A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types.
Summary of "A Joint Graphical Model for Inferring Gene Networks Across Multiple Subpopulations and Data Types."
Reconstructing gene networks from gene expression data is a long-standing challenge. In most applications, the observations can be divided into several distinct but related subpopulations and the gene expression measurements can be collected from multiple data types. Most existing methods are designed to estimate a single gene network from a single dataset. These methods may be suboptimal since they do not exploit the similarities and differences among different subpopulations and data types. In this article, we propose a joint graphical model to estimate the multiple gene networks simultaneously. Our model decomposes each subpopulation-specific gene network as a sum of common and unique components and imposes a group lasso penalty on gene networks corresponding to different data types. The gene network variations across subpopulations can be learned automatically by the decompositions of networks, and the similarities and differences among data types can be captured by the group lasso penalty. The simulation studies demonstrate that our method outperforms the state-of-the-art methods. We also apply our method to the cancer genome atlas breast cancer datasets to reconstruct subtype-specific gene networks. Hub nodes in the estimated subnetworks unique to individual cancer subtypes rediscover well-known genes associated with breast cancer subtypes and provide interesting predictions.
Affiliation
Journal Details
This article was published in the following journal.
Name: IEEE transactions on cybernetics
ISSN: 2168-2275
Pages:
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/31794418
- DOI: http://dx.doi.org/10.1109/TCYB.2019.2952711
PubMed Articles
Differential Network Analysis via Weighted Fused Conditional Gaussian Graphical Model.
The development and prognosis of complex diseases usually involve changes in regulatory relationships among biomolecules. Understanding how the regulatory relationships change with genetic alterations...
Graphical Nash Equilibria and Replicator Dynamics on Complex Networks.
Pairwise-interaction graphical games have been widely used in the study and design of strategic interaction in multiagent systems. With regard to this issue, one entitative problem is actually to unde...
Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression.
To reveal how gene regulatory networks change over cancer development, multiple time-varying differential networks between adjacent cancer stages should be estimated simultaneously. Since the network ...
Altered shoulder kinematics using a new model for multiple dislocations-induced Bankart lesions.
Many active individuals undergo multiple dislocations during the course of a season before surgical treatment without considering the implications of each successive injury. Therefore, the purpose of ...
Prediction of gene function and gene regulatory networks is one of the most active topics in bioinformatics. The accumulation of publicly available gene expression data for hundreds of plant species, ...
Clinical Trials
Development of a Musculoskeletal Model of the PIP Joint
The proximal interphalangeal (PIP) joint is the second joint in the finger from the finger tip. The outcome following replacement surgery of this joint is considered unsatisfactory. In ord...
Evaluation of Motion in the Arthritic Wrist Joint
The scaphotrapeziotrapezoid (STT) joint is a dome shaped joint in the radial wrist that is important in transfer of load from the thumb and radial hand to the scaphoid and the radioscaphoi...
Endothelial Cell Gene Networks of CVD
The objective of this study is to identify relevant signature gene networks of cardiovascular disease in endothelial cells derived from circulating endothelial progenitor cells of individu...
Alpha Defensin and 16S rRNA Gene in Diagnosis of PJI
Total joint replacement is considered one of the most successful surgical procedures in the field of orthopedics. Despite this achievement, prosthetic joint infections is still considered ...
The purpose of this research study is to learn more about the stability over multiple recording sessions of brainwave activity during a computerized task that measures different types of a...
Medical and Biotech [MESH] Definitions
Nomograms
Graphical representation of a statistical model containing scales for calculating the prognostic weight of a value for each individual variable. Nomograms are instruments that can be used to predict outcomes using specific clinical parameters. They use ALGORITHMS that incorporate several variables to calculate the predicted probability that a patient will achieve a particular clinical endpoint.
Multifactor Dimensionality Reduction
A statistical tool for detecting and modeling gene-gene interactions. It is a non-parametric and model-free approach.
Models, Statistical
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
Shoulder
Part of the body in humans and primates where the arms connect to the trunk. The shoulder has five joints; ACROMIOCLAVICULAR joint, CORACOCLAVICULAR joint, GLENOHUMERAL joint, scapulathoracic joint, and STERNOCLAVICULAR joint.
Joint Capsule Release
Surgical procedure to relax the JOINT CAPSULE tissues in a joint that has a reduced range of motion due to CONTRACTURE or TISSUE ADHESIONS or joint deformities.
Quick Links
Advanced Search |
Login |
Subscribe |
RSS 
Relevant Topics
Rheumatology
Arthritis
Fibromyalgia
Gout
Lupus
Rheumatic
Rheumatology is the medical specialty concerned with the diagnosis and management of disease involving joints, tendons, muscles, ligaments and associated structures (Oxford Medical Diction...
Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
Gene Expression
The process of gene expression is used by eukaryotes, prokaryotes, and viruses to generate the macromolecular machinery for life. Steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-tran...
BioPortfolio Twitter Channels (200+ Accounts)
LinkedIn