Model-based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone

Andy B. Chen, Kazunori Hamamura, Guohua Wang, Weirong Xing, Subburaman Mohan, Hiroki Yokota, Yunlong Liu

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Understanding the regulatory mechanism that controls the alteration of global gene expression patterns continues to be a challenging task in computational biology. We previously developed an ant algorithm, a biologically-inspired computational technique for microarray data, and predicted putative transcription-factor binding motifs (TFBMs) through mimicking interactive behaviors of natural ants. Here we extended the algorithm into a set of web-based software, Ant Modeler, and applied it to investigate the transcriptional mechanism underlying bone formation. Mechanical loading and administration of bone morphogenic proteins (BMPs) are two known treatments to strengthen bone. We addressed a question: Is there any TFBM that stimulates both "anabolic responses of mechanical loading" and "BMP-mediated osteogenic signaling"? Although there is no significant overlap among genes in the two responses, a comparative model-based analysis suggests that the two independent osteogenic processes employ common TFBMs, such as a stress responsive element and a motif for peroxisome proliferator-activated receptor (PPAR). The post-modeling in vitro analysis using mouse osteoblast cells supported involvements of the predicted TFBMs such as PPAR, Ikaros 3, and LMO2 in response to mechanical loading. Taken together, the results would be useful to derive a set of testable hypotheses and examine the role of specific regulators in complex transcriptional control of bone formation.

Original languageEnglish
Pages (from-to)158-165
Number of pages8
JournalGenomics, Proteomics and Bioinformatics
Volume5
Issue number3-4
DOIs
StatePublished - Mar 2007

Fingerprint

Transcription factors
Transcription Factor
Bone
Ants
Transcription Factors
Model-based
Bone and Bones
Peroxisome Proliferator-Activated Receptors
Prediction
Osteogenesis
Receptor
Ant Algorithm
Proteins
Protein
Computational Biology
Osteoblasts
Common factor
Computational Techniques
Microarrays
Microarray Data

Keywords

  • ant algorithm
  • bone morphogenic protein
  • mechanical loading
  • microarray
  • transcription-factor binding motif

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Molecular Biology

Cite this

Model-based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone. / Chen, Andy B.; Hamamura, Kazunori; Wang, Guohua; Xing, Weirong; Mohan, Subburaman; Yokota, Hiroki; Liu, Yunlong.

In: Genomics, Proteomics and Bioinformatics, Vol. 5, No. 3-4, 03.2007, p. 158-165.

Research output: Contribution to journalArticle

Chen, Andy B. ; Hamamura, Kazunori ; Wang, Guohua ; Xing, Weirong ; Mohan, Subburaman ; Yokota, Hiroki ; Liu, Yunlong. / Model-based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone. In: Genomics, Proteomics and Bioinformatics. 2007 ; Vol. 5, No. 3-4. pp. 158-165.
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