View - ResearchGate

More documents

Recommendations

Info

Index 337eigenvalue 178, 180–182, 184–185false discovery rate (FDR) 57, 61, 64,66, 68false negative 55, 134, 258, 260false positive 60, 64, 119, 123,126, 130, 134, 257–258, 260,269, 274, 281–282,285–287, 305multiple testing 57, 64, 188mutual information 118–119power 182–186, 257, 260p-value 11, 13, 27, 57–59, 61–62,64–66, 182Shannon entropy 180Z-score 40, 44–45synteny (syntenic) 93–94Ttext mining 35, 157transcriptional regulation 129transcription factor binding site (TFBS)20, 130–139, 141, 144–145, 147transcriptional regulatory element(TRE) 55, 57–58transcription factor (TF) 43, 49–50,76, 317Vvirus 127, 253retrovirus 211–212, 215, 217–220visualization 1–2, 4, 6, 9, 18, 25, 31, 37,42, 49, 53–54, 57–62, 64, 66, 77, 93,95, 100, 176, 194
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 102:
Page 106:
Page 110:
Page 114:
Page 118:
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 148:
Prediction Using PAINT 634.2. Size
Page 152:
65Fig. 4. Localization of enrichmen
Page 156:
Prediction Using PAINT 673. Okubo,
Page 160:
5Prediction of Intrinsic Disorder a
Page 164:
Prediction of ID and Its Use in Fun
Page 168:
Table 1Summary of the Web Servers O
Page 172:
Page 176:
Page 180:
Page 184:
Page 188:
Page 192:
Page 196:
Page 200:
Page 204:
Page 208:
IICOMPUTATIONAL METHODS II
Page 212:
94 Crabtree et al.genomes, which is
Page 216:
96 Crabtree et al.Fig. 2. Sybil pro
Page 220:
98 Crabtree et al.Fig. 3. Computing
Page 224:
100 Crabtree et al.3.1.5.1. FILTER
Page 228:
102 Crabtree et al.3. For the sake
Page 232:
104 Crabtree et al.Fig. 5. Best bid
Page 236:
106 Crabtree et al.17. Some cluster
Page 240:
108 Crabtree et al.19. Chado—The
Page 244:
110 Dateproducts prevents the under
Page 248:
112 DateDetails of these tasks are
Page 252:
114 DateThis step creates additiona
Page 256:
116 Date>hsapiens|gi|20093443 >hsap
Page 260:
118 DateBLAST score from the match
Page 264:
Table 1A Sample of Results From Pro
Page 268:
122 DateFig. 1. A network of functi
Page 272:
124 Datedescribed by Verjovsky Marc
Page 276:
126 Dateor contracts put forth by t
Page 280:
8Bioinformatics Tools for Modeling
Page 284:
Modeling Transcription Factor Targe
Page 288:
VISTA Program to search for TFBSs H
Page 292:
Page 296:
Page 300:
Page 304:
Page 308:
Ac 0 0 0 1 0 1 0 1 0 1 1 0 0 0 0 0
Page 312:
Page 316:
Page 320:
Page 324:
Page 328:
154 Osborne et al.are included in t
Page 332:
156 Osborne et al.Fig. 2. Flowchart
Page 336:
158 Osborne et al.UMLS source abbre
Page 340:
160 Osborne et al.Fig. 3. Querying
Page 344:
162 Osborne et al.3.4.2. Installati
Page 348:
164 Osborne et al.amount of filteri
Page 352:
166 Osborne et al.public class MMTx
Page 356:
168 Osborne et al.Fig. 4. Input tes
Page 360:
10Statistical Methods for Identifyi
Page 364:
Identifying Differentially Expresse
Page 368:
Page 372:
Page 376:
Page 380:
Page 384:
Page 388:
Page 392:
Page 396:
Page 400:
Page 404:
11Gene Function Analysis Using the
Page 408:
Gene Function Analysis Using the Ch
Page 412:
Page 416:
Page 420:
Page 424:
Page 428:
Page 432:
Page 436:
Page 440:
12Design and Application of a shRNA
Page 444:
Design and Application of a shRNA 2
Page 448:
Page 452:
Page 456:
Page 460:
Page 464:
224 Cheng and Chang1. IntroductionR
Page 468:
226 Cheng and ChangFig. 1. Structur
Page 472:
228 Cheng and ChangFig. 2. Sequence
Page 476:
230 Cheng and Chang3. Handheld ultr
Page 480:
232 Cheng and ChangFig. 4. Sequence
Page 484:
234 Cheng and ChangFig. 5. Experime
Page 488:
236 Cheng and Chang3.4. Functional
Page 492:
238 Cheng and Chang3.4.4. Fixation
Page 496:
240 Cheng and Chang16. Player, M. R
Page 500:
14Selection of Recombinant Antibodi
Page 504:
Selection of Recombinant Antibodies
Page 508:
Page 512:
Page 516:
Page 520:
Page 524:
Page 528:
258 Tikhmyanova et al.functionally
Page 532:
260 Tikhmyanova et al.partner was f
Page 536:
262 Tikhmyanova et al.5. pGLS22-Ras
Page 540:
264 Tikhmyanova et al.4. pYESTrp2 p
Page 544:
266 Tikhmyanova et al.Fig. 3. Polyl
Page 548:
268 Tikhmyanova et al.To minimize t
Page 552:
270 Tikhmyanova et al.Fig. 4. Flow
Page 556:
272 Tikhmyanova et al.3.3.1. Transf
Page 560:
274 Tikhmyanova et al.3. At room te
Page 564:
276 Tikhmyanova et al.the frozen ma
Page 568:
278 Tikhmyanova et al.Fig. 6. Detai
Page 572:
Table 3Suggested PCR Reactions and
Page 576:
282 Tikhmyanova et al.15. Prepare a
Page 580:
284 Tikhmyanova et al.6. Assay of m
Page 584:
286 Tikhmyanova et al.of tubes. Fin
Page 588:
288 Tikhmyanova et al.the polylinke
Page 592:
290 Tikhmyanova et al.25. Petermann
Page 596:
292 Serebriiskii et al.for eukaryot
Page 600:
294 Serebriiskii et al.(3,9), yeast
Page 604:
296 Serebriiskii et al.systems has
Page 608:
298 Serebriiskii et al.Table 1Conce
Page 612:
300 Serebriiskii et al.Table 2Plasm
Page 616:
302 Serebriiskii et al.2.7. Miscell
Page 620:
304 Serebriiskii et al.Fig. 4. Char
Page 624:
306 Serebriiskii et al.1. From the
Page 628:
308 Serebriiskii et al.resuspend th
Page 632: 310 Serebriiskii et al.1. Use prime
Page 636: 312 Serebriiskii et al.published us
Page 640: 314 Serebriiskii et al.results obta
Page 644: 17Engineering Cys2His2 Zinc Finger
Page 648: Engineering Cys2His2 Zinc Finger Do
Page 680: IndexAamino acid 69-73, 75-79, 81-8
show all

View - ResearchGate

Create successful ePaper yourself

Delete template?

Save as template?