Project description:This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance. VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity.
Project description:This dataset was used to benchmark the Virtual Inference of Protein-activity by Regulon Readout algorithm (VIPER). Despite recent advances in molecular profiling, proteome-wide assessment of protein activity in individual samples remains a highly elusive target. In stark contrast, protein activity quantitation is increasingly critical to the dissection of key regulatory processes and to the elucidation of biologically relevant mechanisms. Importantly, its value extends to the study of drug activity, as most small molecules inhibit activity of their cognate protein substrates without affecting the protein’s or associated mRNA’s abundance. VIPER leverages the increasingly accurate and context specific knowledge of regulatory networks. Specifically, it uses the expression of the transcriptional targets most directly regulated by a given protein in an individual sample as a reporter for the computational inference of its activity. BCL6 knock down experiments were performed in OCI-Ly7 and Pfeiffer GCB-DLBCL cell lines. Both cell lines were maintained in 10% FBS supplemented IMDM medium and transiently transfected with either a BCL6-specific or a non-target control siRNA oligo in triplicate. Total RNA was isolated 48h after transfection and gene expression was profiled on H-GU133plus2 Affymetrix gene chips.
Project description:We derived two novel rpESC lines and characterized their microRNA signature by Solexa deep sequencing. By characterizing their microRNA signature, we identified 91 novel microRNAs, except those are also detected in other primate ESCs. Moreover, these two novel rpESCs display a unique microRNA signature, comparing to their biparental counterpart ESCs.
Project description:In a post-hoc exploratory analysis of the KING trial to seek molecular markers of outcome, RNAseq was performed on resected tumor specimens at the time of diagnostic surgery before the recurrence from 57 study patients from all arms with adequate selinexor exposure and evidence of either clinical benefit or resistance defined above. RNAseq data were used to infer the activity for 6,203 master regulator proteins using the VIPER algorithm.
Project description:Trimeresurus popeiorum, more popularly known as Pope's Pit Viper, is among the venomous Indian snakes that do not belong to the "Big Four" snake species. The project aims to unveil the venom proteome of Pope's Pit Viper (Trimeresusrus popeiorum) from northeastern India.