Discussion Forum

• Please visit UCSF EGAN Discussions to post comments/questions and search archived discussions.

Tutorials

• EGAN Basic Ideas and Terminology (version 1.4, PPT) - July 2010
• EGAN Basic Ideas and Terminology (version 1.4, PDF) - July 2010
• EGAN tutorial: A basic use-case (version 1.3, PPT) - July 2010
• EGAN tutorial: A basic use-case (version 1.3, PDF) - July 2010

• EGAN tutorial: Interface basics (version 1.1, PPT) - October 2009 by Jesse Paquette
• EGAN tutorial: Loading network data (version 1.1, PPT) - October 2009 by Jesse Paquette
• EGAN tutorial: Loading experiment results (version 1.1, PPT) - October 2009 by Jesse Paquette

Presentations

• Divining Systems Biology Knowledge from High-throughput Experiments Using EGAN (PPT) - July 2010
• Divining Systems Biology Knowledge from High-throughput Experiments Using EGAN (PDF) - July 2010
• Exploratory Gene Association Networks (PPT) - October 2009
• 5 Slides About EGAN (PPT) - October 2009

Publications about EGAN

• Paquette and Tokuyasu, Hypergraph visualization and enrichment statistics: how the EGAN paradigm facilitates organic discovery from Big Data. Proc. SPIE 7865, 78650E (2011).

  Copyright 2009 Society of Photo-Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic electronic or print reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.

• Paquette and Tokuyasu. EGAN: Exploratory Gene Association Networks. Bioinformatics (2010) 26(2):285-286.

Publications using EGAN

• Martin TM, et al. Network analysis of endogenous gene expression profiles after PEI-mediated DNA delivery. J Gene Med. 2013.
• Mak IW, et al. Parathyroid hormone-related protein (PTHrP) modulates adhesion, migration and invasion in bone tumor cells. Bone 2013 Mar 2.
• Daschkey S, et al. MicroRNAs Distinguish Cytogenetic Subgroups in Pediatric AML and Contribute to Complex Regulatory Networks in AML-Relevant Pathways. PLoS One 2013 Feb 2.
• Bansal A, et al. Discovery and Validation of Barrett's Esophagus MicroRNA Transcriptome by Next Generation Sequencing. PLoS One 2013 Jan 23.
• Zhen Li, et al. Expression profiles of microRNAs from lactating and non-lactating bovine mammary glands and identification of miRNA related to lactation. BMC Genomics 2012 Dec 27.
• Wildenhain S, et al. Homeobox protein HB9 binds to the prostaglandin E receptor 2 promoter and inhibits intracellular cAMP mobilization in leukemic cells. J Biol Chem. 2012 Oct 8.
• Parker R, et al. Correlation of proteome-wide changes with social immunity behaviors provides insight into resistance to the parasitic mite, Varroa destructor, in the honey bee (Apis mellifera). Genome Biol. 2012 Sep 28.
• Beyer M, et al. High-Resolution Transcriptome of Human Macrophages. PLoS One. 2012 Sep 21.
• Gysin S, et al. Analysis of mRNA Expression Profiles After MEK1/2 Inhibition Reveals Pathways Involved in Drug Sensitivity. Mol Cancer Res. 2012 Jul 25.
• Gunther J, et al. Catecholamine-related gene expression in blood correlates with tic severity in tourette syndrome. Psychiatry Res. 2012 May 28.
• Guo W, et al. RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nat Med. 2012 May 18.
• Mak IWY, et al. Transcriptomic & proteomic analyses in bone tumor cells: Deciphering parathyroid hormone-related protein (PTHrP) regulation of the cell cycle and apoptosis. J Bone Miner Res. 2012 Apr 16.
• De Lay M, et al. Microarray analysis verifies two distinct phenotypes of glioblastomas resistant to anti-angiogenic therapy. Clin Cancer Res. 2012 Apr 3.
• Chen H, et al. hnRNP Q regulates Cdc42-mediated neuronal morphogenesis. Mol and Cell Biology. 2012 Apr 3.
• Cooke J, et al. Mucosal genome-wide methylation changes in inflammatory bowel disease. Inflamm Bowel Dis. 2012 Mar 14.
• Liu DZ, et al. Integrated analysis of mRNA and microRNA expression in mature neurons, neural progenitor cells and neuroblastoma cells. Gene. 2012 Mar 10.
• Moulos P, et al. Unifying the integration, analysis and interpretation of multi-omic datasets: exploration of the disease networks of Obstructive Nephropathy in children. Conf Proc IEEE Eng Med Biol Soc. 2011 Dec 1.
• Bhattacharya A, et al. Two Distinct Routes to Oral Cancer Differing in Genome Instability and Risk for Cervical Node Metastasis. Clin Cancer Res. 2011 Nov 8.
• Wu J, et al. Analysis of microRNA expression profiling identifies miR-155 and miR-155* as potential diagnostic markers for active tuberculosis: a preliminary study. Hum Immunol. 2011 Oct 14.
• Maslanik T, et al. The impact of acute-stressor exposure on splenic innate immunity: A gene expression analysis. Brain Behav Immun. 2011 Aug 27.
• Tian Y, et al. GABA- and acetylcholine-related gene expression in blood correlate with tic severity and microarray evidence for alternative splicing in Tourette syndrome: A pilot study. Brain Research 2011 Mar 24.
• Lee IH, et al. A filter-based feature selection approach for identifying potential biomarkers for lung cancer. Journal of Clinical Bioinformatics 2011 Mar 21.
• Wolf D, et al. From the Lab to the Clinic: Gene-Expression Profiles That Are Associated with Mek-Inhibitor Sensitivity In Vitro Are Coordinately Co-Expressed in Breast Cancer Biopsy Samples from the I-SPY Trial. Cancer Research 2009, 69 (Meeting Abstract Supplement), 2042.

Reviews referencing EGAN

• Askland K, et al. Ion channels and schizophrenia: a gene set-based analytic approach to GWAS data for biological hypothesis testing. Hum Genet. 2012 Mar.
• Kilian J, et al. Prerequisites, performance and profits of transcriptional profiling the abiotic stress response. Biochim Biophys Acta. 2012 Feb.
• Sanz-Pamplona R, et al. Tools for protein-protein interaction network analysis in cancer research.. Clin Transl Oncol. 2012 Jan 14.