PPT-Pathway and network analysis

Functional interpretation of gene lists Bing Zhang Department of Biomedical Informatics Vanderbilt University bingzhangvanderbiltedu Omics studies generate lists of interesting genes. Dorothy Cheung. Introduction. The problem and its . importance. Missing Pieces. Related . works in summary. Methodology. Data set. Network Generation. Network Analysis. Conclusion. Outline. The problem and its importance. Biostat. & . Bioinfo. short course series. Jianying Li. The Road to Pathway Analysis. Adapted from Werner (2008), Current Opinion in Biotech., 19:50-64. Next Gen RNA-Seq. Acknowledgment. QB for kindly organization. Reactome.db. Package. Utah State University – Spring . 2012. STAT . 6570. : Statistical Bioinformatics. Cody Tramp. References. Ligtenberg. . W. 2011. . Reactome.db. : How to use the . reactome.db. Reactome.db. Package. Utah State University – Spring . 2012. STAT . 6570. : Statistical Bioinformatics. Cody Tramp. References. Ligtenberg. . W. 2011. . Reactome.db. : How to use the . reactome.db. pathway . knowledgebase. Connecting . pathways, networks, and . disease. Robin Haw, PhD . Project Manager and Outreach Coordinator. Ontario Institute for Cancer Research. robin.haw@oicr.on.ca. San Diego. March 15, 2016. www.bioinformatics.ca. 2. Module #: Title of Module. Module . 15. More Depth on Pathway and Network Analysis. Robin Haw. High-Throughput Biology: From Sequence to Networks. March 20-26, 2017. Learning Objectives of Module. Steve Jupe. Motivation for Pathway and Network Analysis in Cancer. “. Exclusivity principle. ”. in cancer.. once a gene is mutated in a pathway, the selective growth advantage incurred by a second mutated gene in the same pathway is minimal.. Beyond the Genome 2012. Informatics Workshop, Sep 27, 2012. Josh Stuart, UC Santa . Cruz. “It . is entirely in line with the accidental nature of mutations that . … . the vast . majority [are] . detrimental. Systematic . In . silico. . analysis using public database. Sung Hwan Lee. 1,4. , Baek Gil . Kim. 2,3. , . Ho Kyoung Hwang. 1,4. , Woo . Jung . Lee. 1,4. , Chang . Moo Kang. 1,4**.  . 1. Department . AACR Annual Meeting 2012. Major Symposium: Designing Rational Combination Therapy for Cancer. Josh Stuart, UC Santa Cruz. Apr 3, 2012. Disclosure. SAB for Five3 Genomics. Overview of pathway-guided approach. www.biostat.wisc.edu/bmi776/ . Spring 2021. Daifeng. Wang. daifeng.wang@wisc.edu. These slides, excluding third-party material, are licensed under . CC BY-NC 4.0. by Anthony Gitter, Mark Craven, Colin Dewey and . Steven Hallam | University of British Columbia. SRI International, 2013. Overview. Through the looking glass…. Environmental Pathway/Genome Databases. MetaPathways. Pipeline Development. 2. Metabolism. Ashish Agarwal. Shannon Chen. The University of Texas . at Austin. Rahul . Tikekar. Ririko. Horvath. Larry May . IRS, RAS. Advisory Roles: . Robert . Hanneman. ( UC Riverside), Lillian Mills (UT Austin). Bikalp. . Chamola. (VAF). Shyam Singh (IRMA). Introduction. What do we already know?. Community based collective actions are solutions to ineffective and inequitable delivery of public goods. Processes of such collective actions are democratic...