ABSTRACT
Regardless of all efforts on community discovery algorithms, it is still an open and challenging subject in network science. Recognizing communities in a multilayer network, where there are several layers (types) of connections, is even more complicated. Here, we concentrated on a specific type of communities called seed-centric local communities in the multilayer environment and developed a novel method based on the information cascade concept, called PLCDM. Our simulations on three datasets (real and artificial) signify that the suggested method outstrips two known earlier seed-centric local methods. Additionally, we compared it with other global multilayer and single-layer methods. Eventually, we applied our method on a biological two-layer network of Colon Adenocarcinoma (COAD), reconstructed from transcriptomic and post-transcriptomic datasets, and assessed the output modules. The functional enrichment consequences infer that the modules of interest hold biomolecules involved in the pathways associated with the carcinogenesis.
Subject(s)
Adenocarcinoma/genetics , Algorithms , Colonic Neoplasms/genetics , Protein Interaction Maps/genetics , Transcriptome/genetics , Adenocarcinoma/metabolism , Carcinogenesis/genetics , Colonic Neoplasms/metabolism , HumansABSTRACT
Complexity of cascading interrelations between molecular cell components at different levels from genome to metabolome ordains a massive difficulty in comprehending biological happenings. However, considering these complications in the systematic modelings will result in realistic and reliable outputs. The multilayer networks approach is a relatively innovative concept that could be applied for multiple omics datasets as an integrative methodology to overcome heterogeneity difficulties. Herein, we employed the multilayer framework to rehabilitate colon adenocarcinoma network by observing co-expression correlations, regulatory relations, and physical binding interactions. Hub nodes in this three-layer network were selected using a heterogeneous random walk with random jump procedure. We exploited local composite modules around the hub nodes having high overlay with cancer-specific pathways, and investigated their genes showing a different expressional pattern in the tumor progression. These genes were examined for survival effects on the patient's lifespan, and those with significant impacts were selected as potential candidate biomarkers. Results suggest that identified genes indicate noteworthy importance in the carcinogenesis of the colon.
Subject(s)
Adenocarcinoma/genetics , Carcinogenesis/genetics , Colonic Neoplasms/genetics , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic/genetics , Transcriptome , Upstream Stimulatory Factors/genetics , Adenocarcinoma/pathology , Colonic Neoplasms/pathology , Disease Progression , E2F1 Transcription Factor/genetics , HumansABSTRACT
BACKGROUND: Complexity and dynamicity of biological events is a reason to use comprehen-sive and holistic approaches to deal with their difficulty. Currently with advances in omics data genera-tion, network-based approaches are used frequently in different areas of computational biology and bio-informatics to solve problems in a systematic way. Also, there are many applications and tools for net-work data analysis and manipulation which their goal is to facilitate the way of improving our under-standings of inter/intra cellular interactions. METHODS: In this article, we introduce CatbNet, a multi network analyzer application which is prepared for network comparison objectives. RESULT AND CONCLUSION: CatbNet uses many topological features of networks to compare their structure and foundations. One of the most prominent properties of this application is classified network analysis in which groups of networks are compared with each other.
