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Bioinformatics platforms for analyzing global gene expression (MBCO AACR 2018)

This video series was recorded on the last day of the RNA-seq Analysis in Cancer Biomarker Discovery and Network Interpretation laboratory from the 2018 American Association for Cancer Research Molecular Biology in Clinical Workshop. This section of the course concerned the interpretation of the final gene list from an RNA-seq analysis of 7 ovarian tumors (OTs) vs. 7 tumor-associated macrophages (TAMs) (Reinartz et al. Genome Biology 2016, 17:108) produced in the initial section of the lab by the workshop participants.


Part 1: Introduction to types of bioinformatics interpretation platforms

Part 1 in this video series gives an introduction to the types of bioinformatics platforms available for pathway mining, network building, data mining and clinical interpretation. Part 2 demonstrates the pathway/network platform STRING using the top 200 genes (by fold change) upregulated in the TAMs vs. OTs. Part 3 introduces the Illumina pathway/data miner, Correlation Engine, by using a larger list of genes upregulated (log2 fold change greater than 2) in the TAMs vs. the OTs. Part 4 deals with using clinical information with our analysis by introducing some of the functionality of Illumina’s Cohort Analyzer.


Part 2: Demonstration of Search Tool for the Retrieval of Interacting Genes/Proteins (STRING)


I would like to thank my co-instructors for this course, Drs. Tzu Phang and Robert Stearman from the University of Colorado Denver and Indiana University School of Medicine, respectively. I would also like to thank Illumina Informatics for donating the use of their platform during and after this course and the American Association for Cancer Research for once again putting on a fantastic workshop.


Part 3: Demonstration of Correlation Engine (Illumina)


I would like to thank my co-instructors for this course, Drs. Tzu Phang and Robert Stearman from the University of Colorado Denver and Indiana University School of Medicine, respectively. I would also like to thank Illumina Informatics for donating the use of their platform during and after this course and the American Association for Cancer Research for once again putting on a fantastic workshop.


Part 4: Demonstration of Cohort Analyzer (Illumina)


All opinions expressed in the video are the speaker’s and do not necessarily reflect those of the companies whose platforms are being demonstrated. Any uses of the products and platforms described in this presentation may be uses that have not been cleared or approved by the FDA or any other applicable regulatory body.

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