Modeling Genetic Regulatory Networks using Gene Expression Profiling and State-Space Models

2005 ◽  
pp. 269-293 ◽  
Author(s):  
Claudia Rangel ◽  
John Angus ◽  
Zoubin Ghahramani ◽  
David L. Wild
Keyword(s):  
Gene Expression ◽  
State Space ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Genetic Regulatory Networks ◽  
State Space Models

scholarly journals Modeling T-cell activation using gene expression profiling and state-space models

2004 ◽  
Vol 20 (9) ◽  
pp. 1361-1372 ◽  
Author(s):  
C. Rangel ◽  
J. Angus ◽  
Z. Ghahramani ◽  
M. Lioumi ◽  
E. Sotheran ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
State Space ◽  
Gene Expression Profiling ◽  
T Cell Activation ◽  
Expression Profiling ◽  
Cell Activation ◽  
State Space Models

scholarly journals NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

2019 ◽  
Vol 47 (W1) ◽  
pp. W234-W241 ◽  
Author(s):  
Guangyan Zhou ◽  
Othman Soufan ◽  
Jessica Ewald ◽  
Robert E W Hancock ◽  
Niladri Basu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Visual Analytics ◽  
Regulatory Networks ◽  
Meta Analysis ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Perform Gene Expression ◽  
And Performance

Abstract The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) networks. It was soon updated for gene expression meta-analysis with improved workflow and performance. Over the years, NetworkAnalyst has been continuously updated based on community feedback and technology progresses. Users can now perform gene expression profiling for 17 different species. In addition to generic PPI networks, users can now create cell-type or tissue specific PPI networks, gene regulatory networks, gene co-expression networks as well as networks for toxicogenomics and pharmacogenomics studies. The resulting networks can be customized and explored in 2D, 3D as well as Virtual Reality (VR) space. For meta-analysis, users can now visually compare multiple gene lists through interactive heatmaps, enrichment networks, Venn diagrams or chord diagrams. In addition, users have the option to create their own data analysis projects, which can be saved and resumed at a later time. These new features are released together as NetworkAnalyst 3.0, freely available at https://www.networkanalyst.ca.

Integrating miRNA and gene expression profiling analysis revealed regulatory networks in gastrointestinal stromal tumors

Epigenomics ◽  
2016 ◽  
Vol 8 (10) ◽  
pp. 1347-1366 ◽  
Author(s):  
Maria Abbondanza Pantaleo ◽  
Gloria Ravegnini ◽  
Annalisa Astolfi ◽  
Vittorio Simeon ◽  
Margherita Nannini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Gastrointestinal Stromal Tumors ◽  
Regulatory Networks ◽  
Stromal Tumors ◽  
Profiling Analysis

scholarly journals DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks

2016 ◽  
Vol 12 (10) ◽  
pp. e1005146 ◽  
Author(s):  
Daifeng Wang ◽  
Fei He ◽  
Sergei Maslov ◽  
Mark Gerstein
Keyword(s):  
Gene Expression ◽  
State Space ◽  
Regulatory Networks ◽  
State Space Models

scholarly journals Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0201071 ◽  
Author(s):  
Chayanin Tangsuwansri ◽  
Thanit Saeliw ◽  
Surangrat Thongkorn ◽  
Weerasak Chonchaiya ◽  
Kanya Suphapeetiporn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Autism Spectrum Disorder ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Autism Spectrum ◽  
Spectrum Disorder

Gene Expression Profiling and Regulatory Networks in Single Cells

2012 ◽  
pp. 1-13
Author(s):  
Fumio Arai ◽  
Kentaro Hosokawa ◽  
Yoshiko Matsumoto ◽  
Hirofumi Toyama ◽  
Toshio Suda
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Regulatory Networks ◽  
Single Cells

Custom microarray for glycobiologists: considerations for glycosyltransferase gene expression profiling

2002 ◽  
Vol 69 ◽  
pp. 135-142 ◽  
Author(s):  
Elena M. Comelli ◽  
Margarida Amado ◽  
Steven R. Head ◽  
James C. Paulson
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Affymetrix Genechip ◽  
Microarray Technology ◽  
Gene Arrays ◽  
Glycosyltransferase Gene

The development of microarray technology offers the unprecedented possibility of studying the expression of thousands of genes in one experiment. Its exploitation in the glycobiology field will eventually allow the parallel investigation of the expression of many glycosyltransferases, which will ultimately lead to an understanding of the regulation of glycoconjugate synthesis. While numerous gene arrays are available on the market, e.g. the Affymetrix GeneChip® arrays, glycosyltransferases are not adequately represented, which makes comprehensive surveys of their gene expression difficult. This chapter describes the main issues related to the establishment of a custom glycogenes array.

278: Gene Expression Profiling of Prostatic Epithelial Cells in Two-Dimensional Versus Three-Dimensional Cultures

2007 ◽  
Vol 177 (4S) ◽  
pp. 93-93
Author(s):  
Toshiyuki Tsunoda ◽  
Junichi Inocuchi ◽  
Darren Tyson ◽  
Seiji Naito ◽  
David K. Ornstein
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Three Dimensional ◽  
Two Dimensional

748: Gene Expression Profiling of Renal Medullary Carcinoma

2004 ◽  
Vol 171 (4S) ◽  
pp. 198-199 ◽  
Author(s):  
Ximing J. Yang ◽  
Jun Sugimura ◽  
Maria S. Tretiakova ◽  
Bin T. Teh
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Medullary Carcinoma ◽  
Renal Medullary Carcinoma
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