Table 2.

Examples of strategies used for co-expression network analysis in regard to the respective biological question addressed.

Review Sections	Biological question	Species	Strategy	References
Data availability for co-expression network analysis	Identify functional modules associated to germination and dormancy	Arabidopsis	Use of a condition dependant approach	Bassel et al., 2011
	Build a comprehensive and functional co-expression network	Arabidopsis, rice	Integration of multiple sources of data in the network construction to support functional gene linkage	Lee et al., 2010, 2011
	Gene functional annotation	Rice	Comparison of condition dependant and condition independent network based approach.	Childs et al., 2011
	Maximize the capture of gene co-expression relationship	Arabidopsis	Pre-clustering of input expression samples to approximate condition dependant approach	Feltus et al., 2013
Gene prioritization	Explore the modular biological organization	Arabidopsis	Arabidopsis gene co-expression network based on 1000 microarrays. Modules were extracted using the Markov Clustering Algorithm (MCL)	Mao et al., 2009
	Infer gene regulatory relationships in gene co-expression modules	Arabidopsis	Identify gene expression modules driven by known cis-regulatory motifs	Ma et al., 2013
	Gene functional annotation	Arabidopsis	Module enrichment for known cis-regulatory elements	Vandepoele et al., 2009
	Identify co-expression modules	Arabidopsis	Development of an Heuristic clustering algorithm	Mutwil et al., 2010
eQTL based co-expression networks	Identify causal genes responsible for glucosinolate variation	Arabidopsis	Use co-expression network as non-genetic (independent) filter to prioritize GWA mapping candidates	Chan et al., 2011
	Identify candidates for shade avoidance	Arabidopsis	Prioritize genes underlying phenotypic QTL using co-expression network analysis, eQTL information and functional classification	Jimenez-Gomez et al., 2010
	Examine natural variation in circadian clock function	Arabidopsis	eQTL mapping using a priori defined phase groups and comparison with metabolomics QTLs	Kerwin et al., 2011
	Examine transcriptional network response to biotic interactions	Arabidopsis	Perform a network eQTL analysis from a priori defined gene expression networks	Kliebenstein et al., 2006
	Identify novel abiotic stress genes	Arabidopsis	Network guided genetic screen: gene ranking combined to co-expression network analysis	Ransbotyn et al., 2014
Temporal resolution for co-expression network	Resolve the chronological regulatory mechanisms involved in the response to pathogen infection	Arabidopsis	Temporal clustering by combining extensive time series data and co-expression network analysis	Windram et al., 2012
	Identify key genes regulating the acquisition of longevity during seed maturation	Medicago Arabidopsis	Developmental time course data and cross species comparison for co-expression network analysis	Righetti et al., 2015
Spatial resolution for dynamic co-expression network	Identify cell-specific molecular mechanisms	Maize	Combine Laser-capture microscopy with RNA-seq	Zhan et al., 2015
Comparative co-expression network analysis	Knowledge transfer between species	Maize rice	Global co-expression network alignment using both gene homology and network topology	Ficklin and Feltus, 2011
	Identify conserved modules across species	Several species	Co-expressed node vicinity networks (NVNS) compared across species.	Mutwil et al., 2011