RMCL-ESA: A Novel Method to Detect Co-regulatory Functional Modules in Cancer

Considering the increasingly large scale of gene expression data, common module identification algorithms exist many problems, such as large search space and long running time. A novel co-regulatory modules identification algorithm RMCL-ESA (Regularized Markov Cluster & Explosion Search Algorithm) based on improved Markov cluster and explosion search strategy has been proposed. Improved Markov cluster is adapted to preprocess gene expression profiles through three subprocedure: expansion, inflation, prune, which filter redundant genes and save computational cost. Then, two-stage explosion search strategy has been explored for identifying co-regulatory modules. Comparing with existing methods on breast cancer and ovary cancer datasets from TCGA, CRMs (Co-regulatory Functional Modules) of RMCL-ESA include more significant biological function GO-terms and regulation pathways with high enrichment score.

[1]  Srinivasan Parthasarathy,et al.  Identifying functional modules in interaction networks through overlapping Markov clustering , 2012, Bioinform..

[2]  Cheng Liang,et al.  Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion , 2014, Bioinform..

[3]  Cheng Liang,et al.  A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations , 2018, Bioinform..

[4]  Qing Zhang,et al.  Fireworks Explosion Optimization algorithm for parameter identification of PV model , 2016, 2016 IEEE 8th International Power Electronics and Motion Control Conference (IPEMC-ECCE Asia).

[5]  Juan Liu,et al.  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules , 2011, Bioinform..

[6]  Ying Tan,et al.  Fireworks Algorithm for Optimization , 2010, ICSI.

[7]  Jiawei Luo,et al.  A path-based measurement for human miRNA functional similarities using miRNA-disease associations , 2016, Scientific Reports.

[8]  Michael I. Jordan,et al.  On Spectral Clustering: Analysis and an algorithm , 2001, NIPS.

[9]  Jiawei Luo,et al.  Identifying Functional Modules in Co-Regulatory Networks Through Overlapping Spectral Clustering , 2018, IEEE Transactions on NanoBioscience.

[10]  Jiawei Luo,et al.  Discovery of microRNAs and Transcription Factors Co-Regulatory Modules by Integrating Multiple Types of Genomic Data , 2017, IEEE Transactions on NanoBioscience.