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Table 4 Comparison of published methods that compare co-expression patterns across different plant species

From: Comparing time series transcriptome data between plants using a network module finding algorithm

Reference Wang et al. [44] Chang et al. [45] This protocol
Species Maize and rice Maize Arabidopsis and rice
Inputs Transcriptomes from multiple segments of one tissue type in two species Time series of transcriptomes from one tissue type under two conditions in one species Time series of transcriptomes from one tissue type in two species
Methods  Correlate developmental gradients by constructing a unified developmental model (UDM)  Co-cluster the fitted maize and rice gene expressions by using K-means clustering method  Construct co-expression networks by using the Pearson correlation coefficients (PCCs)  Infer time-ordered gene co-expression networks (TO-GCNs) by the breadth-first search algorithm  Construct co-expression networks by using the Pearson correlation coefficients (PCCs)  Integrate co-expression networks and pairs of orthologous genes, and infer network modules by using OrthoClust
Results K clusters TO-GCNs Orthologous co-expressed modules
Tool availability Data visualization is provided at: http://bar.utoronto.ca/Maize-Rice_eFP_Portal/ Pipeline software: https://github.com/petitmingchang/TO-GCN Repository of this protocol: https://github.com/LiLabAtVT/CompareTranscriptome