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Table 1Tools That Can Perform Gene Set Functional Association AnalysisTool name Web address Status ReferenceGOStat http://gostat.wehi.edu.au/ Live 22CLENCH http://www.personal.psu.edu/faculty/n/h/nhs109/Clench/ Live 23GoToolBox http://crfb.univ-mrs.fr/GOToolBox/index.php Live 24DAVID/EASEOnline http://apps1.niaid.nih.gov/david/ Live 25GoMiner http://discover.nci.nih.gov/gominer/ Live 26FatiGO http://www.fatigo.org/ Live 27GOTM/WebGestalt htttp://genereg.ornl.gov/gotm Live 15,28Onto-Express http://vortex.cs.wayne.edu/projects.htm Live 29GeneMerge http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge/GeneMerge.html Live 30FuncAssociate http://llama.med.harvard.edu/cgi/func/funcassociate Live 31GoSurfer http://biosun1.harvard.edu/complab/gosurfer/ Live 32EGOn http://www.genetools.no/ Live 33OntologyTraverser http://franklin.imgen.bcm.tmc.edu/rho/services/OntologyTraverser/ Live 34PANTHER http://www.pantherdb.org/ Live 8FuncSpec http://funspec.med.utoronto.ca/ Live 35GoTermFinder http://bair-server.lesc.doc.ic.ac.uk:8088/cgi-bin/GOTermFinder.pl Live 36MAPPFinder http://www.genmapp.org/MAPPFinder.html Live 37GFINDER http://promoter.bioing.polimi.it/gfinder/ Live 3821
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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
Page 16: Prefaceixcolleagues demonstrate how
Page 20: xiiContentsPART III EXPERIMENTAL ME
Page 26: ICOMPUTATIONAL METHODS I
Page 34: 4 BidautTable 1Input File Format Us
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Page 62: 18 BidautReferences1. Hughes, T. R.
Page 66: 20 Kirov et al.way to associate gen
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Page 100: 38 Wang and Ochs1. Download the LS-
Page 104: 40 Wang and OchsFig. 1. The PattRun
Page 108: 42 Wang and OchsFig. 3. The PattRun
Page 112: 44 Wang and OchsFig. 4. The gene ta
Page 116: 46 Wang and Ochsresults posttreatme
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4From Promoter Analysis to Transcri
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Prediction Using PAINT 51even in si
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Prediction Using PAINT 53Fig. 1. A
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Prediction Using PAINT 55first exon
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58 Gonye et al.Fig. 3. A network vi
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60 Gonye et al.exGeneList.txt) is a
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62 Gonye et al.(http://www.tm4.org)
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64 Gonye et al.does not span the en
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66 Gonye et al.4.7. Interpreting th
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68 Gonye et al.18. Dozmorov, M. G.,
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70 Uversky et al.in protein functio
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72 Uversky et al.sequence space and
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Table 1 (Continued)Server name URL
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76 Uversky et al.1.5. When to Use t
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78 Uversky et al.elucidating compos
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Table 2Averaged Frequencies of Diff
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82 Uversky et al.the box Raw Output
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84 Uversky et al.peculiarities of t
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86 Uversky et al.Fig. 4. Prediction
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88 Uversky et al.13. Uversky, V. N.
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90 Uversky et al.50. Vucetic, S., O
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92 Uversky et al.84. Ritter, L. M.,
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6Sybil: Methods and Software for Mu
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Sybil: Multiple Genome Comparison a
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7Estimating Protein Function Using
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Estimating Protein Function Using P
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130 Davuluriinteracting proteins an
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Table 1Web URLs of Promoter, TF Dat
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134 DavuluriPWM-based models do not
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136 DavuluriTF-map alignments of or
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138 Davuluridiscussed which program
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140 DavuluriTable 2ER-a-Responsive
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Table 3Sample Data Matrix Represent
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Table 3 (Continued)Class MYCMAX MYC
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146 DavuluriFig. 3. (A) CART Tree:
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148 Davuluri11. Vlieghe, D., Sandel
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150 Davuluri44. Berezikov, E., Gury
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9Mining Biomedical Data Using MetaM
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Mining Biomedical Data Using MMTx a
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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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