BIT001 Bioinformatics assignments 5 and 6 By: John Yoder … Continue reading →

Mission and Central activities: The GBG's mission is to manage and assess molecular interaction data obtained through multiple platforms, increase the understanding of the effect of those interactions on the chemosensitivity of cancer, and create tools that will facilitate that process. Translation of that information will be directed towards the recognition of diagnostic and therapeutic cancer biomarkers, and directed cancer therapy. Freely available for public use are our professional grade Miner Suite bioinformatics software package, as well as our characterization and annalysis of the NCI-60 cancer cell lines, the DNA, RNA, protein, epigenetic and pharmacological levels (accessible through CellMiner). The Miner Suite of bioinformatic software packages. CellMiner: A database and query tool designed for the cancer research community to facilitate integration of the molecular datasets generated by the GBG and its collaborators on the NCI-60. SpliceCenter: A suite of very user-friendly tools designed for use by every bench biologist who needs to check for the impact of gene splice variation on common molecular biology technologies including RT-PCR, RNAi, expression microarrays, and peptide-based assays. SpliceMiner: A web application for mapping microarrray probes to transcripts in an exon-specific manner. CIMminer: A tool that produces Clustered Image Maps (CIMs) (i.e., clustered heat maps). … Continue reading →

By Estel Grace Masangkay Using a bioinformatics approach, Ohio State University researchers found that isolation of the endothelial progenitor cell might not be necessary to understand and possibly improve cardiovascular health. Instead, stem cells in circulating blood might be used to study cardiovascular health. Nicanor Moldovan, senior author of the study and a research associate professor of cardiovascular medicine at The Ohio State University, said, There are people who still dream that the prototypical progenitors for several components of the cardiovascular tree will be found and isolated. I decided to focus the analysis on the whole nonpurified cell population the blood as it is. The research group decided to skip the traditional method of isolation and keep the entire blood sample for analysis. The team analyzed gene activity at the messenger RNA level, then narrowed the search to detect mRNA for 45 genes in the blood cells. The sorting produced gene clusters which were aggregated into two modules. A total of 15 primitive and cardiovascular genes showed a clear connection in a module. Blood samples from healthy volunteers helped define the cardiovascular-relevant module, which suggested that higher expression of the identified genes were associated with younger age, more flexible vessels, … Continue reading →