scholarly journals Mapping functional transcription factor networks from gene expression data

2013 ◽  
Vol 23 (8) ◽  
pp. 1319-1328 ◽  
Author(s):  
B. C. Haynes ◽  
E. J. Maier ◽  
M. H. Kramer ◽  
P. I. Wang ◽  
H. Brown ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Gene Expression Data ◽  
Expression Data ◽  
Transcription Factor Networks ◽  
Functional Transcription Factor

CLUSTERING AND RE-CLUSTERING FOR PATTERN DISCOVERY IN GENE EXPRESSION DATA

2005 ◽  
Vol 03 (02) ◽  
pp. 281-301 ◽  
Author(s):  
PATRICK C. H. MA ◽  
KEITH C. C. CHAN ◽  
DAVID K. Y. CHIU
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Gene Expression Data ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Pairwise Distance ◽  
Expression Data ◽  
Promoter Regions ◽  
Factor Binding

The combined interpretation of gene expression data and gene sequences is important for the investigation of the intricate relationships of gene expression at the transcription level. The expression data produced by microarray hybridization experiments can lead to the identification of clusters of co-expressed genes that are likely co-regulated by the same regulatory mechanisms. By analyzing the promoter regions of co-expressed genes, the common regulatory patterns characterized by transcription factor binding sites can be revealed. Many clustering algorithms have been used to uncover inherent clusters in gene expression data. In this paper, based on experiments using simulated and real data, we show that the performance of these algorithms could be further improved. For the clustering of expression data typically characterized by a lot of noise, we propose to use a two-phase clustering algorithm consisting of an initial clustering phase and a second re-clustering phase. The proposed algorithm has several desirable features: (i) it utilizes both local and global information by computing both a "local" pairwise distance between two gene expression profiles in Phase 1 and a "global" probabilistic measure of interestingness of cluster patterns in Phase 2, (ii) it distinguishes between relevant and irrelevant expression values when performing re-clustering, and (iii) it makes explicit the patterns discovered in each cluster for possible interpretations. Experimental results show that the proposed algorithm can be an effective algorithm for discovering clusters in the presence of very noisy data. The patterns that are discovered in each cluster are found to be meaningful and statistically significant, and cannot otherwise be easily discovered. Based on these discovered patterns, genes co-expressed under the same experimental conditions and range of expression levels have been identified and evaluated. When identifying regulatory patterns at the promoter regions of the co-expressed genes, we also discovered well-known transcription factor binding sites in them. These binding sites can provide explanations for the co-expressed patterns.

scholarly journals The Hedgehog transcription factor GLI3 is differentially expressed in the tumors of breast cancer patients treated with trastuzumab.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Monoclonal Antibody ◽  
Transcription Factor ◽  
Gene Expression Data ◽  
Differentially Expressed ◽  
Expression Data ◽  
Breast Cancer Patients ◽  
Extracellular Region ◽  
Binding Event

Trastuzumab, a monoclonal antibody that targets HER2, is utilized for the treatment of breast cancer (1). While the mechanism of action of trastuzumab function in breast cancer is ascribed to trastuzumab binding to the extracellular region of HER2 (2), the transcriptional consequences that follow this binding event are less well understood. We report here, using analysis of published microarray and gene expression data (3, 4), that the transcription factor GLI3 (5) is differentially expressed in the tumors of patients with breast cancer treated with trastuzumab.

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