Open Day 2006

From Expression, Through Annotation, to Function

Ohad Manor & Tali Goren

Open Day 2006

Have you ever wondered…

Open Day 2006

Types of Data

Gene Expression (Microarray)GO Annotations

Gene Expression (Microarray)

GO AnnotationsChIP on chipGO AnnotationsGene Expression

(Microarray)GO AnnotationsChIP on chipProtein – Protein Interactions

Sub - Cellular Localization

Systematic view in

genomic large scale

What Characterizes

these data sets?

Open Day 2006

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• A computational tool to check enrichment of data sets

• Implemented in perl

• Interactive command line

• May be scripted…

• Concatenate tests and matrix operations

• Data manipulation functions and queries

What is ?

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Using

• Load biological data

• Check enrichment of crossed data sets

• Extract statistically significant results

• Multiple hypothesis correction

• Cluster gene sets

• Save results

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What is statistically significant?

• How to choose the right test to compare measurements?

• Paired or Unpaired?

• Non – Parametric:– no assumption about sample size or distribution– no parameters such as expectation or variance

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Paired – Binary Version

0 1

0 3 2

1 0 5

RA

P1

Ribosome Assembly

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

RAP1Ribosome Assembly

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Paired – continuous version

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

heat shockGene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

YPDGene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

-1 1

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Unpaired test

Gene1

Gene2

Gene4

Gene5

Gene6

heat shock

Gene3

Gene7

Gene8

Gene10

heat shock

-1 1

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

heat shock

RAP1

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

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Statistics Statistics…….

 

Parametric TestsNon -Parametric

TestsBinary

Measurements

Compare two unpaired groups

Unpaired T test Kolmogorov-Smirnov

Compare two paired groups

Paired T test Wilcoxon test Chi-square test

Quantify association

between two variables

Pearson correlation Spearman Correlation

Goal

Type Of Data

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How About Some Biology?

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S. Cerevisiae Regulation

• Let’s presume we know nothing about the Yeast

• Use ENRICH to construct a basic regulatory network of Yeast

• How can we do that?

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STE12

RAP1

YAP5

MSN2

SFP1

FHL1

GAT1

Binary values

Rib

osom

al

Stre

ss

Cel

l cyc

le

Met

abol

ism

Flow chart

HG test Significance

threshold

Rib

osom

al

Str

ess

Cel

l cyc

le

Met

abol

ism

STE12

RAP1

YAP5

MSN2

SFP1

FHL1

GAT1

P-values

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Rib

osom

al

Stre

ss

Cel

l cyc

le

Met

abol

ism

GO

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Ch

IP

STE

12

RA

P1

MSN

2 F

HL

1

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Metabolism Stress Cell cycle

Yeast regulation network

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FHL1 proteinCase study

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FHL1 – what is known

• Putative transcriptional regulator

• Predicted to be involved in stress response• Required for rRNA processing

• Null mutant shows reduced growth rate• Could we have found all of that alone?

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Experimental various conditions

genes

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Exp.

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

FHL1

Unpaired

T-test

Exp.1

Exp.2

Exp.3

Exp.4

Exp.5

P-values

FHL1

Exp.1

Exp.2

Exp.3

Exp.4

Exp.5

FHL1

Exp.1

Exp.2

Exp.3

Exp.4

Exp.5

Binary values

Conditions

HG test

P-values

FH

L1

Hea

t sh

ock

AA

sta

rvat

ion

osm

otic

str

ess

oxid

ativ

e st

ress

in

vasi

ve g

row

th

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Tell me who are your friends…Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

FHL1

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

ChIP

HG test

RA

P1

FK

H2

MB

P1

GA

T3

S

OK

2

P-values

FH

L1

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Enriched conditions

GrowthStress

response

Enriched GO annotations

Ribosome assembly

RAP1 SFP1 GAT3

Enriched TF’s

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Remember this question?

• What is the connection between the expression level of a gene to its sub-cellular localization?

• Which Transcription Factors regulate Amino Acid Biosynthesis?

• Does a heat shock affect peripheral proteins more than it affects mitochondrial proteins?

MitochondrionCell Periphery

Open Day 2006

Flow chart

genes

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Exp.

Gene1

Gene2

Gene3

Gene4

Gene5

Gene6

Gene7

Gene8

Gene9

Gene10

Localization

Unpaired

T-test

HG testExp.1

Exp.2

Exp.3

Exp.4

Exp.5

P-values

Mit

ocho

ndri

a

B

ud N

eck

V

acuo

le

Cel

l per

iphe

ry

Nuc

leus

Exp.1

Exp.2

Exp.3

Exp.4

Exp.5

Mit

ocho

ndri

a

B

ud N

eck

V

acuo

le

Cel

l per

iphe

ry

Nuc

leus

Exp.1

Exp.2

Exp.3

Exp.4

Exp.5

Binary values

Shor

t H

S M

ediu

m H

S

Lon

g H

S

Seve

re H

S

M

oder

ate

HS

P-values

Short HS Medium HS

Long HS Severe HS

Moderate HS

Cel

l per

iphe

ry

Mit

ocho

ndri

a

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Future plans

• Continue to develop

• More data available out there

• Build Regulation networks for the Yeast and other species

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Questions

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Thanks

• Prof. Nir Friedman

• Tommy Kaplan

• And to you for listening!!!

Open Day 2006