title: DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The program, datasets and supplementary files are available at http://www.jjwanglab.org/DDGni/.
authors.affiliation: Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Department of Biology, Hong Kong Baptist University, Kowloon, Department of Computer Science, Faculty of Engineering and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
authors.forename: Hari Krishna
authors.initials: HK
authors.lastname: Yalamanchili
authors.forename: Bin
authors.initials: B
authors.lastname: Yan
authors.forename: Mulin Jun
authors.initials: MJ
authors.lastname: Li
authors.forename: Jing
authors.initials: J
authors.lastname: Qin
authors.forename: Zhongying
authors.initials: Z
authors.lastname: Zhao
authors.forename: Francis Y L
authors.initials: FY
authors.lastname: Chin
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D014157:Transcription Factors / Q000378:metabolism; D015003:Yeasts / Q000235:genetics / Q000378:metabolism
chemical_list: D014157:Transcription Factors