Research is to see what everybody else has seen and to think what

nobody else has thought.�Albert Szent-Györgyi

Image by J.W. McGuire/NIH

Image from You Don’t Know Jack. Vol 3.

Unsupervised discovery �from large gene expression compendia with ADAGE

Casey Greene

Analysis with Denoising Autoencoders of �Gene Expression (ADAGE)

Tan et al. Pac Sym Bio 2015; Tan et al. In Press. mSystems

ADAGE Identifies Genes’ Pathways

Assign Pathway

… and produces useful networks

The Transcription Factor Anr Controls P.a. Response to Low O2

Low O2

O2

O2

O2

O2

O2 O2

O2 O2

O2

O2

O2

O2

O2

O2

O2 O2

O2

O2 O2

O2

O2

O2 O2

O2

O2

O2 O2 O2

O2 O2

O2

O2

O2

Anr

CF Lung Epithelium

Node42 reflects Anr Activity

E−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr ActivityE−G

EOD

−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

C

New Experiment Validates Node 42’s Low-O2 Signature

CF lung epithelial cells Jack Hammond

E−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr Activity

E−GEO

D−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

CE−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr Activity

E−GEO

D−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

C

ADAGE complements PCA/ICA

E−GEOD−17179} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

O2

Node42

O2

E−GEOD−33160

E−GEOD−52445

PC4 PC7 IC14

} wt

}}Δanr

Δdnr

O2

} wt

}}Δanr

Δdnr

O2

} wt

}}Δanr

Δdnr

O2−0.5 0 0.51Value

Color Key

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

−1 0 1 2Value

Color Key

O2 O2 O2−2−1 0 1 2 3Value

Color Key

O2 O2 O2−0.5 0.5 1.5

Value

Color Key

−2−1 0 1Value

Color Key

−3−2−1 0 1Value

Color Key

−1 0 1Value

Color Key

−1 0 1 2 3 4Value

Color Key

−1.5−0.5 0.5Value

Color Key

−0.5 0 0.5Value

Color Key

−0.4 0 0.4Value

Color Key

−1 0 1 2Value

Color Key

IC49

} wt

}}Δanr

Δdnr

O2

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

O2

Color Key

Color Key

Color Key

−1 0 1Value

Color Key

−0.5 0.5 1.5Value

−0.5 0 0.51Value

−1 0 1 2Value

}}Δanr

wt

}Δanr

wt

Anr-Microarray

Anr-RNAseq

}}Δanr

wt

}}Δanr

wt

}}Δanr

wt

}}Δanr

wt

Value

Color Key

Value

Color Key

Value

Color Key

Value

Color Key

−0.6 0.60 −0.1 0 0.1 −0.1 0 0.1 0.2 −0.1 0 0.1

Value

Color Key

Value

Color Key

Value

Color Key

Value

Color Key

−15 0 10Value

Color Key

Color Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

−5 0 5

Color Key

Value

Color Key

Value

}}}

}}

Δanr

wt

PAO1

J215

}Δanr

wt

}}}

}}

Δanr

wt

PAO1

J215

}Δanr

wt

}}}

}}

Δanr

wt

PAO1

J215

}Δanr

wt

}}}

}}

Δanr

wt

PAO1

J215

}Δanr

wt

}}}

}}

Δanr

wt

PAO1

J215

−10 0 10 −1.5 0 1 −1 0 1 −0.05 0 0.1 −0.2 0 0.2

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

Thompson, Tan, Greene. In Press. PeerJ. https://peerj.com/preprints/1460/ Jeff Thompson

Cross-platform normalization of microarray and RNA-seq data for machine learning applications

Thompson, Tan, Greene. In Press. PeerJ. https://peerj.com/preprints/1460/

New Experiment Validates Node 42’s Low-O2 Signature

CF lung epithelial cells Jack Hammond

E−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr Activity

E−GEO

D−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

CE−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr Activity

E−GEO

D−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

C

E−GEOD−17179

} wt

}}Δanr

Δdnr

E−GEOD−17296

}}}}}}

ΔanrΔroxSR

ΔanrΔroxSR

wt

wt

}}

EXP

STAT

O2

E−GEO

D−52445

O2

Node42 - Anr Activity

E−GEO

D−33160

O2

A

B

−15 0 10Value

Color KeyColor Key

−10 0 10Value

Color Key

Value−10 0 10

−10 0 15

Color Key

Value

}}Δanr

wt

}}Δanr

wt }}Δanr

wt

−5 0 5

Color Key

Value

Color Key

Value−4 0 4

Color Key

Value−2 0 2

Microarray RNAseq PAO1

RNAseq J215

C

ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions�bioRxiv: http://dx.doi.org/10.1101/030650�In Press @ mSystems

How do we move from �this to mechanisms?

What “pathways” did my experiment affect?

ADAGE-based Pathway Analysis of Transcriptomic Changes

ADAGE Webserver coming soon! http://www.greenelab.com/webservers

Jie Tan+ (Grad Student) Gregory Way (Grad Student) Brett Beaulieu-Jones (Grad Student) René Zelaya (Programmer) Matt Huyck (Programmer) Kathy Chen (Undergrad) Mulin Xiong (Undergrad) Deb Hogan (Hogan Lab/Dartmouth) Jack Hammond (Hogan Lab/Dartmouth) Jeff Thompson (Marsit Lab/Dartmouth) Data: All investigators who publicly release their gene expression data. Images: Artists who release their work under a Creative Commons license. Funding: G&B Moore Investigator in Data-Driven Discovery National Science Foundation Cystic Fibrosis Foundation Norris Cotton Cancer Center Prouty Grant American Cancer Society Dartmouth SYNERGY +Neukom Institute Graduate Fellowship Find us online: http://www.greenelab.com Twitter: @GreeneScientist