miRNAtools: Advanced Training Using the miRNA Web of Knowledge

Abstract

Micro-RNAs (miRNAs) are small non-coding RNAs that act as negative regulators of the genomic output. Their intrinsic importance within cell biology and human disease is well known. Their mechanism of action based on the base pairing binding to their cognate targets have helped the development not only of many computer applications for the prediction of miRNA target recognition but also of specific applications for functional assessment and analysis. Learning about miRNA function requires practical training in the use of specific computer and web-based applications that are complementary to wet-lab studies. In order to guide the learning process about miRNAs, we have created miRNAtools (), a web repository of miRNA tools and tutorials. This article compiles tools with which miRNAs and their regulatory action can be analyzed and that function to collect and organize information dispersed on the web. The miRNAtools website contains a collection of tutorials that can be used by students and tutors engaged in advanced training courses. The tutorials engage in analyses of the functions of selected miRNAs, starting with their nomenclature and genomic localization and finishing with their involvement in specific cellular functions.

Pathway analysis of genes identified through Post-GWAS to understand prostate cancer aetiology

“…The comparison of post-GWAS genes dysregulated genes was performed, separately, for primary tumour versus normal and metastatic samples investigating for overlapped genes based on Entrez gene identifiers. Oncomine originated studies utilised in the study are: 1) Taylor dataset (Oncomine ID: n9205) including 150 prostate carcinoma tissue specimens (131 specimens from primary and 19 metastatic tumours) and 29 paired normal adjacent prostate tissue specimens [38], 2) Yu (Oncomine ID: n5345) that used 23 normal prostate and 64 prostate carcinoma samples [22] and 3) Grasso dataset (Oncomine ID: n6252) that describes 59 localized prostate carcinoma and 28 benign prostate tissue specimens [39].…”

Proteomic profiling of exosomes derived from pancreatic beta-cells cultured under hyperglycemia

“…Secreted EVs reflect the physiology and pathology of the cell of their origin, and they have an important function in cellular homeostasis, disease pathogenesis, and diagnostics. Moreover, EVs are gaining attention in clinics as therapeutics and drug delivery vehicles, transferring bioactive molecules such as miRNAs [5][6][7][8], proteins [9,10], genes [11], and other therapeutic agents to target cells for therapeutic purposes [12]. Recent in vivo and in vitro studies have shown that the molecular composition of EVs is changing because of hyperglycemia (HG) [13,14], and these changes can be considered as diagnostic and prognostic biomarkers.…”