Inter-module connectivity, which tend to connect different communities and maintain network architectural integrity, is contributing to functional coordination and information flow between modules in perturbations. Detecting the strength of inter-module connection is essential to characterize the reactive bio-systematical variation. A quantitative evaluation method for inter-module connections is needed. Here, based on the high-throughput microarray data from mouse, an evaluation approach (named as IMCC) for inter-module connectivity was developed. The IMCC model, which is an integration of direct and indirect inter-module connections, successfully excluded inter-module connections without statistical significance or below the cutoff value, and provided a more comprehensive landscape of inter-module relationships. We showed that the IMCC method reflected a more precise functional coordination between modules according to KEGG database, were validated by topological parameter. Application of IMCC in genome-scale stroke networks deciphered characteristic pathological “core-periphery” structure of modular map and functional coordination module pair.
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