• Corpus ID: 245836877

Automatically layout and visualize the biological pathway map with spectral graph theory

  title={Automatically layout and visualize the biological pathway map with spectral graph theory},
  author={Li Xiao and Yanfei Wang and Shiying Li and Lingxi Chen and Shuaicheng Li},
The pathway is a biological term that refers to a series of interactions between molecules in a cell that cause a certain product or a change in the cell [NIH20]. Pathway analysis is a powerful method for gene expression analysis [Cir17]. Through pathway maps, the lists of genes that are differently expressed across the given phenotypes are translated into various biological phenomena [Nguyen2019]. Visualizing a pathway map manually is a common practice nowadays because of the limitations of… 

A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants

The visualization options of the tools that were identified by a literature review are described in order to provide insight for improvements in this developing field, and the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data is reported.

A General Introduction To Graph Visualization Techniques

This survey aims to provide an introduction on graph visualization techniques helping the reader to gain a first insight into the most fundamental techniques.

Introduction to spectral graph theory

We write M ∈ Rn×n to denote that M is an n×n matrix with real elements, and v ∈ Rn to denote that v is a vector of length n. Vectors are usually taken to be column vectors unless otherwise specified.

Singular Value Decomposition

  • C. Tomasi
  • Computer Science
    Encyclopedia of Social Network Analysis and Mining
  • 2014
Mainly this thesis focus on a specific matrix factorization called Singular Value Decomposition (SVD) used to solve complicated inverses and identifying systems in signal processing.

Singular Value Decomposition (SVD) tutorial

  • Sept.
  • 2002

Biological Pathways Fact Sheet

  • Aug.
  • 2020

PATHWAY: map04115

  • June
  • 2020