Table 1.

Comparison of TissueNexus with existing functional gene network databases

Databases	Tissues	Gene expression technology	Tissue gene expression	#Datasetsa (all/expression)	#Samples	Methods	References
mouseNet	Not tissue-wise	Microarray	No	340/333	13,634	Bayesian	(2)
						classifier
diseaseQUEST	Multiple tissues	Microarray	No	174/169	2,736	Bayesian	(5)
						classifier
GIANT	Multiple tissues	Microarray	No	987/980	38,000	Bayesian	(1)
						classifier
HumanNet	Not tissue-wise	Microarray (125 datasets)	No	NAb/158	16,220	Bayesian	(6)
		RNA-seq (33 datasets)				likelihood
BaiHui	Brain only	Microarray	Yes	216/213	4,688	Bayesian	(8)
						classifier
TissueNexus	Multiple tissues	RNA-seq	Yes	1,345/1,341	52,087	XGBoost	This work

^aIn the Datasets column, all and expression indicate the numbers of all genomic datasets and only the gene expression datasets used to build functional networks in each database, respectively. Expression is the dominant data type used to construct networks.

^bThe number of all integrated datasets is not provided in the original paper.