TarPiD (Targets of piRNA Database) offers comprehensive information on piRNA and its targets, including their expression, methodologies (high-throughput or low-throughput) for target identification/validation, cells/tissue types, diseases, target regulation types, target binding regions, and important biological functions driven by piRNAs through target interactions.
Our RNAi laboratory has performed next-generation sequencing of small RNA and transcriptomes in tissues and cell lines of multiple cancer types to decode the cancerome. This is aimed at developing novel diagnostic and therapeutic strategies.
GEO Accession Nos: GSE197508, GSE196674, GSE196688, GSE83945, GSE83794, GSE85075.
SoCeR predicts, gauges, and compares the propensity of the ceRNAs of a gene of interest based on a miRNA-mediated ‘tug-of-war’ model. It precisely envisages which among a ceRNA pair exerts a stronger pull on the shared miRNA pool. This tool predicts ceRNAs in 32 cancer types with a true positive rate of 79%.
Published in: miRNA-mediated 'tug-of-war' model reveals ceRNA propensity of genes in cancers. Molecular Oncology, 12(6):855-868, 2018.
StarMir predicts both seed and seedless target sites in all three regions of target mRNAs (5’UTR, CDS, 3’UTR) using prediction models based on V-CLIP (human), HITS-CLIP (mouse), and ALG1-CLIP (worm). This was developed while working at Wadsworth Center, NY.
Publications: Nucleic Acids Res. 41(14): e138, 2013 | RNA Biology 13 (6), 554-560, 2016.
RiNAcyc (RNA interacting Nodes in Acyclic Path) identifies acyclic paths in complex biological networks to map key regulatory feedback circuits.
Published in: Unraveling novel TF-miRNA regulatory crosstalk in metastasis of Soft Tissue Sarcoma. Scientific Reports, 5:9742, 2015.
