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» Analyzing time series gene expression data
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BMCBI
2010
131views more  BMCBI 2010»
13 years 7 months ago
Prediction of epigenetically regulated genes in breast cancer cell lines
Background: Methylation of CpG islands within the DNA promoter regions is one mechanism that leads to aberrant gene expression in cancer. In particular, the abnormal methylation o...
Leandro A. Loss, Anguraj Sadanandam, Steffen Durin...
BMCBI
2006
119views more  BMCBI 2006»
13 years 7 months ago
Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip stu
Background: The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with know...
Zihua Hu, Gail R. Willsky
BMCBI
2008
98views more  BMCBI 2008»
13 years 7 months ago
Empirical Bayes models for multiple probe type microarrays at the probe level
Background: When analyzing microarray data a primary objective is often to find differentially expressed genes. With empirical Bayes and penalized t-tests the sample variances are...
Magnus Åstrand, Petter Mostad, Mats Rudemo
BMCBI
2005
114views more  BMCBI 2005»
13 years 7 months ago
Signal transduction pathway profiling of individual tumor samples
Background: Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to anal...
Thomas Breslin, Morten Krogh, Carsten Peterson, Ca...
BMCBI
2010
144views more  BMCBI 2010»
13 years 7 months ago
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
Background: Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is gen...
Xin He, Moushumi Sen Sarma, Xu Ling, Brant W. Chee...