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22 Kirov et al.based on a study associating expression patterns in the adult mouse brain withthe development of the mouse embryo (16).Websites of interest and related to this work include:• WebGestalt: http://genereg.ornl.gov/webgestalt.• GOTree Machine: http://genereg.ornl.gov/gotm.• GeneKeyDB: http://genereg.ornl.gov/gkdb or http://sourceforge.net/projects/genekeydb.• Entrez gene: http://ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene.• UCSC genome browser: http://genome.ucsc.edu/cgi-bin/hgGateway.• CGAP: http://cgap.nci.nih.gov/.• SourceForge: http://www.sf.net.• Biocarta (Biocarta, Inc., San Diego, CA): http://www.biocarta.com/index.asp.• KEGG: http://www.genome.ad.jp/kegg/.• GO consortium: http://www.geneontology.org/.• OBO: http://obo.sourceforge.net/.• PANTHER: www.pantherdb.org.• STRING: http://string.embl.de/.• DAVID: http://david.abcc.ncifcrf.gov/.• GSB: http://www.cisreg.ca/gsb/.• EnsMART: http://www.ensembl.org/Multi/martview.Additional important sites and mailing lists are described in Note 1.3. MethodsThe methods that are described require minimal set of computer skills: usingspreadsheet and simple text editing software and accessing the Internet. The stepsneeded to define a gene set based on expression or other high-throughput experimentaldesign are out of the scope of this chapter and could require high computer/biostatisticsproficiency and access to specialized software. As a startingpoint it is assumed that an interesting gene set (based on experimental or otherevidence) is already compiled.3.1. ID Conversion and Gene Set Management3.1.1. Gene Set Upload and ID ConversionUsually commercial microarrays designate the genes printed on the chipusing their own IDs. This contributes to the already significant set of existinggene designators. Therefore, often the first step that needs to be undertakenis the conversion of gene IDs. Although it might seem trivial, this stepcould lead to misleading results if not performed correctly (see Note 2). Itis strongly advised against the use of gene symbols (see Note 3). It wouldbe best if the input gene IDs are Entrez gene ID (formerly Locuslink ID)
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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
Page 20: xiiContentsPART III EXPERIMENTAL ME
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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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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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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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