8. Node42 reflects Anr Activity
E−GEOD−17179
}wt
}
}
Δanr
Δdnr
E−GEOD−17296
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
wt
wt
}
}
EXP
STAT
O2
E−GEOD−52445
O2
Node42 - Anr Activity
E−GEOD−33160
O2
A
−15 0 10
Value
Color Key Color Key
−10 0 10
Value
Color Key
Value
−10 0 10
−10 0 15
Color Key
Value
9. New Experiment Validates Node 42’s
Low-O2 Signature
CF lung epithelial cells
Jack Hammond
E−GEOD−17179 E−GEOD−17296
B
}
}
Δanr
wt
}
}Δanr
wt }
}Δan
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
}
}
Δanr
Δdnr
E−GEOD−17296
}
}
}Δanr
ΔroxSR
wt
}STAT
D−52445
D−33160
B
}
}
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
10. ADAGE complements PCA/ICA
E−GEOD−17179
}wt
}
}
Δanr
Δdnr
E−GEOD−17296
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
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 0.51
Value
Color Key
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
wt
wt
}
}
EXP
STAT
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
wt
wt
}
}
EXP
STAT
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
wt
wt
}
}
EXP
STAT
−1 0 1 2
Value
Color Key
O2 O2 O2−2−1 0 1 2 3
Value
Color Key
O2 O2 O2
−0.5 0.5 1.5
Value
Color Key
−2−1 0 1
Value
Color Key
−3−2−1 0 1
Value
Color Key
−1 0 1
Value
Color Key
−1 0 1 2 3 4
Value
Color Key
−1.5−0.5 0.5
Value
Color Key
−0.5 0 0.5
Value
Color Key
−0.4 0 0.4
Value
Color Key
−1 0 1 2
Value
Color Key
IC49
}wt
}
}
Δanr
Δdnr
O2
}
}
}
}
}
}
Δanr
ΔroxSR
Δanr
ΔroxSR
wt
wt
}
}
EXP
STAT
O2
O2
Color Key
Color Key
Color Key
−1 0 1
Value
Color Key
−0.5 0.5 1.5
Value
−0.5 0 0.51
Value
−1 0 1 2
Value
}
}
Δanr
wt
Anr-Microarray
}
}
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
−15 0 10
Value
Color Key
Color Key
−10 0 10
Value
Color Key
Value
−10 0 10
−10 0 15
Color Key
Value
−5 0 5
Color Key
Value
11. 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
12. Cross-platform normalization of microarray and
RNA-seq data for machine learning applications
Thompson, Tan, Greene. In Press. PeerJ. https://peerj.com/preprints/1460/
13. New Experiment Validates Node 42’s
Low-O2 Signature
CF lung epithelial cells
Jack Hammond
E−GEOD−17179 E−GEOD−17296
B
}
}
Δanr
wt
}
}Δanr
wt }
}Δan
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
}
}
Δanr
Δdnr
E−GEOD−17296
}
}
}Δanr
ΔroxSR
wt
}STAT
D−52445
D−33160
B
}
}
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
}
}
Δanr
Δdnr
E−GEOD−17296
}
}
}Δanr
ΔroxSR
wt
}STAT
D−52445
D−33160
B
}
}
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
14. 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
15. How do we move from
this to mechanisms?
What “pathways” did my
experiment affect?
18. 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