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Table 3 (Continued)Class MYCMAX MYC VMYB GATA2 P53 TCF11 EFC CETS168 MAZ STAT4 CRX SOX5 FOXD3 HNF3α E2A AP3 AML1 E47 TCF4 HIF1Me 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0Me 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 1 0 0Me 0 0 0 1 1 1 0 0 1 1 1 1 0 0 0 0 0 1 1 0Me 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0Me 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 1 0 0 0Me 1 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0Me 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0Me 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0Me 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0Me 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0Me 0 0 0 0 0 0 0 0 0 1 1 0 1 1 0 0 0 0 1 0The first column is the class variable (y), which is a categorical variable with two values; Ac–Acetylated promoter and Me–Methylatedpromoter. The rest of the columns represent different Transcription Factor Binding Sites (TFBS), used as feature (predictor) variables for runningRandom Forest and CART/rpart. It is a binary matrix, where 1 and 0 stand for the presence and absence of TFBS (column) in the correspondingpromoter (row).144
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Gene Function Analysis
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METHODS IN MOLECULAR BIOLOGYGene Fu
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PrefaceThis volume of Methods in Mo
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Prefaceixcolleagues demonstrate how
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xiiContentsPART III EXPERIMENTAL ME
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ICOMPUTATIONAL METHODS I
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4 BidautTable 1Input File Format Us
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6 BidautTable 2Folder Layout to Use
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8 Bidaut• alphaA: this is the num
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10 Bidautcomputing the maximum corr
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12 BidautFig. 3. The complete Clutr
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Table 3Some Identified Patterns (5,
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16 BidautFig. 4. This is a comparis
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18 BidautReferences1. Hughes, T. R.
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20 Kirov et al.way to associate gen
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22 Kirov et al.based on a study ass
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24 Kirov et al.1. Retrieve the gene
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26Fig. 1. Functional associations f
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28 Kirov et al.Fig. 2. Pathway anal
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30 Kirov et al.3. Gene symbols usag
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32 Kirov et al.9. OBO_Team, Open Bi
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3Estimating Gene Function With Leas
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Estimating Gene Function With LS-NM
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50 Gonye et al.activity and problem
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52 Gonye et al.Currently, PAINT can
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54 Gonye et al.dynamic nature of th
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Prediction Using PAINT 57represente
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Prediction Using PAINT 59In PAINT,
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Prediction Using PAINT 6114. On the
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Prediction Using PAINT 634.2. Size
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65Fig. 4. Localization of enrichmen
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Prediction Using PAINT 673. Okubo,
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5Prediction of Intrinsic Disorder a
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Prediction of ID and Its Use in Fun
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Table 1Summary of the Web Servers O
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IICOMPUTATIONAL METHODS II
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94 Crabtree et al.genomes, which is
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96 Crabtree et al.Fig. 2. Sybil pro
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98 Crabtree et al.Fig. 3. Computing
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100 Crabtree et al.3.1.5.1. FILTER
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102 Crabtree et al.3. For the sake
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104 Crabtree et al.Fig. 5. Best bid
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106 Crabtree et al.17. Some cluster
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108 Crabtree et al.19. Chado—The
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110 Dateproducts prevents the under
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112 DateDetails of these tasks are
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114 DateThis step creates additiona
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116 Date>hsapiens|gi|20093443 >hsap
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Page 276: 126 Dateor contracts put forth by t
Page 280: 8Bioinformatics Tools for Modeling
Page 284: Modeling Transcription Factor Targe
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Page 322: 150 Davuluri44. Berezikov, E., Gury
Page 326: 9Mining Biomedical Data Using MetaM
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172 Ho et al.Fig. 1. Artificial exa
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174 Ho et al.allowing for cases whe
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176 Ho et al.A different measure is
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178 Ho et al.3.1.3. LA and Generali
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180 Ho et al.The ECF-statistic can
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182 Ho et al.In the special case of
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184 Ho et al.Fig. 5. An illustratio
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186 Ho et al.Fig. 7. The power curv
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188 Ho et al.this section were not
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190 Ho et al.References1. Schena, M
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IIIEXPERIMENTAL METHODS
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194 Caldwell et al.for sequences th
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196 Caldwell et al.query because it
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198 Caldwell et al.Fig. 1. (A) Prot
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200 Caldwell et al.outside primer o
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202 Caldwell et al.5. Targeting scr
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204 Caldwell et al.will allow the s
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206 Caldwell et al.3.1.6. Plasmid P
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208 Caldwell et al.PCR amplify the
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210 Caldwell et al.8. Thawing cells
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212 Zhang et al.Going one step beyo
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214 Zhang et al.Fig. 2. Generation
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216 Zhang et al.Perform PCR cycles,
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218 Zhang et al.Fig. 4. Schematic m
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220 Zhang et al.Fig. 5. Replacement
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13Construction of Simple and Effici
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DNA Vector-Based shRNA-Expression S
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244 Hust et al.overcome by two appr
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246 Hust et al.Fig. 1. Schematic de
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248 Hust et al.interaction during p
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250 Hust et al.3.4. Titering1. Inoc
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252 Hust et al.10. Shortly before u
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254 Hust et al.activity by preservi
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15A Bacterial/Yeast Merged Two-Hybr
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Screening in Yeast With a Bacterial
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16A Bacterial/Yeast Merged Two-Hybr
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Dual Bait-Compatible Bacterial Two-
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318 Thibodeau-Beganny and Joungbeen
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320 Thibodeau-Beganny and JoungFig.
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324 Thibodeau-Beganny and JoungTypi
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328 Thibodeau-Beganny and JoungPCR
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330 Thibodeau-Beganny and Joung16-1
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332 Thibodeau-Beganny and Joung2. P
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334 Thibodeau-Beganny and Joung11.
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336 IndexKknockin (gene knockin) 19
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