MARQ 0.0.1

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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 +29 -0
  6. data/bin/marq_config +170 -0
  7. data/install_scripts/CustomDS/Rakefile +223 -0
  8. data/install_scripts/GEO/Rakefile +258 -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
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  270. data/install_scripts/GEO/series/GSE10521.yaml +56 -0
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  272. data/install_scripts/GEO/series/GSE1073.yaml +127 -0
  273. data/install_scripts/GEO/series/GSE10860.yaml +25 -0
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  300. data/install_scripts/GEO/series/GSE12104.yaml +10 -0
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  302. data/install_scripts/GEO/series/GSE12150.yaml +32 -0
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  305. data/install_scripts/GEO/series/GSE1365.yaml +14 -0
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  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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@@ -0,0 +1,16 @@
1
+ ---
2
+ :title: Adaptive evolution in yeast
3
+ :description: |-
4
+ A Saccharomyces cerevisiae population was cultured for many generations under conditions to which it is not optimally adapted. These experiments were designed to investigate adaptive evolution under natural selection.
5
+ This study is described in more detail in Ferea TL, et al. 1999. Proc Natl Acad Sci USA 96:9721-6
6
+ Keywords: other
7
+ :arrays:
8
+ GSM1093:
9
+ treatment: Control
10
+ GSM1094:
11
+ treatment: Parent vs Evolved
12
+ GSM904:
13
+ treatment: Parent vs Evolved
14
+ GSM905:
15
+ treatment: Parent vs Evolved
16
+ :platform: GPL58
@@ -0,0 +1,35 @@
1
+ ---
2
+ :title: Genome-wide transcriptional dependencies on TAF1 functional domains
3
+ :description: |-
4
+ TFIID plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TAF subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse. Yeast (Saccharomyces cerevisiae) TAF1 reportedly possesses at least four distinct activities including a histone acetyltransferase, and TBP, TAF, and promoter binding. Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability. To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature sensitive taf1ts2 yeast strain. After galactose-induction and temperature inactivation of the temperature-sensitive allele, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription. Virtually all TAF1-dependent genes, which comprise ~90% of the yeast genome, displayed a strong dependency upon all regions of TAF1 that were tested. This might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or that all TAF1-dependent genes require the many activities of TAF1. Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes.
5
+ Keywords: genetic modification
6
+ :arrays:
7
+ GSM65312:
8
+ condition: HT4
9
+ GSM65313:
10
+ condition: PB1
11
+ GSM65302:
12
+ condition: FHT-WT1
13
+ GSM65314:
14
+ condition: "null"
15
+ GSM65303:
16
+ condition: DT1
17
+ GSM65315:
18
+ condition: homotypic
19
+ GSM65304:
20
+ condition: TF1
21
+ GSM65305:
22
+ condition: HT4
23
+ GSM65306:
24
+ condition: PB1
25
+ GSM65307:
26
+ condition: "null"
27
+ GSM65308:
28
+ condition: homotypic
29
+ GSM65309:
30
+ condition: FHT-WT1
31
+ GSM65310:
32
+ condition: DT1
33
+ GSM65311:
34
+ condition: TF1
35
+ :platform: GPL1220
@@ -0,0 +1,18 @@
1
+ ---
2
+ :title: "Functional Genomic Analysis of Commercial Baker\xE2\x80\x99s Yeast during Initial Stages of Model Dough-Fermentation"
3
+ :description: "Gene expression profiles of baker\xE2\x80\x99s yeast during initial dough-fermentation were investigated using liquid fermentation media to obtain insights at the molecular level into rapid adaptation mechanisms of baker\xE2\x80\x99s yeast. Results showed that onset of fermentation caused drastic changes in gene expression profiles within 15 min. Genes involved in the tricarboxylic acid (TCA) cycle were down-regulated and genes involved in glycolysis were up-regulated, indicating a metabolic shift from respiration to fermentation. Genes involved in ethanol production (PDC genes and ADH1), in glycerol synthesis (GPD1 and HOR2), and in low-affinity hexose transporters (HXT1 and HXT3) were up-regulated at the beginning of model dough-fermentation. Among genes up-regulated at 15 min, several genes classified as transcription were down-regulated within 30 min. These down-regulated genes are involved in messenger RNA splicing and ribosomal protein biogenesis, in zinc finger transcription factor proteins, and in transcriptional regulator (SRB8, MIG1). In contrast, genes involved in amino acid metabolism and in vitamin metabolism, such as arginine biosynthesis, riboflavin biosynthesis, and thiamin biosynthesis, were subsequently up-regulated after 30 min. Interestingly, the genes involved in the unfolded protein response (UPR) pathway were also subsequently up-regulated. Our study presents the first overall description of the transcriptional response of baker\xE2\x80\x99s yeast during dough-fermentation, and will thus help clarify genomic responses to various stresses during commercial fermentation processes.\n\
4
+ Keywords: fermentation"
5
+ :arrays:
6
+ GSM66920:
7
+ treatment: fermentation 15 min
8
+ GSM66919:
9
+ treatment: before fermentation
10
+ GSM66921:
11
+ treatment: fermentation 15 min
12
+ GSM66922:
13
+ treatment: fermentation 30 min
14
+ GSM66923:
15
+ treatment: fermentation 60 min
16
+ GSM65640:
17
+ treatment: before fermentation
18
+ :platform: GPL90
@@ -0,0 +1,12 @@
1
+ ---
2
+ :title: Aft2 in yeast iron regulation
3
+ :description: |-
4
+ Iron homeostasis in the yeast Saccharomyces cerevisiae is regulated at the transcriptional level by Aft1p, which activates the expression of its target genes in response to low-iron conditions. The yeast genome contains a paralog of AFT1, which has been designated AFT2. To establish whether AFT1 and AFT2 have overlapping functions, a mutant containing a double aft1aft2 deletion was generated. Growth assays established that the single aft2 strain exhibited no iron-dependent phenotype. However, the double-mutant aft1aft2 strain was more sensitive to low-iron growth conditions than the single-mutant aft1 strain. A mutant allele of AFT2 (AFT2-1up), or overexpression of the wild-type AFT2 gene, led to partial complementation of the respiratory- deficient phenotype of the aft1 strain. The AFT2-1up allele also increased the uptake of 59Fe in an aft1 strain. DNA microarrays were used to identify genes regulated by AFT2. Some of the AFT2-regulated genes are known to be regulated by Aft1p; however, AFT2-1up-dependent activation was independent of Aft1p. The kinetics of induction of two genes activated by the AFT2-1up allele are consistent with Aft2p acting as a direct transcriptional factor. Truncated forms of Aft1p and Aft2p bound to a DNA duplex containing the Aft1p binding site in vitro. The wild-type allele of AFT2 activated transcription in response to growth under low-iron conditions. Together, these data suggest that yeast has a second regulatory pathway for the iron regulon, with AFT1 and AFT2 playing partially redundant roles.
5
+ Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
6
+ Keywords: Logical Set
7
+ :arrays:
8
+ GSM69766:
9
+ condition: AFT2 vector
10
+ GSM69767:
11
+ condition: AFT2 mutant vector
12
+ :platform: GPL2668
@@ -0,0 +1,12 @@
1
+ ---
2
+ :title: Unfolded Protein Response
3
+ :arrays:
4
+ GSM69854:
5
+ condition: Kb vs. Ctrl
6
+ GSM69855:
7
+ condition: Tunicamycin vs. Ctrl
8
+ :description: |-
9
+ To dissect the requirements of membrane protein degradation from the ER, we expressed the mouse major histocompatibility complex class I heavy chain H-2K(b) in yeast. Like other proteins degraded from the ER, unassembled H-2K(b) heavy chains are not transported to the Golgi but are degraded in a proteasome-dependent manner. The overexpression of H-2K(b) heavy chains induces the unfolded protein response (UPR). In yeast mutants unable to mount the UPR, H-2K(b) heavy chains are greatly stabilized. This defect in degradation is suppressed by the expression of the active form of Hac1p, the transcription factor that upregulates UPR-induced genes. These results indicate that induction of the UPR is required for the degradation of protein substrates from the ER.
10
+ Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
11
+ Keywords: Logical Set
12
+ :platform: GPL2650
@@ -0,0 +1,118 @@
1
+ ---
2
+ :arrays:
3
+ GSM70645:
4
+ knockdown: RAS
5
+ GSM70634:
6
+ knockdown: E2F3
7
+ GSM70623:
8
+ knockdown: Src
9
+ GSM70612:
10
+ knockdown: Myc
11
+ GSM70601:
12
+ knockdown: GFP
13
+ GSM70646:
14
+ knockdown: RAS
15
+ GSM70635:
16
+ knockdown: E2F3
17
+ GSM70624:
18
+ knockdown: Bcat
19
+ GSM70613:
20
+ knockdown: Myc
21
+ GSM70602:
22
+ knockdown: GFP
23
+ GSM70647:
24
+ knockdown: RAS
25
+ GSM70636:
26
+ knockdown: E2F3
27
+ GSM70625:
28
+ knockdown: Bcat
29
+ GSM70614:
30
+ knockdown: Myc
31
+ GSM70603:
32
+ knockdown: GFP
33
+ GSM70648:
34
+ knockdown: RAS
35
+ GSM70637:
36
+ knockdown: E2F3
37
+ GSM70626:
38
+ knockdown: Bcat
39
+ GSM70615:
40
+ knockdown: Myc
41
+ GSM70604:
42
+ knockdown: GFP
43
+ GSM70650:
44
+ knockdown: RAS
45
+ GSM70649:
46
+ knockdown: RAS
47
+ GSM70638:
48
+ knockdown: E2F3
49
+ GSM70627:
50
+ knockdown: Bcat
51
+ GSM70616:
52
+ knockdown: Myc
53
+ GSM70605:
54
+ knockdown: GFP
55
+ GSM70651:
56
+ knockdown: RAS
57
+ GSM70640:
58
+ knockdown: E2F3
59
+ GSM70639:
60
+ knockdown: E2F3
61
+ GSM70628:
62
+ knockdown: Bcat
63
+ GSM70617:
64
+ knockdown: Src
65
+ GSM70606:
66
+ knockdown: GFP
67
+ GSM70641:
68
+ knockdown: E2F3
69
+ GSM70630:
70
+ knockdown: Bcat
71
+ GSM70629:
72
+ knockdown: Bcat
73
+ GSM70618:
74
+ knockdown: Src
75
+ GSM70607:
76
+ knockdown: Myc
77
+ GSM70597:
78
+ knockdown: GFP
79
+ GSM70642:
80
+ knockdown: RAS
81
+ GSM70631:
82
+ knockdown: Bcat
83
+ GSM70620:
84
+ knockdown: Src
85
+ GSM70619:
86
+ knockdown: Src
87
+ GSM70608:
88
+ knockdown: Myc
89
+ GSM70598:
90
+ knockdown: GFP
91
+ GSM70643:
92
+ knockdown: RAS
93
+ GSM70632:
94
+ knockdown: Bcat
95
+ GSM70621:
96
+ knockdown: Src
97
+ GSM70610:
98
+ knockdown: Myc
99
+ GSM70609:
100
+ knockdown: Myc
101
+ GSM70599:
102
+ knockdown: GFP
103
+ GSM70644:
104
+ knockdown: RAS
105
+ GSM70633:
106
+ knockdown: E2F3
107
+ GSM70622:
108
+ knockdown: Src
109
+ GSM70611:
110
+ knockdown: Myc
111
+ GSM70600:
112
+ knockdown: GFP
113
+ :description: |-
114
+ Signatures of Oncogenic Pathway Deregulation in Human Cancers
115
+ The ability to define cancer subtypes, recurrence of disease, and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies. Such data is also of substantial importance to the analysis of cellular signaling pathways central to the oncogenic process. With this focus, we have developed a series of gene expression signatures that reliably reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumors, and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumor sub-types. Clustering tumors based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Furthermore, predictions of pathway deregulation in cancer cell lines are shown to coincide with sensitivity to therapeutic agents that target components of the pathway, underscoring the potential for such pathway prediction to guide the use of targeted therapeutics.
116
+ Keywords: other
117
+ :title: Oncogene Signature Dataset
118
+ :platform: GPL570
@@ -0,0 +1,31 @@
1
+ ---
2
+ :title: Exploring the scope of TOR/PKA co-regulation in MDN
3
+ :arrays:
4
+ GSM70809:
5
+ condition: TPK versus tpk1-3 deletion MDN
6
+ GSM70747:
7
+ condition: BCY1 Rapamycin MDN versus bcy1 deletion Rapamycin MDN
8
+ GSM70749:
9
+ condition: TPK MDN -/ Rapamycin
10
+ GSM70752:
11
+ condition: tpk1-3 deletion MDN -/ Rapamycin
12
+ GSM70753:
13
+ condition: TPK versus tpk1-3 deletion MDN
14
+ GSM70742:
15
+ condition: BCY1 MDN -/ Rapamycin
16
+ GSM70806:
17
+ condition: BCY1 MDN -/ Rapamycin
18
+ GSM70807:
19
+ condition: BCY1 versus bcy1 deletion MDN
20
+ GSM70755:
21
+ condition: TPK verus tpk1-3 deletion MDN -/ Rapamycin
22
+ GSM70744:
23
+ condition: bcy1 deletion MDN -/ Rapamycin
24
+ GSM70808:
25
+ condition: TPK MDN -/ Rapamycin
26
+ GSM70745:
27
+ condition: BCY1 versus bcy1 deletion MDN
28
+ :description: |-
29
+ To identify genes co-regulated by TOR and PKA during growth in MDN
30
+ Keywords: Media, Wild type and mutant strains, and dose response
31
+ :platform: GPL2763
@@ -0,0 +1,14 @@
1
+ ---
2
+ :title: Response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.
3
+ :arrays:
4
+ GSM71741:
5
+ condition: Y10 mRNP vs. Poly
6
+ GSM71742:
7
+ condition: G0 mRNP vs. Poly
8
+ GSM71743:
9
+ condition: Y5 mRNP vs. Poly
10
+ :description: |-
11
+ The global gene expression program that accompanies the adaptation of Saccharomyces cerevisiae to an abrupt transfer from a fermentable to a nonfermentable carbon source was characterized by using a cDNA microarray to monitor the relative abundances and polysomal distributions of mRNAs. Features of the program included a transient reduction in global translational activity and a severe decrease in polysome size of transcripts encoding ribosomal proteins.
12
+ A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
13
+ Keywords: replicate_design
14
+ :platform: GPL53
@@ -0,0 +1,36 @@
1
+ ---
2
+ :title: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1
3
+ :arrays:
4
+ GSM72035:
5
+ condition: 03II01 batch p12
6
+ GSM72036:
7
+ condition: 03II01 batch p4
8
+ GSM72025:
9
+ condition: Low-D chemostat vs. High-D chemostat
10
+ GSM72037:
11
+ condition: 03II01 batch p5
12
+ GSM72026:
13
+ condition: 03II01 batch p6
14
+ GSM72027:
15
+ condition: 03II01 batch p7
16
+ GSM72028:
17
+ condition: 03II01 batch p8
18
+ GSM72029:
19
+ condition: 03II01 batch p9
20
+ GSM72030:
21
+ condition: 03II01 batch p1
22
+ GSM72031:
23
+ condition: 03II01 batch p10
24
+ GSM72032:
25
+ condition: 03II01 batch p2
26
+ GSM72033:
27
+ condition: 03II01 batch p11
28
+ GSM72034:
29
+ condition: 03II01 batch p3
30
+ :description: |-
31
+ Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours.
32
+ Groups of assays that are related as part of a time series.
33
+ FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time
34
+ FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition
35
+ Keywords: time_series_design
36
+ :platform: GPL2638
@@ -0,0 +1,23 @@
1
+ ---
2
+ :title: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2
3
+ :arrays:
4
+ GSM72038:
5
+ condition: batch 02X25 10.5h
6
+ GSM72039:
7
+ condition: batch 02X25 6h
8
+ GSM72040:
9
+ condition: batch 02X25 8h
10
+ GSM72041:
11
+ condition: batch 02X25 9h
12
+ GSM72042:
13
+ condition: batch 02X25 11h
14
+ GSM72043:
15
+ condition: batch 02X25 9.5h
16
+ GSM72044:
17
+ condition: batch 02X25 10h
18
+ :description: |-
19
+ Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) samples were grown in batch for the indicated time.
20
+ Groups of assays that are related as part of a time series.
21
+ FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 6 h; name: 34357_Elapsed Time; Measurement: time(absolute) 10.5 h; name: 34365_Elapsed Time; Measurement: time(absolute) 8 h; name: 34358_Elapsed Time; Measurement: time(absolute) 9 h; name: 34359_Elapsed Time; Measurement: time(absolute) 11 h; name: 34368_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 34360_Elapsed Time; Measurement: time(absolute) 10 h; name: 34362_Elapsed Time
22
+ Keywords: time_series_design
23
+ :platform: GPL2638
@@ -0,0 +1,13 @@
1
+ ---
2
+ :title: ssa1/2 deletion mutant
3
+ :description: |-
4
+ Yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain.
5
+ Keywords: Stress response
6
+ :arrays:
7
+ GSM74505:
8
+ condition: ssa1/2 deletion mutant
9
+ GSM74506:
10
+ condition: ssa1/2 deletion mutant
11
+ GSM74507:
12
+ condition: ssa1/2 deletion mutant
13
+ :platform: GPL2674
@@ -0,0 +1,15 @@
1
+ ---
2
+ :title: Saccharomyces cerevisiae Sko1-HA strain MAP37, W303-1A background
3
+ :description: |-
4
+ These three replicates were analyzed in "Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae.
5
+ ", by Proft M, Gibbons FD, Copeland M, Roth FP, Struhl K; published in Eukaryot Cell. 2005 Aug;4(8):1343-52.
6
+ A new analysis algorithm for Chip-chip data ('Chipper') is described in Genome Biology. Manuscript entitled "Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization." by FD Gibbons, M Proft, K Struhl, and FP Roth. Accepted, no publication date as yet.
7
+ Keywords: ChIP-chip
8
+ :arrays:
9
+ GSM73628:
10
+ condition: Sko1-HA
11
+ GSM73626:
12
+ condition: Sko1-HA
13
+ GSM73627:
14
+ condition: Sko1-HA
15
+ :platform: GPL1689
@@ -0,0 +1,31 @@
1
+ ---
2
+ :title: Prp4-1 temperature shift
3
+ :description: "Prp4-1 and wt strains were grown at 26\xC2\xB0C to A600 of 1.0, then an equal volume of 48\xC2\xB0C media was added to bring the temperature to 37\xC2\xB0C. Both strains were allowed to grow at 37\xC2\xB0C and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature.\n\
4
+ Keywords = splicing\n\
5
+ Keywords: time-course"
6
+ :arrays:
7
+ GSM1506:
8
+ condition: prp4-TempShift-30mins
9
+ GSM1507:
10
+ condition: prp4-TempShift-30mins
11
+ GSM1508:
12
+ condition: prp4-TempShift-60mins
13
+ GSM1509:
14
+ condition: prp4-TempShift-60mins
15
+ GSM1510:
16
+ condition: prp4-TempShift-120mins
17
+ GSM1511:
18
+ condition: prp4-TempShift-120mins
19
+ GSM1500:
20
+ condition: prp4-TempShift-0mins
21
+ GSM1501:
22
+ condition: prp4-TempShift-0mins
23
+ GSM1502:
24
+ condition: prp4-TempShift-5mins
25
+ GSM1503:
26
+ condition: prp4-TempShift-5mins
27
+ GSM1504:
28
+ condition: prp4-TempShift-15mins
29
+ GSM1505:
30
+ condition: prp4-TempShift-15mins
31
+ :platform: GPL108
@@ -0,0 +1,15 @@
1
+ ---
2
+ :title: Heme Deficient vs Wild Type in Low Iron
3
+ :description: |-
4
+ Heme Deficient or Wild Type (normal heme) for 6 hrs with iron chelation by BPS.
5
+ Keywords: Cell Type Comparison
6
+ :arrays:
7
+ GSM78518:
8
+ condition: heme deficient
9
+ GSM78519:
10
+ condition: wt
11
+ GSM78520:
12
+ condition: wt
13
+ GSM78521:
14
+ condition: heme deficient
15
+ :platform: GPL2983
@@ -0,0 +1,80 @@
1
+ ---
2
+ :title: Non-essential mRNA processing factors
3
+ :description: |-
4
+ Set of experiments done on yeast deletion strains of various non-essential mRNA processing factors.
5
+ Keywords = splicing
6
+ Keywords: repeat sample
7
+ :arrays:
8
+ GSM1495:
9
+ condition: upf3
10
+ GSM1484:
11
+ condition: nam8
12
+ GSM1473:
13
+ condition: hsp104
14
+ GSM1462:
15
+ condition: prp4
16
+ GSM1496:
17
+ condition: upf3
18
+ GSM1485:
19
+ condition: prp17
20
+ GSM1474:
21
+ condition: hsp104
22
+ GSM1463:
23
+ condition: brr1
24
+ GSM1486:
25
+ condition: prp17
26
+ GSM1475:
27
+ condition: msl1
28
+ GSM1464:
29
+ condition: brr1
30
+ GSM1487:
31
+ condition: prp18
32
+ GSM1476:
33
+ condition: msl1
34
+ GSM1465:
35
+ condition: cus2
36
+ GSM1488:
37
+ condition: prp18
38
+ GSM1477:
39
+ condition: mud1
40
+ GSM1466:
41
+ condition: cus2
42
+ GSM1490:
43
+ condition: snu17
44
+ GSM1489:
45
+ condition: snu17
46
+ GSM1478:
47
+ condition: mud1
48
+ GSM1467:
49
+ condition: dbr1
50
+ GSM1491:
51
+ condition: snu40
52
+ GSM1480:
53
+ condition: mud13
54
+ GSM1479:
55
+ condition: mud13
56
+ GSM1468:
57
+ condition: dbr1
58
+ GSM1492:
59
+ condition: snu40
60
+ GSM1481:
61
+ condition: mud2
62
+ GSM1470:
63
+ condition: ecm2
64
+ GSM1469:
65
+ condition: ecm2
66
+ GSM1493:
67
+ condition: snu66
68
+ GSM1482:
69
+ condition: mud2
70
+ GSM1471:
71
+ condition: gcr3
72
+ GSM1494:
73
+ condition: snu66
74
+ GSM1483:
75
+ condition: nam8
76
+ GSM1472:
77
+ condition: gcr3
78
+ GSM1461:
79
+ condition: prp4
80
+ :platform: GPL105