Welcome to the q-bio Summer School and Conference!

Network analysis and gene-list enrichment analysis in systems biology

From Q-bio

Avi Ma’ayan, PhD

Assistant Professor

Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York, Experimental Therapeutics Institute, Mount Sinai School of Medicine, Icahn Medical Institute 1425 Madison Ave., New York NY 10029

avi.maayan@mssm.edu

Abstract

The workshop will be divided into three separate 50 minutes lectures introducing applications of graph theory and network analysis as well as gene list enrichment analysis in systems biology. The first lecture will cover the description of different types of intracellular networks, methods to construct biological networks, and different types of graphs used to represent regulatory intracellular networks. The second lecture will survey milestones and key concepts in network analysis introducing topological measures, random networks, growing network models, and topological observations from molecular biological systems abstracted to networks. The last lecture will discuss methods to analyze lists of genes from experimental data in the context of prior knowledge networks and gene list libraries to make predictions for functional experimental validation. Specific instructions for using the tools ChEA, GATE, Lists2Networks, KEA, and Genes2Networks will be provided.

  1. Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, and Ma’ayan A. ChEA: Transcription Factor Regulation Inferred from Integrating Genome-Wide ChIP-X Experiments. Bioinformatics, 26, 2438-44 (2010) PMID: 20709693 http://amp.pharm.mssm.edu/lib/chea.jsp
  2. Macarthur BD, Lachmann A, Lemischka IR, Ma’ayan A. GATE: Software for the Analysis and Visualization of High-Dimensional Time-series Expression Data. Bioinformatics. 26, 143-144 (2010) PMID: 19892805 http://amp.pharm.mssm.edu/maayan-lab/gate.htm
  3. Lachmann A, Ma’ayan A. Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics 11, 87 (2010) PMID: 20152038 http://www.lists2networks.org
  4. Lachmann A, Ma’ayan A. KEA: Kinase Enrichment Analysis. Bioinformatics 25, 684-6 (2009) PMID: 19176546 http://amp.pharm.mssm.edu/lib/kea.jsp
  5. Berger SI, Posner JM, Ma’ayan A. Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks. BMC Bioinformatics 8, 372 (2007) PMID: 17916244 http://actin.pharm.mssm.edu/genes2networks
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