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 | Â Correlate developmental gradients by constructing a unified developmental model (UDM) Â Co-cluster the fitted maize and rice gene expressions by using K-means clustering method | Â Construct co-expression networks by using the Pearson correlation coefficients (PCCs) Â Infer time-ordered gene co-expression networks (TO-GCNs) by the breadth-first search algorithm | Â Construct co-expression networks by using the Pearson correlation coefficients (PCCs) Â 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 |