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Estimating Gene Function With LS-NMF 45variability within a pattern. Herein the process using a spreadsheet program isdescribed, as these are widely available.1. Output the A (distribution) matrix for the best simulation from the PattRun programby pressing the Export button once the results are viewed. Provide a namefor the output file in the Save dialog. Check only the box for the Distribution andthen press the Save button.2. Open the output file with a spreadsheet program. The top lines of the file willlook likecdc25-sep160147.00Wed Sep 13 13:42:57 2006DistributionSPAC222.09 10.03 3.53 5.75 0 1.28 0SPAC977.10 10.79 0 0 10.98 0 0.12SPAC821.06 5.59 0.02 5.10 0.31 6.88 2.09SPAC821.09 0 0 14.49 0 0 7.31with a header providing the name of the data set, the χ 2 value, and the date of theLS-NMF analysis. After the header, each row provides the gene name and thestrength of assignment of that gene to each of the six patterns.3. Choose the pattern of interest; herein again focus is on pattern 3 (column D inthe spreadsheet). Calculate the mean and standard deviation of the column byreplacing cell D3 with “=average(d6:dN)”, where N is the last row with dataand replacing cell D4 with “=stdev(d6:dN).” Using cut and paste these can becalculated for all patterns, if one wishes.4. In an empty column, move to the sixth cell and enter “=(d6-$d$4)/$d$5” andreturn. Then copy this cell and fill down. These are the Z-scores for the genes.5. Copy the first column (gene names) and the Z-scores, so they are side-by-side.If pasting into a new spreadsheet or page, choose to paste values. Sort thecolumns by the Z-score.6. Again, one must choose a cutoff to produce a gene list; however in general, thelarger the magnitude of the Z-score the more strongly a gene is associated with apattern. This allows one to compare the strength of association of a gene acrossdifferent patterns. Comparison with the list from ClutrFree will show the genes arein the same order, but the values have changed.4. Notes1. In addition, two command line C++ versions, one for single workstation (DesktopLS-NMF) and one for Beowulf cluster (LAM/MPI LS-NMF), are available foradvanced users. Both versions are coded in C++, should be compiled using a standardC++ and mpiCC. Packages are downloadable in tar ball form, and aREADME file is included with all necessary steps for installation. Other than theLS-NMF code itself, two Perl scripts are included under API subdirectory for
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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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Page 66: 20 Kirov et al.way to associate gen
Page 70: 22 Kirov et al.based on a study ass
Page 74: 24 Kirov et al.1. Retrieve the gene
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Page 82: 28 Kirov et al.Fig. 2. Pathway anal
Page 86: 30 Kirov et al.3. Gene symbols usag
Page 90: 32 Kirov et al.9. OBO_Team, Open Bi
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Page 132: Prediction Using PAINT 55first exon
Page 138: 58 Gonye et al.Fig. 3. A network vi
Page 142: 60 Gonye et al.exGeneList.txt) is a
Page 146: 62 Gonye et al.(http://www.tm4.org)
Page 150: 64 Gonye et al.does not span the en
Page 154: 66 Gonye et al.4.7. Interpreting th
Page 158: 68 Gonye et al.18. Dozmorov, M. G.,
Page 162: 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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