Identifying regulatory networks by combinatorial analysis of promoter elements
Several computational methods based on microarray data are currently used to study
genome-wide transcriptional regulation. Few studies, however, address the combinatorial …
genome-wide transcriptional regulation. Few studies, however, address the combinatorial …
Systematic determination of genetic network architecture
Technologies to measure whole-genome mRNA abundances 1, 2, 3 and methods to
organize and display such data 4, 5, 6, 7, 8, 9, 10 are emerging as valuable tools for systems …
organize and display such data 4, 5, 6, 7, 8, 9, 10 are emerging as valuable tools for systems …
[PDF][PDF] Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
The combination of genome-wide expression patterns and full genome sequences offers a
great opportunity to further our understanding of the mechanisms and logic of transcriptional …
great opportunity to further our understanding of the mechanisms and logic of transcriptional …
[HTML][HTML] Identifying combinatorial regulation of transcription factors and binding motifs
Background Combinatorial interaction of transcription factors (TFs) is important for gene
regulation. Although various genomic datasets are relevant to this issue, each dataset …
regulation. Although various genomic datasets are relevant to this issue, each dataset …
Identification of regulatory elements using a feature selection method
Motivation: Many methods have been described to identify regulatory motifs in the
transcription control regions of genes that exhibit similar patterns of gene expression across …
transcription control regions of genes that exhibit similar patterns of gene expression across …
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
A major focus of genome research has been to decipher the cis-regulatory code that
governs complex transcriptional regulation. We report a computational approach for …
governs complex transcriptional regulation. We report a computational approach for …
Functional genomics as applied to mapping transcription regulatory networks
N Banerjee, MQ Zhang - Current opinion in microbiology, 2002 - Elsevier
The sequencing of the human genome and the entire genomes of many model organisms
has resulted in the identification of many genes. Many large-scale experiments for …
has resulted in the identification of many genes. Many large-scale experiments for …
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a
limited number of studies have characterized this aspect on a whole-genome level. We have …
limited number of studies have characterized this aspect on a whole-genome level. We have …
Genetic reconstruction of a functional transcriptional regulatory network
Z Hu, PJ Killion, VR Iyer - Nature genetics, 2007 - nature.com
Although global analyses of transcription factor binding provide one view of potential
transcriptional regulatory networks,, regulation also occurs at levels distinct from …
transcriptional regulatory networks,, regulation also occurs at levels distinct from …
Regulatory element detection using correlation with expression
HJ Bussemaker, H Li, ED Siggia - Nature genetics, 2001 - nature.com
We present here a new computational method for discovering cis-regulatory elements that
circumvents the need to cluster genes based on their expression profiles. Based on a model …
circumvents the need to cluster genes based on their expression profiles. Based on a model …