Abstract
We present a hierarchical Bayes model for determining genes in the sporulation pathway of Bacillus subtilis (B. subtilis) using two complementary replicated cDNA microarray experimental designs. The first design involves the mutation of a transcription factor, Sigma factor E (σE), and the second is an overexpression of this factor. We first normalize the microarray data using a rank invariant method. Genes found to be overexpressed in both experimental designs are further examined experimentally to determine their role in the sporulation pathway. Through statistical and experimental methods we found 181 genes that had not been previously described as controlled by σE. We identify the chromosome locations of clusters of σE-controlled genes using a nearest neighbor scan-statistic, and determine B. subtilis functional categories that are over-represented in subsets of expressed genes.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1-18 |
| Number of pages | 18 |
| Journal | Journal of Multivariate Analysis |
| Volume | 90 |
| Issue number | 1 SPEC. ISS. |
| DOIs | |
| State | Published - Jul 2004 |
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Keywords
- Bayesian models
- CDNA microarrays
- Functional category
- Gene location cluster
- MCMC
- Scan statistics
ASJC Scopus subject areas
- Statistics, Probability and Uncertainty
- Numerical Analysis
- Statistics and Probability
Cite this
Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. / Conlon, Erin M.; Eichenberger, Patrick; Liu, Jun S.
In: Journal of Multivariate Analysis, Vol. 90, No. 1 SPEC. ISS., 07.2004, p. 1-18.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs
AU - Conlon, Erin M.
AU - Eichenberger, Patrick
AU - Liu, Jun S.
PY - 2004/7
Y1 - 2004/7
N2 - We present a hierarchical Bayes model for determining genes in the sporulation pathway of Bacillus subtilis (B. subtilis) using two complementary replicated cDNA microarray experimental designs. The first design involves the mutation of a transcription factor, Sigma factor E (σE), and the second is an overexpression of this factor. We first normalize the microarray data using a rank invariant method. Genes found to be overexpressed in both experimental designs are further examined experimentally to determine their role in the sporulation pathway. Through statistical and experimental methods we found 181 genes that had not been previously described as controlled by σE. We identify the chromosome locations of clusters of σE-controlled genes using a nearest neighbor scan-statistic, and determine B. subtilis functional categories that are over-represented in subsets of expressed genes.
AB - We present a hierarchical Bayes model for determining genes in the sporulation pathway of Bacillus subtilis (B. subtilis) using two complementary replicated cDNA microarray experimental designs. The first design involves the mutation of a transcription factor, Sigma factor E (σE), and the second is an overexpression of this factor. We first normalize the microarray data using a rank invariant method. Genes found to be overexpressed in both experimental designs are further examined experimentally to determine their role in the sporulation pathway. Through statistical and experimental methods we found 181 genes that had not been previously described as controlled by σE. We identify the chromosome locations of clusters of σE-controlled genes using a nearest neighbor scan-statistic, and determine B. subtilis functional categories that are over-represented in subsets of expressed genes.
KW - Bayesian models
KW - CDNA microarrays
KW - Functional category
KW - Gene location cluster
KW - MCMC
KW - Scan statistics
UR - http://www.scopus.com/inward/record.url?scp=8844270991&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=8844270991&partnerID=8YFLogxK
U2 - 10.1016/j.jmva.2004.02.007
DO - 10.1016/j.jmva.2004.02.007
M3 - Article
AN - SCOPUS:8844270991
VL - 90
SP - 1
EP - 18
JO - Journal of Multivariate Analysis
JF - Journal of Multivariate Analysis
SN - 0047-259X
IS - 1 SPEC. ISS.
ER -