DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment

Hari Krishna Yalamanchili, Bin Yan, Mulin Jun Li, Jing Qin, Zhongying Zhao, Francis Y L Chin, Junwen Wang

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Motivation: Inferring gene-regulatory networks is very crucial in decoding various complex mechanisms in biological systems. Synthesis of a fully functional transcriptional factor/protein from DNA involves series of reactions, leading to a delay in gene regulation. The complexity increases with the dynamic delay induced by other small molecules involved in gene regulation, and noisy cellular environment. The dynamic delay in gene regulation is quite evident in high-temporal live cell lineage-imaging data. Although a number of gene-network-inference methods are proposed, most of them ignore the associated dynamic time delay.Results: Here, we propose DDGni (dynamic delay gene-network inference), a novel gene-network-inference algorithm based on the gapped local alignment of gene-expression profiles. The local alignment can detect short-term gene regulations, that are usually overlooked by traditional correlation and mutual Information based methods. DDGni uses 'gaps' to handle the dynamic delay and non-uniform sampling frequency in high-temporal data, like live cell imaging data. Our algorithm is evaluated on synthetic and yeast cell cycle data, and Caenorhabditis elegans live cell imaging data against other prominent methods. The area under the curve of our method is significantly higher when compared to other methods on all three datasets.Availability: The program, datasets and supplementary files are available at http://www.jjwanglab.org/DDGni/.Contact: Supplementary Information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)377-383
Number of pages7
JournalBioinformatics
Volume30
Issue number3
DOIs
StatePublished - Feb 1 2014
Externally publishedYes

Fingerprint

Gene Networks
Gene Regulatory Networks
Alignment
Genes
Gene expression
Gene Regulation
Imaging
Imaging techniques
Cell
Artificial Cells
Nonuniform Sampling
Caenorhabditis elegans
Cell Lineage
Gene Expression Profile
Computational Biology
Transcriptome
Gene Regulatory Network
Cell Cycle
Biological systems
Area Under Curve

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

DDGni : Dynamic delay gene-network inference from high-temporal data using gapped local alignment. / Yalamanchili, Hari Krishna; Yan, Bin; Li, Mulin Jun; Qin, Jing; Zhao, Zhongying; Chin, Francis Y L; Wang, Junwen.

In: Bioinformatics, Vol. 30, No. 3, 01.02.2014, p. 377-383.

Research output: Contribution to journalArticle

Yalamanchili, Hari Krishna ; Yan, Bin ; Li, Mulin Jun ; Qin, Jing ; Zhao, Zhongying ; Chin, Francis Y L ; Wang, Junwen. / DDGni : Dynamic delay gene-network inference from high-temporal data using gapped local alignment. In: Bioinformatics. 2014 ; Vol. 30, No. 3. pp. 377-383.
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