- Xin Y, Chanrion B, O’Donnell AH,
Milekic M, Costa R, Ge Y, Haghighi FG
(2012) MethylomeDB: a database of DNA
methylation profiles of the brain. Nucleic
Acids Res 40(Database issue):
D1245–D1249. https://doi.org/10.1093/
nar/gkr1193
- Wishart DS, Jewison T, Guo AC, Wilson M,
Knox C, Liu Y, Djoumbou Y, Mandal R,
Aziat F, Dong E, Bouatra S, Sinelnikov I,
Arndt D, Xia J, Liu P, Yallou F, Bjorndahl T,
Perez-Pineiro R, Eisner R, Allen F, Neveu V,
Greiner R, Scalbert A (2013) HMDB 3.0—
the human metabolome database in 2013.
Nucleic Acids Res 41(Database issue):
D801–D807. https://doi.org/10.1093/
nar/gks1065
- Mitchell A, Bucchini F, Cochrane G,
Denise H, ten Hoopen P, Fraser M,
Pesseat S, Potter S, Scheremetjew M,
Sterk P, Finn RD (2016) EBI metagenomics
in 2016—an expanding and evolving resource
for the analysis and archiving of metagenomic
data. Nucleic Acids Res 44(D1):D595–D603.
https://doi.org/10.1093/nar/gkv1195
- Friedman A, Perrimon N (2007) Genetic
screening for signal transduction in the era of
network biology. Cell 128(2):225–231.
https://doi.org/10.1016/j.cell.2007.01.
007
- Barabasi AL, Oltvai ZN (2004) Network biol-
ogy: understanding the cell’s functional orga-
nization. Nat Rev Genet 5(2):101–113.
https://doi.org/10.1038/nrg1272
- Goymer P (2008) Network biology: why do
we need hubs? Nat Rev Genet 9(9):650
- Hu JX, Thomas CE, Brunak S (2016) Net-
work biology concepts in complex disease
comorbidities. Nat Rev Genet 17
(10):615–629. https://doi.org/10.1038/
nrg.2016.87
- New AM, Lehner B (2015) Systems biology:
network evolution hinges on history. Nature
523(7560):297–298. https://doi.org/10.
1038/nature14537
- Chatr-Aryamontri A, Oughtred R,
Boucher L, Rust J, Chang C, Kolas NK,
O’Donnell L, Oster S, Theesfeld C,
Sellam A, Stark C, Breitkreutz BJ,
Dolinski K, Tyers M (2017) The BioGRID
interaction database: 2017 update. Nucleic
Acids Res 45(D1):D369–D379.https://doi.
org/10.1093/nar/gkw1102
- Szklarczyk D, Franceschini A, Wyder S,
Forslund K, Heller D, Huerta-Cepas J,
Simonovic M, Roth A, Santos A, Tsafou KP,
Kuhn M, Bork P, Jensen LJ, von Mering C
(2015) STRING v10: protein-protein
interaction networks, integrated over the
tree of life. Nucleic Acids Res 43(Database
issue):D447–D452. https://doi.org/10.
1093/nar/gku1003
- Kanehisa M, Furumichi M, Tanabe M, Sato Y,
Morishima K (2017) KEGG: new perspectives
on genomes, pathways, diseases and drugs.
Nucleic Acids Res 45(D1):D353–D361.
https://doi.org/10.1093/nar/gkw1092
- Fabregat A, Sidiropoulos K, Garapati P,
Gillespie M, Hausmann K, Haw R, Jassal B,
Jupe S, Korninger F, McKay S, Matthews L,
May B, Milacic M, Rothfels K, Shamovsky V,
Webber M, Weiser J, Williams M, Wu G,
Stein L, Hermjakob H, D’Eustachio P
(2016) The reactome pathway knowledge-
base. Nucleic Acids Res 44(D1):
D481–D487. https://doi.org/10.1093/
nar/gkv1351
- Bohler A, Wu G, Kutmon M, Pradhana LA,
Coort SL, Hanspers K, Haw R, Pico AR,
Evelo CT (2016) Reactome from a WikiPath-
ways perspective. PLoS Comput Biol 12(5):
e1004941. https://doi.org/10.1371/jour
nal.pcbi.1004941
- Tyner C, Barber GP, Casper J, Clawson H,
Diekhans M, Eisenhart C, Fischer CM,
Gibson D, Gonzalez JN, Guruvadoo L,
Haeussler M, Heitner S, Hinrichs AS,
Karolchik D, Lee BT, Lee CM, Nejad P,
Raney BJ, Rosenbloom KR, Speir ML,
Villarreal C, Vivian J, Zweig AS, Haussler D,
Kuhn RM, Kent WJ (2017) The UCSC
Genome Browser database: 2017 update.
Nucleic Acids Res 45(D1):D626–D634.
https://doi.org/10.1093/nar/gkw1134
- Koch A, De Meyer T, Jeschke J, Van Crie-
kinge W (2015) MEXPRESS: visualizing
expression, DNA methylation and clinical
TCGA data. BMC Genomics 16:636.
https://doi.org/10.1186/s12864-015-
1847-z
- van ’t Veer LJ, Dai H, van de Vijver MJ, He
YD, Hart AA, Mao M, Peterse HL, van der
Kooy K, Marton MJ, Witteveen AT, Schreiber
GJ, Kerkhoven RM, Roberts C, Linsley PS,
Bernards R, Friend SH (2002) Gene expres-
sion profiling predicts clinical outcome of
breast cancer. Nature 415(6871):530–536.
https://doi.org/10.1038/415530a
- Zeng T, Li J (2010) Maximization of negative
correlations in time-course gene expression
data for enhancing understanding of molecu-
lar pathways. Nucleic Acids Res 38(1):e1.
https://doi.org/10.1093/nar/gkp822
- Zeng T, Guo X, Liu J (2014) Negative corre-
lation based gene markers identification in
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