Expression analysis platforms
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Expression Analysis Platforms. Friday's Class. 4:00-5:00 140 SH Work in the Laboratory of Signal Processing of the EESC / USP revolves around modeling biological systems. Currently, our lines of research are: diagnosing speech pathology, ultrasound signal processing, and

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Expression Analysis Platforms

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Expression analysis platforms

Expression Analysis Platforms

Friday s class

Friday's Class


140 SH

Work in the Laboratory of Signal Processing of the EESC / USP revolves around modeling biological systems. Currently, our lines of research are: diagnosing speech pathology, ultrasound signal processing, and

bioinformatics (particularly for phylogeny). All lines of research involve clustering algorithms.

The work on clustering seeks to determine the natural number of groups and to validate the clustering algorithms. Several techniques have been applied to genomic databases, among them are: resampling, analysis of missing data, using assumptions about a priori information. Now we are focusing on probabilistic models and validation of structural models. The studies are conducted on information generated by electrophoresis of species with agricultural applications, and are provided by Embrapa ( Now we are working with 3 doctoral students focusing on the area of binder phenotypic and genotypic information for varieties of corn.

Other courses

Other Courses

  • Intro to Informatics (in CS)

  • Intro to Bioinformatics (51:121)

    • provides a first exposure to some available computational techniques and resources

    • however, the emphasis is on utilization

  • In this course (51:123) -- I try to emphasize tools and techniques that you would use to go about developing your own computational resources (software, systems, tools, etc).

  • Computational Methods in Molecular Biology (51:122 -- Casavant, Bair)

    • advanced topics

Bioinformatics certificate

Bioinformatics Certificate

  • Offered by the Graduate College (MS/PhD)


Final exam

Final Exam

  • 25 questions – mostly short answer/T/F

    • 1 paper

    • 1 genome sequencing

    • 2 Ensembl

    • 1 references

    • 1 array

    • 2 programming

    • 1 pattern matching

    • 2 expression

    • 3 other

    • 3 p-genes

    • 1 Blast/Blat

    • 5 Hash questions

    • 1 N-W

    • 1 sequencing



  • What is expression

  • Platforms

    • ChIP on Chip

    • Gene expression

    • Exon arrays

    • Tiling arrays

    • SNP chips

  • Applied S/W for Expression "Library" -- OTDB

  • Alternative Splicing

  • Association Study Example -- AMD

  • How to analyze

What is expression

What is expression?

Gene expression

mRNA - transcription

- microRNAs

Protein - translation

A typical experiment

A Typical Experiment

Case vs. Control

Ex. Retina cells +/- 7-keto-cholesterol

3x redundancy

Look for differentially expressed genes

t-test, ANOVA


Result --> set of genes

But there s so much more

But there’s so much more…

  • Differential expression of genes

  • Time-courses

  • Alternative splicing

  • ChIP-on-chip

  • High-density SNP genotyping

  • Using chips to select genomic fragments for re-sequencing

  • Additional annotation/analyses

Definition of microarray

Definition of Microarray

  • What is a gene expression array?

    • “A microarray is a small analytical device that allows genomic exploration with speed and precision unprecedented in the history of biology” - Schena 2003

Expression analysis platforms


graphics by Jiang Long

Physical spotting

Physical Spotting

Expression analysis platforms

Advantages to arrays

Advantages to Arrays

  • A single array permits monitoring thousands of genes in parallel

  • Provides information at genomic scale

    • Reveals gene function and gene interactions

    • Identifies relationship between genetic and biochemical pathways

    • Identifies traits associated with multigenic origins

  • Caveat - further modifications may occur

    • Post-transcriptional

    • Translational

    • Protein

Microarray research

Microarray Research

  • Ubiquitous in biology & agriculture research

  • Interdisciplinary disciplines

    • Biology

    • Computer Science

    • Statistics

  • Experiments require teams of individuals

  • Analysis presents many obstacles that need to be overcome

Statement of the problem

Statement of the Problem

  • Obstacles impeding analysis process

    • Analysis is complex with multiple steps

    • Requires multiple discipline expertise

      • Bio - understand underlying biology

      • Stats - normalization & statistical measures

      • Comp Sci - programmatic solutions, computation resources

  • Necessity for centralized analysis system

    • Robust

    • Extensible

    • Portable



Gene Expression Arrays

Exon Arrays

Tiling Arrays

SNP chips

Venders: Affymetrix, Nimblegene, Agilent, others

An aside

An Aside

  • State-of-the-art sequencing technology + microarray == ?

  • 454-, pyro-, pyrophosphate sequencing

Expression analysis platforms

Margulies, et. al, Nature, 2005

Gs 20 system brochure 454 roche

GS 20 System Brochure 454/Roche

Gene chip sequencing

Gene Chip + Sequencing

454, pyro- or pyrophosphate sequencing

Genome sequencing in microfabricated high-density picolitre reactors, Margulies, et. al, Nature, 2005

Nature 2007

Sequence capture

Sequence Capture

Gene expression arrays

Gene Expression Arrays

Traditional method, typically provides one or more probes that interrogate the expression level of a gene.

U133Plus2 - 54,000 probes

Exon arrays

Exon Arrays

Target each exon of a gene individually

1,400,000 probe sets

Different levels of confidence/quality

300,000 exons from full-length mRNAs

880,000+ exons from gene predictions

500,000+ “control” exons

Available for human, mouse and rat

Tiling array

Tiling Array

Tiling arrays

Tiling Arrays

Covering the entire genome with probes

Probes every 35 bp across the genome

7-14 chips (depending on the application)

… or can focus on a specific area

10,000 bp proximal promoter of every gene

1 chip

Tiling arrays applications

Tiling Arrays - Applications



protein-DNA interaction

DNA modifications



Anywhere in the genome!

Expression analysis platforms

  • What can you use tiling arrays for?

Encode project

ENCODE Project

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Nature, V 447, June 14, 2007

Transcript connectivity

Transcript Connectivity

  • protein-coding loci are more transcriptionally complex than previously thought

  • 19% of pseudogenes transcribed

  • genes had, on average, 10 different transcriptional start sites

Chip on chip

ChIP on Chip

Snp chips

SNP chips

SNPs - single nucleotide polymorphisms

Affymetrix 6.0 Array

  • 906,600 SNPs

  • 946,000 (non-polymorphic) "monomorphic" SNPs



    Association Studies

    Changes in Copy Number (deletions/duplications)




allele frequenciesA1A2A1A2

SNP 10.740.260.750.25

SNP 20.700.300.100.90

Power increases with more samples, and more SNPs

Alternative splicing in the eye

Alternative Splicing in the Eye


To identify the splicing variants expressed in retina, retinal pigment epithelia, and optic nerve head. (3x biological replicates)


To guide/focus screening efforts to those exons that are expressed.

In collaboration with Rob Mullins

Show probes

Show Probes

Ocular tissue expression database

Ocular Tissue Expression Database

Survey of 10 ocular tissues

GOAL: catalog which genes are expressed across tissues of specific interest in ocular

In collaboration with Abe Clark at Alcon

Ocular tissue expression database1

Ocular Tissue Expression Database

Ocular tissue expression database2

Ocular Tissue Expression Database

Expression analysis platforms


Amd association study

AMD Association Study


Identify the major susceptibility regions for age-related macular degeneration.

Several regions have been reported

  • How may susceptibility regions are there?

    Genotyping 400 AMD patients and controls with high-density SNP chips

    400,000,000 genotypes




allele frequenciesA1A2A1A2

SNP 10.740.260.750.25

SNP 20.700.300.100.90

Power increases with more samples, and more SNPs

How to analyze the data

How to analyze the data?

First step is acquiring the data!





Differential Expression




Time series (all of the above)

Correlation of expression

Early response vs. late response



DAVID Database for Annotation, Visualization and Integrated Discovery

  • Look for conservation of a particular function or annotation in the set of differentially expressed genes.

    GSEA Gene Set Enrichment Analysis

  • Look for annotations that are differentially expressed (as a group).

    Ex. Tour de France

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