Literature DB >> 26991351

Circular piecewise regression with applications to cell-cycle data.

Cristina Rueda1, Miguel A Fernández1, Sandra Barragán1, Kanti V Mardia2, Shyamal D Peddada3.   

Abstract

Applications of circular regression models appear in many different fields such as evolutionary psychology, motor behavior, biology, and, in particular, in the analysis of gene expressions in oscillatory systems. Specifically, for the gene expression problem, a researcher may be interested in modeling the relationship among the phases of cell-cycle genes in two species with differing periods. This challenging problem reduces to the problem of constructing a piecewise circular regression model and, with this objective in mind, we propose a flexible circular regression model which allows different parameter values depending on sectors along the circle. We give a detailed interpretation of the parameters in the model and provide maximum likelihood estimators. We also provide a model selection procedure based on the concept of generalized degrees of freedom. The model is then applied to the analysis of two different cell-cycle data sets and through these examples we highlight the power of our new methodology.
© 2016, The International Biometric Society.

Entities:  

Keywords:  Change points; Circular data; Circular-circular regression; Gene expression; Generalized AIC; Von Mises distribution

Mesh:

Year:  2016        PMID: 26991351      PMCID: PMC5026859          DOI: 10.1111/biom.12512

Source DB:  PubMed          Journal:  Biometrics        ISSN: 0006-341X            Impact factor:   2.571


  12 in total

1.  A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions.

Authors:  Delong Liu; Clarice R Weinberg; Shyamal D Peddada
Journal:  Bioinformatics       Date:  2004-04-15       Impact factor: 6.937

2.  Efficient change point detection for genomic sequences of continuous measurements.

Authors:  Vito M R Muggeo; Giada Adelfio
Journal:  Bioinformatics       Date:  2010-11-18       Impact factor: 6.937

3.  The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle.

Authors:  Tata Pramila; Wei Wu; Shawna Miles; William Stafford Noble; Linda L Breeden
Journal:  Genes Dev       Date:  2006-08-15       Impact factor: 11.361

Review 4.  The circadian clock and pathology of the ageing brain.

Authors:  Anna A Kondratova; Roman V Kondratov
Journal:  Nat Rev Neurosci       Date:  2012-03-07       Impact factor: 34.870

5.  Generalized Degrees of Freedom and Adaptive Model Selection in Linear Mixed-Effects Models.

Authors:  Bo Zhang; Xiaotong Shen; Sunni L Mumford
Journal:  Comput Stat Data Anal       Date:  2012-03-01       Impact factor: 1.681

6.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors:  P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal:  Mol Biol Cell       Date:  1998-12       Impact factor: 4.138

7.  Estimation of Parameters Subject to Order Restrictions on a Circle With Application to Estimation of Phase Angles of Cell Cycle Genes.

Authors:  Cristina Rueda; Miguel A Fernández; Shyamal Das Peddada
Journal:  J Am Stat Assoc       Date:  2009-03-01       Impact factor: 5.033

8.  Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species.

Authors:  Miguel A Fernández; Cristina Rueda; Shyamal D Peddada
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

9.  Exaggerated trait allometry, compensation and trade-offs in the New Zealand giraffe weevil (Lasiorhynchus barbicornis).

Authors:  Christina J Painting; Gregory I Holwell
Journal:  PLoS One       Date:  2013-11-27       Impact factor: 3.240

10.  Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes.

Authors:  Alberto Santos; Rasmus Wernersson; Lars Juhl Jensen
Journal:  Nucleic Acids Res       Date:  2014-11-05       Impact factor: 19.160

View more
  1 in total

1.  Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data.

Authors:  Nicholas L Panchy; John P Lloyd; Shin-Han Shiu
Journal:  BMC Genomics       Date:  2020-02-13       Impact factor: 3.969

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.