Literature DB >> 25519431

Detecting differential patterns of interaction in molecular pathways.

Masanao Yajima1, Donatello Telesca2, Yuan Ji3, Peter Müller4.   

Abstract

We consider statistical inference for potentially heterogeneous patterns of association characterizing the expression of bio-molecular pathways across different biologic conditions. We discuss a modeling approach based on Gaussian-directed acyclic graphs and provide computational and methodological details needed for posterior inference. Our application finds motivation in reverse phase protein array data from a study on acute myeloid leukemia, where interest centers on contrasting refractory versus relapsed patients. We illustrate the proposed method through both synthetic and case study data.
© The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Entities:  

Keywords:  Conditional independence; Directed acyclic graphs; Gaussian Markov models; Reversible jumps MCMC

Mesh:

Year:  2014        PMID: 25519431      PMCID: PMC4441103          DOI: 10.1093/biostatistics/kxu054

Source DB:  PubMed          Journal:  Biostatistics        ISSN: 1465-4644            Impact factor:   5.899


  9 in total

1.  Detecting differential gene expression with a semiparametric hierarchical mixture method.

Authors:  Michael A Newton; Amine Noueiry; Deepayan Sarkar; Paul Ahlquist
Journal:  Biostatistics       Date:  2004-04       Impact factor: 5.899

2.  Sparse inverse covariance estimation with the graphical lasso.

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3.  MODELING DEPENDENT GENE EXPRESSION.

Authors:  Donatello Telesca; Peter Müller; Giovanni Parmigiani; Ralph S Freedman
Journal:  Ann Stat       Date:  2012-06-11       Impact factor: 4.028

4.  Joint estimation of multiple graphical models.

Authors:  Jian Guo; Elizaveta Levina; George Michailidis; Ji Zhu
Journal:  Biometrika       Date:  2011-02-09       Impact factor: 2.445

5.  Sparse covariance estimation in heterogeneous samples.

Authors:  Abel Rodríguez; Alex Lenkoski; Adrian Dobra
Journal:  Electron J Stat       Date:  2011-09-15       Impact factor: 1.125

6.  Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells.

Authors:  Raoul Tibes; Yihua Qiu; Yiling Lu; Bryan Hennessy; Michael Andreeff; Gordon B Mills; Steven M Kornblau
Journal:  Mol Cancer Ther       Date:  2006-10       Impact factor: 6.261

7.  Simultaneous activation of multiple signal transduction pathways confers poor prognosis in acute myelogenous leukemia.

Authors:  Steven M Kornblau; Matthew Womble; Yi Hua Qiu; C Ellen Jackson; Wenjing Chen; Marina Konopleva; Elihu H Estey; Michael Andreeff
Journal:  Blood       Date:  2006-06-08       Impact factor: 22.113

8.  The joint graphical lasso for inverse covariance estimation across multiple classes.

Authors:  Patrick Danaher; Pei Wang; Daniela M Witten
Journal:  J R Stat Soc Series B Stat Methodol       Date:  2014-03       Impact factor: 4.488

9.  Modeling Protein Expression and Protein Signaling Pathways.

Authors:  Donatello Telesca; Peter Müller; Steven M Kornblau; Marc A Suchard; Yuan Ji
Journal:  J Am Stat Assoc       Date:  2011       Impact factor: 5.033

  9 in total
  4 in total

1.  A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD.

Authors:  Elin Shaddox; Francesco C Stingo; Christine B Peterson; Sean Jacobson; Charmion Cruickshank-Quinn; Katerina Kechris; Russell Bowler; Marina Vannucci
Journal:  Stat Biosci       Date:  2016-10-28

Review 2.  Bayesian graphical models for modern biological applications.

Authors:  Yang Ni; Veerabhadran Baladandayuthapani; Marina Vannucci; Francesco C Stingo
Journal:  Stat Methods Appt       Date:  2021-05-27

3.  A random covariance model for bi-level graphical modeling with application to resting-state fMRI data.

Authors:  Lin Zhang; Andrew DiLernia; Karina Quevedo; Jazmin Camchong; Kelvin Lim; Wei Pan
Journal:  Biometrics       Date:  2020-09-11       Impact factor: 2.571

4.  Bayesian graphical models for computational network biology.

Authors:  Yang Ni; Peter Müller; Lin Wei; Yuan Ji
Journal:  BMC Bioinformatics       Date:  2018-03-21       Impact factor: 3.169

  4 in total

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