REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
BLCA1 dataset	(van der Heijden et al., 2016)44	GEO: GSE57813
BLCA2 dataset	(Kim et al., 2010)45	GEO: GSE13507
BLCA3 dataset	(Sjodahl et al., 2012)46	GEO: GSE32894
BLCA4 dataset	(Dyrskjøt et al., 2005)47	https://doi.org/10.1158/1078-0432.CCR-04-2095
BLCA5 dataset	(Hedegaard et al., 2016)48	ArrayExpress: E-MTAB-4321
BRCA1 dataset	(Hatzis et al., 2011)49	GEO: GSE25055
BRCA2 dataset	(Hatzis et al., 2011)49	GEO: GSE25065
BRCA3 dataset	(Edlund et al., 2021)50	GEO: GSE140494
BRCA4 dataset	(Birkbak et al., 2018)51	GEO: GSE103668
BRCA5 dataset	(Popovici et al., 2010; Shi et al., 2010)52,53	GEO: GSE20194
BRCA6 dataset	(Shen et al., 2012; Tabchy et al., 2010)54,55	GEO: GSE20271
BRCA7 dataset	(Miyake et al., 2012)56	GEO: GSE32646
PCA1 dataset	(Jain et al., 2018)57	GEO: GSE116918
PCA2 dataset	(Ragnum et al., 2015)58	GEO: GSE55935
PCA3 dataset	(Ross et al., 2014)59	GEO: GSE51066
PCA4 dataset	(Erho et al., 2013)60	GEO: GSE46691
PCA5 dataset	(Boormans et al., 2013)61	GEO: GSE41408
PCA6 dataset	(Ross et al., 2016)62	JHU Natural History cohort
PCA7 dataset	(Ross-Adams et al., 2015)63	GEO: GSE70769
TF-target and TF-miRNA interactions	(Rouillard et al., 2016)66	Harmonizome
miRNA-target interactions1	(Agarwal et al., 2015)68	TargetScan
miRNA-target interactions2	(Chou et al., 2021)69	miRTarBase
miRNA-target interactions3	(Sticht et al., 2018)70	miRWalk
The feed-forward loops mechanism	This paper	GitHub repository
The NOTCH-MYC signaling mechanism	This paper	GitHub repository
The cell-cell adhesion, activation, and O2 response mechanism	This paper	GitHub repository
The Alzheimer disease mechanism	This paper	GitHub repository
The diabetes mechanism	This paper	GitHub repository
The viral infection mechanism	This paper	GitHub repository
Code for reproducibility	This paper	GitHub repository
Software and algorithms
R (v4.0.3)	(Ihaka and Gentleman, 1996)	https://www.r-project.org/
MergeMaid (v3.1)	(Cope et al., 2004)84	https://bioconductor.riken.jp/packages/3.1/bioc/html/MergeMaid.html
SwitchBox (v1.24.0)	(Afsari et al., 2015)85	https://www.bioconductor.org/packages/release/bioc/html/switchBox.html
caret (v6.0-86)	(Kuhn, 2008)86	https://topepo.github.io/caret/
limma (v3.44.3)	(Ritchie et al., 2015)	https://bioconductor.org/packages/release/bioc/html/limma.html
boot (v1.3-25)	(Davison and Hinkley, 1997)89	https://cran.r-project.org/web/packages/boot/index.html
randomForest (v4.6-14)	(Breiman, 2001)79	https://cran.r-project.org/web/packages/randomForest/index.html
kernlab (v0.9-29)	(Karatzoglou et al., 2004)87	https://cran.r-project.org/web/packages/kernlab/index.html
xgboost (v1.2.0.1)	(Chen and Guestrin, 2016)80	https://cran.r-project.org/web/packages/xgboost/index.html
pROC (v1.16.2)	(Robin et al., 2011)	https://cran.r-project.org/package=pROC
MsigDB (v6.1)	(Subramanian et al., 2005)71	https://www.gsea-msigdb.org/gsea/msigdb/
igraph (v1.3.0)	(Csardi and Nepusz, 2005)90	https://cran.r-project.org/web/packages/igraph/index.html
enrichR (v3.0)	(Jawaid, 2022; Xie et al., 2021)91,92	https://cran.r-project.org/web/packages/enrichR/index.html