title: MicroRNA mediated network motifs in autoimmune diseases and its crosstalk between genes, functions and pathways.
abstract: Autoimmune diseases (AIDs) are incurable but suppressible diseases whose molecular mechanisms are yet to be elucidated. In this work, we selected five systemic autoimmune diseases such as Rheumatoid Arthritis (RA), Type 1 Diabetes (T1D), Inflammatory Bowel Disease (IBD), Autoimmune Thyroid Disease (ATD) and Systemic Lupus Erythematosus (SLE). Heterogeneous data such as miRNA, transcription factor (TF), target genes and protein-protein interactions involved in these AIDs were integrated to understand their roles at different functional levels of miRNA such as transcription initiation, gene regulatory network formation and post transcriptional regulation. To understand the functional characteristics of these complex biological networks, they can be simplified as network motifs (sub networks) and motif-motif interacting pairs (MMIs). The network motif patterns and motif-motif interacting pairs that occur for the selected five diseases were identified. To further understand the functional association between AIDs, functions and pathways were determined using gene set enrichment analysis and five selected immune signaling pathways (ISPs). The crosstalk within AIDs and between the immune signaling pathways (ISPs) could provide novel insights in deciphering disease mechanisms. This study represents the first investigation of miRNA-TF regulatory network for AIDs and its association with ISPs using sub-network motifs.
authors.affiliation: Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore 641 046, India. Electronic address: archana.prabahar@gmail.com.
authors.forename: Archana
authors.initials: A
authors.lastname: Prabahar
authors.affiliation: Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore 641 046, India. Electronic address: n.jeyakumar@yahoo.co.in.
authors.forename: Jeyakumar
authors.initials: J
authors.lastname: Natarajan
mesh_terms: D000465:Algorithms; D001327:Autoimmune Diseases / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D015551:Autoimmunity / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D010363:Pattern Recognition, Automated; D060066:Protein Interaction Maps; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors
keywords: Autoimmune diseases; Crosstalk; Immune signaling pathways; Network motifs; microRNA