Systems Biology (Methods in Molecular Biology)

two species (although given the very large TCGA cohort size,

some overlap between cancer and normal is seen for the TCGA

dataset).

Acknowledgments

This work was supported by the National Science Foundation

(award 1553728-DBI), the PhRMA Foundation (Research

Starter Grant in Informatics), the Medical Research Foundation of

Oregon (New Investigator Grant), and the Animal Cancer Founda-

tion (Comparative Oncology Award). S.A.R. thanks Shay Bracha

and Cheri Goodall for kindly providing the dog bladder RNA sam-

ples that were used in the transcriptome profiling study [3], Tanjin

Xu for assistance with the mRNA-seq data processing, Brent Kron-

miller for help with designing the dog mRNA-seq study, and Ilya

Shmulevich, Sheila Reynolds, and Matti Nykter for advice.

References

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2. Lister R, O’Malley RC, Tonti-Filippini J et al
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3. Ramsey SA, Xu T, Goodall C et al (2017) Cross-
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−5.0

−2.5

0.0

2.5

5.0

−4 0 4

log 2 (cancer normal)in dog

log

( 2

cancer

normal

)

in human

Fig. 3Scatter plot of gene expression ratios of 1788 pairs of gene orthologs

(human-dog) in bladder cancer vs. normal bladder. Up- or downregulation of a

gene in human bladder cancer is highly predictive of up- or downregulation of

its dog ortholog in bladder cancer (odds ratio¼29.8,p< 10 ^15 , Fisher’s

exact test)

304 Stephen A. Ramsey