Biology Reference
In-Depth Information
TABLE 18.2
Pipeline and Data Analysis Steps of Transcriptome, Proteome and Metabolome Datasets Obtained from Same Experiments, Prior to Integration
Steps
Data analysis procedures Transcriptome
Proteome
Internal metabolites
External metabolites
1
Analytical method
Affymetrix YG-S98
GeneChip
iTRAQ
GC-TOF-MS
GC-TOF-MS
Growth rates (h-1)
0.07, 0.1, 0.2
0.1, 0.2
0.07, 0.1, 0.2
0.07, 0.1, 0.2
Nutr. limitations
C, N, P, S
C, N, P, S
C, N, P, S
C, N, P, S
Replicates
4
1
3
3
2
Identification and
quantification
Affymetrix GCOS
software
[a]
Genome Annotating Proteomic
Pipeline
[h]
(GAPP) system,
Mascot score and
link to the quantification data in
a relational database
Mass spectral libraries, reverse
match score
Mass spectral libraries, reverse match
score
700 and analysis of
700 , and analysis of pure
standards
>
>
pure standards
3
Heavily-tailed distribution
Data logged
Data logged
Data logged
Data logged
4
Experiment-wise
normalization
—
Each run normalized to pooled
standard
—
—
5
Sample-wise normalization RMA
[b
d]
normalization
MAD (median absolute
deviation)
[e]
Normalized to internal standard
Normalized to internal standard
e
6
Missing value imputation
(MVI)
Not required
MVI
[f]
MVI
[f]
MVI
[f]
7
Measurement-wise
normalization
MAD
[e]
MAD
[e]
MAD
[e]
MAD
[e]
8
Principal Components
Analysis (PCA)
NIPALS
[g]
NIPALS
[g]
NIPALS
[g]
NIPALS
[g]
RMA, robust multichip average (RMA) quantile normalization; MVI, missing-value imputation. MAD (median absolute deviation) normalization; non-linear iterative partial least squares (NIPALS) algorithm.
a
Affymetrix website [
http://www.affymetrix.com
]
b
Bolstad BM, Irizarry RA, Astrand M, Speed, TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19: 185
193.
e
c
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31: e15.
d
RMAExpress software [
http://rmaexpress.bmbolstad.com/
]
e
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res
2002, 30: e15.
f
Oba S, Sato MA, Takemasa I, Monden M, Matsubara K, Ishii S: A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 2003, 19: 2088
2096.
g
Wold H: Estimation of Principal Components and Related Models by Iterative Least Squares. In Multivariate Analysis. Edited by Krishnaiah PR. New York: Academic Press; 1966: 391
e
e
420.
h
Genome Annotating Proteomic Pipeline (GAPP) [
http://www.gapp.info
]
(
[53]
; Suppl. File 4. Supplementary Methods, with permission).
