A Statistical Test for Differential Network Analysis Based on Inference of Gaussian Graphical Model.

08:00 EDT 26th July 2019 | BioPortfolio

Summary of "A Statistical Test for Differential Network Analysis Based on Inference of Gaussian Graphical Model."

Differential network analysis investigates how the network of connected genes changes from one condition to another and has become a prevalent tool to provide a deeper and more comprehensive understanding of the molecular etiology of complex diseases. Based on the asymptotically normal estimation of large Gaussian graphical model (GGM) in the high-dimensional setting, we developed a computationally efficient test for differential network analysis through testing the equality of two precision matrices, which summarize the conditional dependence network structures of the genes. Additionally, we applied a multiple testing procedure to infer the differential network structure with false discovery rate (FDR) control. Through extensive simulation studies with different combinations of parameters including sample size, number of vertices, level of heterogeneity and graph structure, we demonstrated that our method performed much better than the current available methods in terms of accuracy and computational time. In real data analysis on lung adenocarcinoma, we revealed a differential network with 3503 nodes and 2550 edges, which consisted of 50 clusters with an FDR threshold at 0.05. Many of the top gene pairs in the differential network have been reported relevant to human cancers. Our method represents a powerful tool of network analysis for high-dimensional biological data.


Journal Details

This article was published in the following journal.

Name: Scientific reports
ISSN: 2045-2322
Pages: 10863


DeepDyve research library

PubMed Articles [39148 Associated PubMed Articles listed on BioPortfolio]

Direct interaction network and differential network inference from compositional data via lasso penalized D-trace loss.

The development of high-throughput sequencing technologies for 16S rRNA gene profiling provides higher quality compositional data for microbe communities. Inferring the direct interaction network unde...

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...

A unified method for improved inference in random effects meta-analysis.

Random effects meta-analyses have been widely applied in evidence synthesis for various types of medical studies. However, standard inference methods (e.g. restricted maximum likelihood estimation) us...

Proteomic investigation of intra-tumor heterogeneity using network-based contextualization - A case study on prostate cancer.

Cancer is a heterogeneous disease, confounding the identification of relevant markers and drug targets. Network-based analysis is robust against noise, potentially offering a promising approach toward...

Identification of differential risk hotspots for collision and vehicle type in a directed linear network.

Traffic accidents can take place in very different ways and involve a substantially distinct number and types of vehicles. Thus, it is of interest to know which parts of a road structure present an ov...

Clinical Trials [11735 Associated Clinical Trials listed on BioPortfolio]

Model-Free Time Curves for Longitudinal Data Analysis

To enhance statistical methods for epidemiological studies by extending the Disturbed Highest Derivative Polynomial (DHDP) to models for binary-logistic and Poisson data and by including r...

Establishing the Language Network With Independent Component Analysis of Resting State MRI

Proceed to an analysis of sensitivity and specificity results of the fMRI language network obtained in two ways: by providing a conventional language test and independent component analysi...

Knowledge Accessibility and Availability in Forming Knowledge-to-Text Inferences Among Middle Grade Readers

Recent adolescent-based research shows that inference making improves across grades 6-12, uniquely accounts for variance in sentence- and passage-level comprehension, and that individual d...

Differential Clinical and Serologic Response in Psoriasis and Psoriatic Arthritis to Drug Treatment

Psoriasis is a multifactorial cutaneous disorders which affects about 100000 patients in Taiwan. Psoriatic arthritis is also present in about 20~30 percents. Many drugs have been shown to ...

Proteomics for Identification of Hyperoxia-induced Changes in Protein Expression

Aim of the present study is to investigate the influence of hyperoxia on the protein expression using the differential analysis of protein expression in tissues (proteomics). In the study,...

Medical and Biotech [MESH] Definitions

Meta-analysis of randomized trials in which estimates of comparative treatment effects are visualized and interpreted from a network of interventions that may or may not have been evaluated directly against each other. Common considerations in network meta-analysis include conceptual and statistical heterogeneity and incoherence.

A distribution in which a variable is distributed like the sum of the squares of any given independent random variable, each of which has a normal distribution with mean of zero and variance of one. The chi-square test is a statistical test based on comparison of a test statistic to a chi-square distribution. The oldest of these tests are used to detect whether two or more population distributions differ from one another.

Differential thermal analysis in which the sample compartment of the apparatus is a differential calorimeter, allowing an exact measure of the heat of transition independent of the specific heat, thermal conductivity, and other variables of the sample.

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.

The use of statistical methods in the analysis of a body of literature to reveal the historical development of subject fields and patterns of authorship, publication, and use. Formerly called statistical bibliography. (from The ALA Glossary of Library and Information Science, 1983)

Quick Search

DeepDyve research library

Relevant Topics

Pulmonary relating to or associated with the lungs eg Asthma, chronic bronchitis, emphysema, COPD, Cystic Fibrosis, Influenza,  Lung Cancer, Pneumonia, Pulmonary Arterial Hypertension, Sleep Disorders etc Follow and track Lung Cancer News ...

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...

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...

Searches Linking to this Article