Network & Systems Modeling 29 June 2009 NCSU GO Workshop.

Slides:

Advertisements

Similar presentations

MitoInteractome : Mitochondrial Protein Interactome Database Rohit Reja Korean Bioinformation Center, Daejeon, Korea.

Advertisements

GO-based tools for functional modeling GO Workshop 3-6 August 2010.

Pathways & Networks analysis COST Functional Modeling Workshop April, Helsinki.

Gene Ontology John Pinney

STRING Modeling of biological systems through cross-species data integration.

Separation of Scales. Interpretation of Networks Most publications do not consider this.

Gene expression analysis summary Where are we now?

27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.

Gene Co-expression Network Analysis BMI 730 Kun Huang Department of Biomedical Informatics Ohio State University.

COG and GO tutorial.

Bioinformatics: a Multidisciplinary Challenge Ron Y. Pinter Dept. of Computer Science Technion March 12, 2003.

Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break 14:45 – 15:15Regulatory pathways lecture 15:15 – 15:45Exercise.

ONCOMINE: A Bioinformatics Infrastructure for Cancer Genomics

Biological networks Tutorial 12. Protein-Protein interactions –STRING Protein and genetic interactions –BioGRID Signaling pathways –SPIKE Network visualization.

Systems Biology Biological Sequence Analysis

27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.

Biological networks Construction and Analysis. Recap Gene regulatory networks –Transcription Factors: special proteins that function as “keys” to the.

Modeling Functional Genomics Datasets CVM Lesson 1 13 June 2007Bindu Nanduri.

Computational Biology Networks and Pathways Lecture Slides Week 11.

Introduction to molecular networks Sushmita Roy BMI/CS 576 Nov 6 th, 2014.

Genetics: From Genes to Genomes

Pathway Informatics 6 th July, 2015 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University of.

GO Enrichment analysis COST Functional Modeling Workshop April, Helsinki.

Pathways Database System: An Integrated System For Biological Pathways L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan.

Modeling Functional Genomics Datasets CVM Lessons 4&5 10 July 2007Bindu Nanduri.

Systematic Analysis of Interactome: A New Trend in Bioinformatics KOCSEA Technical Symposium 2010 Young-Rae Cho, Ph.D. Assistant Professor Department of.

341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London

Protein-protein interactions Chapter 12. Stable complex Transient Interaction Transient Signaling Complex Rap1A – cRaf1 Interface 1310 Å 2 Stable complex:

Ch10. Intermolecular Interactions and Biological Pathways

Cytoscape A powerful bioinformatic tool Mathieu Michaud

Review of Ondex Bernice Rogowitz G2P Visualization and Visual Analytics Team March 18, 2010.

PutidaNET :Interactome database service and network analysis of Pseudomonas putida KT2440 (P. putida KT2440) Korean BioInformation Center (KOBIC) Seong-Jin,

Overview  Introduction  Biological network data  Text mining  Gene Ontology  Expression data basics  Expression, text mining, and GO  Modules and.

Hyun Seok Kim, Ph.D. Assistant Professor, Severance Biomedical Research Institute, Yonsei University College of Medicine Lecture 13. Network Analysis MES

Modeling Functional Genomics Datasets CVM Lesson 6 11 July 2007Bindu Nanduri.

Biological Pathways & Networks

Bioinformatics Dr. Víctor Treviño BT4007

1 Bio-Trac 40 (Protein Bioinformatics) October 8, 2009 Zhang-Zhi Hu, M.D. Associate Professor Department of Oncology Department of Biochemistry and Molecular.

EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands 1 François Moreews SIGENAE, INRA, Rennes Cytoscape.

A Method for Protein Functional Flow Configuration and Validation Woo-Hyuk Jang 1 Suk-Hoon Jung 1 Dong-Soo Han 1

GO-based tools for functional modeling TAMU GO Workshop 17 May 2010.

From Functional Genomics to Physiological Model: Using the Gene Ontology Fiona McCarthy, Shane Burgess, Susan Bridges The AgBase Databases, Institute of.

Intel Confidential – Internal Only Co-clustering of biological networks and gene expression data Hanisch et al. This paper appears in: bioinformatics 2002.

Workshop Aims NMSU GO Workshop 20 May Aims of this Workshop  WIIFM? modeling examples background information about GO modeling  Strategies for.

Ontology based analyses methods ++ develop a grammar for making productions using mf, bp, cl: –derive a higher level grammar for next level of productions.

Getting Started: a user’s guide to the GO GO Workshop 3-6 August 2010.

Other biological databases and ontologies. Biological systems Taxonomic data Literature Protein folding and 3D structure Small molecules Pathways and.

Getting Started: a user’s guide to the GO TAMU GO Workshop 17 May 2010.

Computations using pathways and networks Nigam Shah

EB3233 Bioinformatics Introduction to Bioinformatics.

BBN Technologies Copyright 2009 Slide 1 The S*QL Plugin for Cytoscape Visual Analytics on the Web of Linked Data Rusty (Robert J.) Bobrow Jeff Berliner,

Genome Biology and Biotechnology The next frontier: Systems biology Prof. M. Zabeau Department of Plant Systems Biology Flanders Interuniversity Institute.

Introduction to biological molecular networks

341- INTRODUCTION TO BIOINFORMATICS Overview of the Course Material 1.

A database of biological pathways and processes (borrowed from a presentation created by Steve Jupe)

GO based data analysis Iowa State Workshop 11 June 2009.

Getting GO: how to get GO for functional modeling Iowa State Workshop 11 June 2009.

 Signal Transduction transmits signals from outside to the inside of the cell  Integer Linear Programming model is used to unravel STN.

Biological Networks. Can a biologist fix a radio? Lazebnik, Cancer Cell, 2002.

Predicting Protein Function Annotation using Protein- Protein Interaction Networks By Tamar Eldad Advisor: Dr. Yanay Ofran Computational Biology.

High throughput biology data management and data intensive computing drivers George Michaels.

RDF based on Integration of Pathway Database and Gene Ontology SNU OOPSLA LAB DongHyuk Im.

 What is MSA (Multiple Sequence Alignment)? What is it good for? How do I use it?  Software and algorithms The programs How they work? Which to use?

Pathway Informatics 30 th March, 2016 Ansuman Chattopadhyay, PhD Head, Molecular Biology Information Services Health Sciences Library System University.

Lecture 4.31 Protein Pathways and Pathway Databases Shan Sundararaj University of Alberta Edmonton, AB

Gene Annotation & Gene Ontology May 24, Gene lists from RNAseq analysis What do you do with a list of 100s of genes that contain only the following.

CSCI2950-C Lecture 12 Networks

1. SELECTION OF THE KEY GENE SET 2. BIOLOGICAL NETWORK SELECTION

Schedule for the Afternoon

Presentation transcript:

Network & Systems Modeling 29 June 2009 NCSU GO Workshop

GO Enrichment: the structure of the GO allows its to be queried in a hierarchical manner.  use the GO DAG Structure to cluster differentially expressed gene sets  determine which GO terms are statistically over- represented in the set Systems biology: study of complex interactions in biological systems  integrates data from multiple experimental types  develop networks describing interactions within the system GO Enrichment & Systems Biology

GO Enrichment Analysis DAVID: GOStat: EasyGO: AmiGO bin/amigo/term_enrichment (does not use IEA) bin/amigo/term_enrichment Onto-Express & OE2GO GOEAST Comparison of enrichment analysis tools : Nucleic Acids Research, 2009, Vol. 37, No. 1 1–13 (Tool_Comparison_09.pdf)

Database for Annotation, Visualization and Integrated Discovery

Species represented in Onto-Express For uploading your own annotations use OE2GO

Comparison Onto-Express, EasyGO, GOstat and DAVID Test set: 60 randomly selected chicken genes Used AgBase GO annotations as baseline annotations Vandenberg et al (BMC Bioinformatics, in review)

Systems Biology Models interactions of components in the system (dynamic). Nanduri B. and McCarthy F.M. (2007). "AgBase - a tool for systems biology in agricultural species." CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 2(078):13-26.

Systems Biology Workflow Nanduri & McCarthy CAB reviews, 2008

Pathways & Networks A network is a collection of interactions Pathways are a subset of networks Network of interacting proteins that carry out biological functions such as metabolism and signal transduction All pathways are networks of interactions NOT ALL NETWORKS ARE PATHWAYS

Biological Networks Networks often represented as graphs Nodes represent proteins or genes that code for proteins Edges represent the functional links between nodes (ex regulation) Small changes in graph’s topology/architecture can result in the emergence of novel properties

Nature 411, 2001, H. Jeong, et al Yeast Protein-Protein Interaction Map

Types of interactions protein (enzyme) – metabolite (ligand) metabolic pathways protein – protein cell signaling pathways, protein complexes protein – gene genetic networks

PLoS Computational Biology March 2007, Volume 3 e42 Database/URL/FTP DIP BIND MPact/MIPS STRING MINT IntAct BioGRID HPRD ProtCom 3did, Interprets Pibase, Modbase CBM ftp://ftp.ncbi.nlm.nih.gov/pub/cbmftp://ftp.ncbi.nlm.nih.gov/pub/cbm SCOPPI iPfam InterDom DIMA Prolinks Predictomehttp://predictome.bu.edu/

KEGG BioCyc Reactome GenMAPP BioCarta Pathguide – the pathway resource list Some resources

I have interactions what next? Evaluate the quality of interactions i.e. type of method used for identification….what exactly are these methods? Visualize these interactions as a network and analyze.