Methods in Enzymology - DNA ...

Methods in Enzymology - DNA Microarrays [part B] - A. Kimmel, Książki, Biochemia

[ Pobierz całość w formacie PDF ]
METHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF
John N. Abelson Melvin I. Simon
DIVISION OF BIOLOGY
CALIFORNIA INSTITUTE OF TECHNOLOGY
PASADENA, CALIFORNIA
FOUNDING EDITORS
Sidney P. Colowick and Nathan O. Kaplan
Table of Contents
C
ONTRIBUTORS TO
V
OLUME
411................. ix
V
OLUMES IN
S
ERIES
. . . . . . . . . . . . . . . . . . . . .
xiii
1. RNA Extraction for Arrays
L
AKSHMI
V. M
ADABUSI
,
G
ARY
J. L
ATHAM
,
AND
B
ERNARD
F. A
NDRUSS
1
2. Analyzing Micro-RNA Expression Using
Microarrays
T
IMOTHY
S. D
AVISON
,
C
HARLES
D. J
OHNSON
,
AND
B
ERNARD
F. A
NDRUSS
14
3. Troubleshooting Microarray Hybridizations B
RIAN
E
ADS
,
A
MY
C
ASH
,
K
EVIN
B
OGART
,
J
AMES
C
OSTELLO
,
AND
J
USTEN
A
NDREWS
34
4. Use of External Controls in Microarray
Experiments
I
VANA
V. Y
ANG
50
5. Standards in Gene Expression Microarray
Experiments
M
ARC
S
ALIT
63
6. Scanning Microarrays: Current Methods and
Future Directions
J
ERILYN
A. T
IMLIN
79
7. An Introduction to BioArray Software
Environment
C
ARL
T
ROEIN
,J
OHAN
V
ALLON
-C
HRISTERSSON
,
AND
L
AO
H. S
AAL
99
8. Bioconductor: An Open Source Framework
for Bioinformatics and Computational
Biology
M
ARK
R
EIMERS AND
V
INCENT
J. C
AREY
119
v
vi
TABLE OF CONTENTS
9. TM4 Microarray Software Suite
A
LEXANDER
I. S
AEED
,
N
IRMAL
K. B
HAGABATI
,
J
OHN
C. B
RAISTED
,
W
EI
L
IANG
,
V
ASILY
S
HAROV
,
E
LEANOR
A. H
OWE
,
J
IANWEI
L
I
,
M
ATHANGI
T
HIAGARAJAN
,
J
OSEPH
A. W
HITE
,
AND
J
OHN
Q
UACKENBUSH
134
10. Clustering Microarray Data
J
EREMY
G
OLLUB AND
G
AVIN
S
HERLOCK
194
11. Analysis of Variance of Microarray Data
J
ULIEN
F. A
YROLES AND
G
REG
G
IBSON
214
12. Microarray Quality Control
J
AMES
M. M
INOR
233
13. Analysis of a Multifactor Microarray Study
Using Partek Genomics Solution
T
OM
D
OWNEY
256
14. Statistics for ChIP-chip and DNase
Hypersensitivity Experiments on
NimbleGen Arrays
P
ETER
C. S
CACHERI
,
G
REGORY
E. C
RAWFORD
,
AND
S
EAN
D
AVIS
270
15. Extrapolating Traditional DNA Microarray
Statistics to Tiling and Protein
Microarray Technologies
T
HOMAS
E. R
OYCE
,
J
OEL
S. R
OZOWSKY
,
N
ICHOLAS
M. L
USCOMBE
,
O
LOF
E
MANUELSSON
,
H
AIYUAN
Y
U
,
X
IAOWEI
Z
HU
,
M
ICHAEL
S
NYDER
,
AND
M
ARK
B. G
ERSTEIN
282
16. Random Data Set Generation to Support
Microarray Analysis
D
ANIEL
Q. N
AIMAN
312
17. Using Ontologies to Annotate
Microarray Experiments
P
ATRICIA
L. W
HETZEL
,
H
ELEN
P
ARKINSON
,
AND
C
HRISTIAN
J. S
TOECKERT
,J
R
325
18. Interpreting Experimental Results Using
Gene Ontologies
T
IM
B
EISSBARTH
340
19. Gene Expression Omnibus:
Microarray Data Storage, Submission,
Retrieval, and Analysis
T
ANYA
B
ARRETT AND
R
ON
E
DGAR
352
TABLE OF CONTENTS
vii
20. Data Storage and Analysis in ArrayExpress A
LVIS
B
RAZMA
,
M
ISHA
K
APUSHESKY
,
H
ELEN
P
ARKINSON
,
U
GIS
S
ARKINS
,
AND
M
OHAMMAD
S
HOJATALAB
370
21. Clustering Methods for Analyzing Large
Data Sets: Gonad Development,
A Study Case
J
´
R
ˆ
ME
H
ENNETIN AND
M
ICHEL
B
ELLIS
387
22. Visualizing Networks
G
EORGE
W. B
ELL AND
F
RAN
L
EWITTER
408
23. Random Forests for Microarrays
A
DELE
C
UTLER AND
J
OHN
R. S
TEVENS
422
A
UTHOR
I
NDEX.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
433
S
UBJECT
I
NDEX .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
461
[ Pobierz całość w formacie PDF ]

zanotowane.pl

doc.pisz.pl

pdf.pisz.pl

sylwina.xlx.pl