7845
41
+ stimulation: LPS
42
+ GSM146691:
43
+ treatment: none
44
+ stimulation: none
45
+ :description: "Transrepression mediated by PPARg and LXRs agonists (GW7845 and GW3965) in primary macrophages stimulated with LPS or poly I:C. Thioglycollate-elicited macrophages were isolated from mice by peritoneal lavage 3 days following peritoneal injection of 2.5 ml 3% thioglycollate (DIFCO). Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after 5 h the medium was removed and cells were fed with fresh medium containing 0.5% fetal bovine serum. Cells were treated with LPS (Sigma) a concentration of 100 ng/ml or poly I:C (100 ng/ml) in the absence or presence of receptor-specific agonists for PPAR\xCE\xB3 (GW7845) or LXR (GW3965) at 1 \xC2\xB5M concentrations. Results suggest signal-dependent nuclear receptors transrepression pathways.\n\
46
+ Reference: Molecular Determinants of Crosstalk between Nuclear Receptors and Toll-like Receptors Mediating Counter-regulation of Inflammatory Responses. Sumito Ogawa, Jean Lozach, Chris Benner, Gabriel Pascual, Rajendra K. Tangirala, Stefan Westin, Alexander Hoffmann, Shankar Subramaniam, Michael David, Michael G. Rosenfeld, and Christopher K. Glass. Cell, Vol 122, 707-721, 9 September 2005.\n\
47
+ Keywords: PPARg and LXRs agonists"
48
+ :title: Differential repression of TLR responses by PPARg and LXRs
49
+ :platform: GPL1310