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Figure  1 shows an illustrative example of the construction of functional similarity interactions between two protein complexes.

Values were log2 transformed and each column was then normalized to have a mean of 0 and a variance of 1. EV values for each data compendium is given in Additional file 12. Functional similarity interactions (Fun-Net) were constructed using Gene Ontology (GO) annotations as defined in the Entrez Gene database, and also metabolic pathway annotations in the KEGG database.

Given two protein complexes Ci = { p k | k = 1…m} and Cj = { p l | l = 1…n}, where p k, p l are protein elements of Ci and Cj, m and n are the number of protein elements belonging to Ci and Cj, respectively, we here defined three kinds of functional similarity interactions between Ci and Cj based on shared protein elements, shared annotating GO terms and protein interactions.

However, while sequence similarity often implies functional similarity, interaction data is not well conserved even for proteins with high sequence similarity.

In this study, we additionally used that method to define a functional similarity interaction between two protein complexes based on protein interaction network.

Therefore, to construct functional similarity protein complex networks where each node is a protein complex, we defined a functional similarity interaction between two protein complexes based on: i) shared protein elements; ii) shared annotating GO terms; and iii) protein interactions.

Therefore, we additionally constructed a functional similarity interaction between two protein complexes based on shared annotating GO terms, where a list of genes and annotating GO terms were collected from NCBI Entrez Gene FTP site (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ gene2go.gz).

Therefore, as we did in our previous study [ 21], we defined a functional similarity interaction between two protein complexes based on their shared protein elements as follows: Two protein complexes are functionally interacted with each other if they share at least one protein element.

For example, TaCIPK14 and TaCIPK15, which had 81%% similarity, showed similar interactions with five TaCBLs (TaCBL1, 2, 3, 4 and 7) but different interactions with TaCBL6 and 9. Compared with TaCIPK14/15, other TaCIPKs showed lower amino acid sequence similarity and more diverse interaction specificity.

Two pairs are considered as similar interactions while their interaction similarity is greater than 0.6.

Although the three unique linker subunits share structural similarity, their interactions with each other and the hemoglobin subunits display striking diversity.