GEO—Gene Expression Omnibus

IBGP705

TA: Lee Cooper

February 18, 2009

Today’s lab

• Complete tutorial

• Email answers to questions to TA by 6pm today

Today’s lab

• Accessing GEO

• GEO Datasets

• GEO Profiles

• The “Help” Section

• BRB Array Tools

Preparing and carrying out a microarray experiment

Analysis of microarray data: clustering

Potential problems with microarray

Dealing with microarray problems

• Best answer = normalization

• Selection of normalization method/s

• Software

• Core lab

Today’s lab: GEO

• Various ways to visually examine microarray data to determine special need for normalization/ initial quality of data

• Accessing GEO

• GEO Datasets

• GEO Profiles

• The “Help” Section

• BRB Array Tools

Accessing GEO

GEO Datasets

GEO Datasets (old interface)

GEO Datasets (new interface)

Check distribution (normalization) and experimental design

Clustering (Algorithms and Parameters)

GEO Datasets: Analysis

GEO Profiles

BRB Array Tools

GEO—Gene Expression Omnibus

Documents

Transcript of GEO—Gene Expression Omnibus

Omnibus Rules

GEO (Gene Expression Omnibus)

Gene Expression and Microarrays - GitHub PagesGene Expression Omnibus (GEO) •A GEO sample(GSM*) describes an individual sample, including the experimental conditions in which it

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Research Article Identification of Differentially Expressed …GEO (Gene Expression Omnibus) database (ID: GSE ) [ , ]. In this present study, based on the microarray data of GSE ,

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1 1,2 3 1,2 Author Manuscript NIH Public Access 1,5 …...All data have been deposited into the NCBI Gene Expression Omnibus (GEO) portal under the accession numbers GSE21291 (RNA-seq),

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6. The Gene Expression Omnibus (GEO): A Gene Expression ...

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

Bioinformatics analysis on multiple Gene Expression ......RESEARCH ARTICLE Open Access Bioinformatics analysis on multiple Gene Expression Omnibus datasets of the hepatitis B virus

Omnibus Certification

Home | DNA Methylation Age Calculator - How to upload the ... · Web viewThese DNA methylation data were downloaded from the Gene Expression Omnibus data base (GEO accession GSE38608).

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International Journal of Computational Intelligence and ... · from National Center for Biotechnology and Information Gene Expression Omnibus datasets. The entire datasets contain

Gene expression and in situ protein profiling of candidate ... · nonsmokers were obtained from the NCBI Gene Expression Omnibus (GEO) database [33, 34]. This resulted in a total

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