'Gene sets' presentation slideshows

Agenda

Agenda. Biological databases related to microarray Gene Ontology KEGG Biocarta Reactome MSigDB Pathway enrichment analysis GSEA GSA Ingenuity Pathway Analysis (IPA) Motif finding. 1. Databases. Biological pathways and knowledge are very complex:.

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Mechanistic Models of Cancer Progression in the Space of Pathways

Mechanistic Models of Cancer Progression in the Space of Pathways. Elena Edelman eje2@duke.edu Computational Biology and Bioinformatics Program Institute of Genome Policy and Science Duke University. Outline. I. Biological Background Problems with single gene analysis

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DAVID slides May 2014 version 5. Appendix Edited and expanded subset of slides on DAVID * (NIAID) from the class:.

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Reactome Functional Interaction (FI) Network

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TRI C LUSTER An Effective Algorithm for Mining Coherent Clusters in 3D Microarray Data

TRI C LUSTER An Effective Algorithm for Mining Coherent Clusters in 3D Microarray Data. Mohammed J. Zaki & Lizhuang Zhao Department of Computer Science, Rensselaer Polytechnic Institute (RPI), Troy, NY {zhaol2, zaki}@cs.rpi.edu. Microarray Data.

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Integrating Biology and Statistics: Gene Set Methods

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Keith Skubitz 1 , Princy Francis 2 , Amy Skubitz 1 , Xianghua Luo 1 , and Mef Nilbert 2,3

Use of gene expression to identify heterogeneity of metastatic behavior among high-grade pleomorphic soft tissue sarcomas. Keith Skubitz 1 , Princy Francis 2 , Amy Skubitz 1 , Xianghua Luo 1 , and Mef Nilbert 2,3 1 University of Minnesota, 2 Lund University, 3 Hvidovre Hospital.

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Gene-set analysis

Gene-set analysis. Danielle Posthuma & Christiaan de Leeuw Dept. Complex Trait Genetics, VU University Amsterdam //danielle/2017/PW_dp.ppt. Boulder, TC31, March 8 2017. SNP associations. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. SNP. Gene. Gene.

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MAKER Annotation Process Example of Glossina

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Differential Analysis

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On utility of gene set signatures in gene expression-based class prediction

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Differential Analysis

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Gene Set Enrichment Analysis (GSEA)

Gene Set Enrichment Analysis (GSEA). Gene Set Enrichment. Example: human diabetes. Skeletal muscle biopsies. No single gene was found to be significantly regulated

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Gene Set Enrichment Analysis (GSEA)

Gene Set Enrichment Analysis (GSEA). Gene Set Enrichment. Example: human diabetes. Skeletal muscle biopsies. No single gene was found to be significantly regulated

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Gene Set Enrichment Analysis (GSEA)

Gene Set Enrichment Analysis (GSEA). Gene Set Enrichment. Example: human diabetes. Skeletal muscle biopsies. No single gene was found to be significantly regulated

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Genomic Analysis of Hepatocellular Carcinoma With Active Hepatitis B Virus Replication

Genomic Analysis of Hepatocellular Carcinoma With Active Hepatitis B Virus Replication. Huat Chye Lim, MD, and John Gordan, MD, PhD Divisions of Hospital Medicine and Hematology/Oncology University of California, San Francisco. Introduction. Synopsis.

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Applying Topic Maps to Genome Research

Applying Topic Maps to Genome Research. Torsten Semmler RZPD German Resource Center for Genome Research www.rzpd.de. Background. genes in their biological context proteins encoded by genes act as enzymes in reactions the defined order of such reactions is called a biological pathway

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