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234 Cheng and ChangFig. 5. Experimental procedure for constructing the DNA vector-based shRNAexpressioncassette. (A) Preparation of DNA vector-based shRNA-expression vector.The improved DNA vector-based shRNA-expression vector is digested with restrictionenzymes ClaI and HindIII, simultaneously, to remove the stuffer Puro R DNA fragment.(B) Cloning of shRNA-expression cassette. The ClaI/HindIII-digested shRNA-expressionvector is ligated with an annealed oligonucleotide duplex that contains a specificshRNA-expression sequence with a row of five Ts as a transcription termination signaland two unique restriction enzyme ClaI and HindIII compatible ends. (C) Screening ofshRNA expressed recombinant DNA clone. The DNA construct containing the shRNAexpressionsequence is identified by simply mapping with restriction enzymes ClaI andHindIII, and further confirmed by directly DNA sequencing with oligonucleotideprimer against T7 or SP6 promoter. The positive recombinant clones contain the restrictionenzyme HindIII site but usually lose the restriction enzyme ClaI site.
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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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118 DateBLAST score from the match
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Table 1A Sample of Results From Pro
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122 DateFig. 1. A network of functi
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124 Datedescribed by Verjovsky Marc
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126 Dateor contracts put forth by t
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8Bioinformatics Tools for Modeling
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Modeling Transcription Factor Targe
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VISTA Program to search for TFBSs H
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Ac 0 0 0 1 0 1 0 1 0 1 1 0 0 0 0 0
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154 Osborne et al.are included in t
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156 Osborne et al.Fig. 2. Flowchart
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158 Osborne et al.UMLS source abbre
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160 Osborne et al.Fig. 3. Querying
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162 Osborne et al.3.4.2. Installati
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164 Osborne et al.amount of filteri
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166 Osborne et al.public class MMTx
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168 Osborne et al.Fig. 4. Input tes
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10Statistical Methods for Identifyi
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Identifying Differentially Expresse
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11Gene Function Analysis Using the
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Gene Function Analysis Using the Ch
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Page 464: 224 Cheng and Chang1. IntroductionR
Page 468: 226 Cheng and ChangFig. 1. Structur
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Page 502: 244 Hust et al.overcome by two appr
Page 506: 246 Hust et al.Fig. 1. Schematic de
Page 510: 248 Hust et al.interaction during p
Page 514: 250 Hust et al.3.4. Titering1. Inoc
Page 518: 252 Hust et al.10. Shortly before u
Page 522: 254 Hust et al.activity by preservi
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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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