View - ResearchGate

More documents

Recommendations

Info

Prediction Using PAINT 634.2. Size of the Gene ListAnother key issue in TRNA is the size of the gene list. Based on the resultsfrom multiple studies, it is recommended that the gene list correspond to at least30 genes. Whereas a formal assessment of the robustness of PAINT to “noise”in the gene list (i.e., containing genes that do not “belong” in the coregulatedset) has not been made, available experience on multiple data sets indicate thatthe results are not critically dependent on 100% accuracy of the gene list correspondingto truly coregulated genes. This has a significant impact in the clusterbasedanalysis, so that small inaccuracies (
Page 2:
Gene Function Analysis
Page 6:
METHODS IN MOLECULAR BIOLOGYGene Fu
Page 12:
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
Page 38:
6 BidautTable 2Folder Layout to Use
Page 42:
8 Bidaut• alphaA: this is the num
Page 46:
10 Bidautcomputing the maximum corr
Page 50:
12 BidautFig. 3. The complete Clutr
Page 54:
Table 3Some Identified Patterns (5,
Page 58:
16 BidautFig. 4. This is a comparis
Page 62:
18 BidautReferences1. Hughes, T. R.
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
Page 78:
26Fig. 1. Functional associations f
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
Page 94:
3Estimating Gene Function With Leas
Page 98: Estimating Gene Function With LS-NM
Page 122: 50 Gonye et al.activity and problem
Page 126: 52 Gonye et al.Currently, PAINT can
Page 130: 54 Gonye et al.dynamic nature of th
Page 136: Prediction Using PAINT 57represente
Page 140: Prediction Using PAINT 59In PAINT,
Page 144: Prediction Using PAINT 6114. On the
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
Page 166: 72 Uversky et al.sequence space and
Page 170: Table 1 (Continued)Server name URL
Page 174: 76 Uversky et al.1.5. When to Use t
Page 178: 78 Uversky et al.elucidating compos
Page 182: Table 2Averaged Frequencies of Diff
Page 186: 82 Uversky et al.the box Raw Output
Page 190: 84 Uversky et al.peculiarities of t
Page 194: 86 Uversky et al.Fig. 4. Prediction
Page 198:
88 Uversky et al.13. Uversky, V. N.
Page 202:
90 Uversky et al.50. Vucetic, S., O
Page 206:
92 Uversky et al.84. Ritter, L. M.,
Page 210:
6Sybil: Methods and Software for Mu
Page 214:
Sybil: Multiple Genome Comparison a
Page 218:
Page 222:
Page 226:
Page 230:
Page 234:
Page 238:
Page 242:
7Estimating Protein Function Using
Page 246:
Estimating Protein Function Using P
Page 250:
Page 254:
Page 258:
Page 262:
Page 266:
Page 270:
Page 274:
Page 278:
Page 282:
130 Davuluriinteracting proteins an
Page 286:
Table 1Web URLs of Promoter, TF Dat
Page 290:
134 DavuluriPWM-based models do not
Page 294:
136 DavuluriTF-map alignments of or
Page 298:
138 Davuluridiscussed which program
Page 302:
140 DavuluriTable 2ER-a-Responsive
Page 306:
Table 3Sample Data Matrix Represent
Page 310:
Table 3 (Continued)Class MYCMAX MYC
Page 314:
146 DavuluriFig. 3. (A) CART Tree:
Page 318:
148 Davuluri11. Vlieghe, D., Sandel
Page 322:
150 Davuluri44. Berezikov, E., Gury
Page 326:
9Mining Biomedical Data Using MetaM
Page 330:
Mining Biomedical Data Using MMTx a
Page 334:
Page 338:
Page 342:
Page 346:
Page 350:
Page 354:
Page 358:
Page 362:
172 Ho et al.Fig. 1. Artificial exa
Page 366:
174 Ho et al.allowing for cases whe
Page 370:
176 Ho et al.A different measure is
Page 374:
178 Ho et al.3.1.3. LA and Generali
Page 378:
180 Ho et al.The ECF-statistic can
Page 382:
182 Ho et al.In the special case of
Page 386:
184 Ho et al.Fig. 5. An illustratio
Page 390:
186 Ho et al.Fig. 7. The power curv
Page 394:
188 Ho et al.this section were not
Page 398:
190 Ho et al.References1. Schena, M
Page 402:
IIIEXPERIMENTAL METHODS
Page 406:
194 Caldwell et al.for sequences th
Page 410:
196 Caldwell et al.query because it
Page 414:
198 Caldwell et al.Fig. 1. (A) Prot
Page 418:
200 Caldwell et al.outside primer o
Page 422:
202 Caldwell et al.5. Targeting scr
Page 426:
204 Caldwell et al.will allow the s
Page 430:
206 Caldwell et al.3.1.6. Plasmid P
Page 434:
208 Caldwell et al.PCR amplify the
Page 438:
210 Caldwell et al.8. Thawing cells
Page 442:
212 Zhang et al.Going one step beyo
Page 446:
214 Zhang et al.Fig. 2. Generation
Page 450:
216 Zhang et al.Perform PCR cycles,
Page 454:
218 Zhang et al.Fig. 4. Schematic m
Page 458:
220 Zhang et al.Fig. 5. Replacement
Page 462:
13Construction of Simple and Effici
Page 466:
DNA Vector-Based shRNA-Expression S
Page 470:
Page 474:
Page 478:
Page 482:
Page 486:
Page 490:
Page 494:
Page 498:
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
Page 526:
15A Bacterial/Yeast Merged Two-Hybr
Page 530:
Screening in Yeast With a Bacterial
Page 534:
Page 538:
Page 542:
Page 546:
Page 550:
Page 554:
Page 558:
Page 562:
Page 566:
Page 570:
Page 574:
Page 578:
Page 582:
Page 586:
Page 590:
Page 594:
16A Bacterial/Yeast Merged Two-Hybr
Page 598:
Dual Bait-Compatible Bacterial Two-
Page 602:
Page 606:
Page 610:
Page 614:
Page 618:
Page 622:
Page 626:
Page 630:
Page 634:
Page 638:
Page 642:
Page 646:
318 Thibodeau-Beganny and Joungbeen
Page 650:
320 Thibodeau-Beganny and JoungFig.
Page 654:
Page 658:
324 Thibodeau-Beganny and JoungTypi
Page 662:
Page 666:
328 Thibodeau-Beganny and JoungPCR
Page 670:
330 Thibodeau-Beganny and Joung16-1
Page 674:
332 Thibodeau-Beganny and Joung2. P
Page 678:
334 Thibodeau-Beganny and Joung11.
Page 682:
336 IndexKknockin (gene knockin) 19
show all

View - ResearchGate

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?