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DNA Vector-Based shRNA-Expression Systems 229Fig. 3. Constructs of improved DNA vector-based shRNA-expression systems. ThePuro R is cloned between restriction enzyme ClaI and HindIII sites in the pHsH1, pHsU6,pMmH1, and pMmU6 constructs as a stuffer that is convenient for the cloning of theshRNA-coding sequences. The resulting improved DNA constructs are redesignated aspHsH1puro (A), pHsU6puro (B), pMmH1puro (C), and pMmU6puro (D) vectors.5. 3% Paraformaldehyde (Merck, Darmstadt, Germany).6. 0.5% Triton X-100 (Merck, Darmstadt, Germany).7. Bicinchoninic acid assay (Pierce, Rockford, IL) stored at room temperature.8. Bovine serum albumin (Sigma, St Louis, MO) stored at room temperature.9. Dual-luciferase reporter assay system (Promega) stored in aliquots at −80°C.10. Enhanced chemiluminescence Western blotting detection reagents (AmershamBiosciences, Arlington Heights, IL) stored at 4°C.2.5. Instruments1. Microcentrifuges (Heraeus Biofuge Pico and Heraeus Biofuge Fresco, KendroLaboratory Products, Sollentum, Germany).2. Dri-block heater (Techne DRI-BLOCK DB 20, Techne, Cambridge, UK).
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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 478: DNA Vector-Based shRNA-Expression S
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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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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