Gene Expression Omnibus (GEO)

Slides:

Advertisements

Similar presentations

Support.ebsco.com Nursing Reference Center Tutorial.

Advertisements

Support.ebsco.com Company View Tutorial. Welcome to EBSCOs Company View tutorial, designed to provide users with an overview of how to use the Company.

Jeopardy Objects Navigation Buttons True/False Parts of a Report Vocabulary Q $100 Q $200 Q $300 Q $400 Q $500 Q $100 Q $200 Q $300 Q $400 Q $500 Final.

Welcome to the Tutorial

PubMed and its search options Jan Emmerich, Sonja Jacobi, Kerstin Müller (5th Semester Library Management)

Oncomine Database Lauren Smalls-Mantey Georgia Institute of Technology June 19, 2006 Note: This presentation contains animation.

The National Center for Biotechnology Information (NCBI) a primary resource for molecular biology information Database Resources.

Library Online Catalog Tutorial Pentagon Library Last Updated March 2008.

The Rice Functional Genomics Program of China cDNA microarray database (RIFGP-CDMD) consists of complete datasets, including the probe sequences, microarray.

Working with gene lists: Finding data using GEO & BioMart June 5, 2014.

1 Welcome to the Protein Database Tutorial This tutorial will describe how to navigate the section of Gramene that provides collective information on proteins.

IAEA International Atomic Energy Agency INIS Collection Search: Introduction and main features INIS Training Seminar 7-11 October 2013, Vienna Domenico.

How to use the web for bioinformatics Molecular Technologies Ethan Strauss X 1171

Acquisitions and Serials in 2005 and beyond Georgia Fujikawa Manager, Training Programs.

Lecture 2.21 Retrieving Information: Using Entrez.

Kate Milova MolGen retreat March 24, Microarray experiments: Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Biological Databases Notes adapted from lecture notes of Dr. Larry Hunter at the University of Colorado.

ONCOMINE: A Bioinformatics Infrastructure for Cancer Genomics

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Data Extraction cDNA arrays Affy arrays. Stanford microarray database.

1 Self Service Banner FOAP AND NAVIGATION Fall 2005 Ver 7.1 Presented by the Auburn University Business Office.

NCBI resources III: GEO and expression data analysis Yanbin Yin Fall

Using ArrayExpress. ArrayExpress is an international public repository for well-annotated microarray data, including gene expression, comparative genomic.

Midterm project Course: Statistics in Bioinformatics Date: 指導教授 : 陳光琦學生 : 吳昱賢.

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

An introduction to using the AmiGO Gene Ontology tool.

Introduction The goal of translational bioinformatics is to enable the transformation of increasingly voluminous genomic and biological data into diagnostics.

PubMed/How to Search, Display, Download & (module 4.1)

ArrayExpress and Gene Expression Atlas: Mining Functional Genomics data Gabriella Rustici, PhD Functional Genomics Team EBI-EMBL

Gene expression services: ArrayExpress and the Gene Expression Atlas Contact: Gabriella Rustici, PhD Functional Genomics Team EBI-EMBL

Erice 2008 Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discovery Erice, 29 May - 8 June Peter Rose

IAGAP Access Database A Tutorial. Databases There are several databases available from the IAGAP Project. There are several databases available from the.

Gene Expression Omnibus (GEO)

ArrayExpress and Gene Expression Atlas: Mining Functional Genomics data Gabriella Rustici, PhD Functional Genomics Team EBI-EMBL

Copyright OpenHelix. No use or reproduction without express written consent1.

ArrayExpress and Expression Atlas: Mining Functional Genomics data Gabriella Rustici, PhD Functional Genomics Team EBI-EMBL

1 Welcome to the GrameneMart Tutorial A tool for batch data sequence retrieval 1.Select a Gramene dataset to search against. 2.Add filters to the dataset.

Basic features for portal users. Agenda - Basic features Overview –features and navigation Browsing data –Files and Samples Gene Summary pages Performing.

Part 1 – PubMed Interface, Display options, Saving, Printing, and ing results. Instructions This part of the course is a PowerPoint demonstration.

1 maxdLoad The maxd website: © 2002 Norman Morrison for Manchester Bioinformatics.

Lesson 1: Exploring Access Learning Objectives After studying this lesson, you will be able to: Start Access and identify elements of the application.

Gene expression analysis

Browsing the Genome Using Genome Browsers to Visualize and Mine Data.

Analysis of GEO datasets using GEO2R Parthav Jailwala CCR Collaborative Bioinformatics Resource CCR/NCI/NIH.

Copyright OpenHelix. No use or reproduction without express written consent1.

Mercury – A Service Oriented Web-based system for finding and retrieving Biogeochemical, Ecological and other land- based data National Aeronautics and.

Copyright OpenHelix. No use or reproduction without express written consent1.

Microarray Technology. Introduction Introduction –Microarrays are extremely powerful ways to analyze gene expression. –Using a microarray, it is possible.

SUPPLEMENTAL FIGURES AND TABLES. Supplementary Table 1: List of new and improved features in GSEA-P version 2 Java software. Examples and screenshots.

Primary vs. Secondary Databases Primary databases are repositories of “raw” data. These are also referred to as archival databases. -This is one of the.

Applied Bioinformatics Week 9 Jens Allmer. Theory I Gene Expression Microarray.

Copyright OpenHelix. No use or reproduction without express written consent1.

IAEA International Atomic Energy Agency INIS Collection Search: Introduction and main features The Role of the International Nuclear Information System.

Copyright OpenHelix. No use or reproduction without express written consent1.

Introduction and Applications of Microarray Databases Chen-hsiung Chan Department of Computer Science and Information Engineering National Taiwan University.

Tutorial 8 Gene expression analysis 1. How to interpret an expression matrix Expression data DBs - GEO Clustering –Hierarchical clustering –K-means clustering.

Copyright OpenHelix. No use or reproduction without express written consent1.

HOW TO FIND RESEARCH PROJECT PAPER HOW TO FIND RESEARCH PROJECT PAPER Click here to begin.

Bioinformatics Shared Resource Introduction to Gene Expression Omnibus (GEO) bsrweb.sanfordburnham.org

PubMed Basics Barbara A. Wood, MLIS Calder Library University of Miami Miller School of Medicine.

ArrayExpress Ugis Sarkans EMBL - EBI

1 © 2004 Cisco Systems, Inc. All rights reserved. Session Number Presentation_ID Cisco Technical Support Seminar Using the Cisco Technical Support Website.

Improving gene expression similarity measurement using pathway-based analytic dimension Changwon Keum BMDRC.

MESA A Simple Microarray Data Management Server. General MESA is a prototype web-based database solution for the massive amounts of initial data generated.

GEO (Gene Expression Omnibus) Deepak Sambhara Georgia Institute of Technology 21 June, 2006.

Using ArrayExpress.

Platforms A Platform record describes the list of elements on the array (e.g., cDNAs, oligonucleotide probesets, ORFs, antibodies) or the list.

Gene Expression Omnibus (GEO)

Welcome to the Quantitative Trait Loci (QTL) Tutorial

Presentation transcript:

Gene Expression Omnibus (GEO)

Microarrays in gene expression A typical gene expression analysis experiment: 1. Differential systems – e.g. cancer vs. normal, drug vs. no drug 2. Choose/prepare the microarray 3. Extract total mRNA (transcriptome) 4. Reverse transcription/dye labelling 5. Combine equal amounts 6. Hybridize 7. Scan 8. ANALYSE AND INTERPRET THE RESULTS – this is the tricky part…

Microarrays in gene expression

SPOTS

Hybridization

SCAN

A public repository for the archiving and distribution of gene expression data submitted by the scientific community. Curated, online resource for gene expression data browsing, query, analysis and retrieval. Convenient for deposition of gene expression data, as required by funding agencies and journals. Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository

GEO Architecture Platform (GPL) = the technology used and the features detected. Sample (GSM) = preparation and description of the sample. Series (GSE) defines a set of samples and how they are related. DataSets (GDS) sample data collections assembled by GEO staff. GEO has four kinds of data records

GPL Platform descriptions GSM Raw/processed spot intensities from a single slide/chip GSE Grouping of slide/chip data “a single experiment” GDS Grouping of experiments Curated by NCBI Submitted by Experimentalists Submitted by Manufacturer GEO Architecture

GEO Home Page Simple interface to:  show status  find documentation  query data  browse data

Platform Accession Page Platform details: Description Type Organism Manufacturer Related samples and series NOTE THE TOP BAR (SCOPE)

Sample Accession Page Sample details: Description Type Organism Source Related platforms and series

Sample File Data Table Data table field descriptions Truncated data table from Quick view Total data rows and file size Supplementary raw data file

Series Accession Page Biological sample summary Design summary Publication information Related platforms and samples

DATASET or GENE PROFILE search GEO data can be queried as: Datasets: experiment-centric view using Entrez GEO DataSets Gene profiles: gene-centric view using Entrez GEO Profiles Selecting either takes you to a similar Entrez introduction page

Querying GEO DataSets Start a GEO DataSets search with the Query>DataSets text box This brings up an Entrez GEO DataSets results form

DataSet Search Results

GEO DataSet Record

GEO Gene Profiles

Querying GEO with IDs from Papers A common way to access GEO data is through accessions from papers. Online journals include hyperlinks to the GEO accession page. Or, at the GEO home page enter the accession into the Query>GEO accession text box

GEO Links in PubMed Search Results One option for displaying PubMed search results is GEO DataSet links. When present, the results page is actually from Entrez GEO DataSets.

GEO BLAST