Gene Expression Analysis (Bioinformatics S12E1)

An in-depth look at how we to measure and analyze tens of thousands of DNA probes simultaneously using RT-qPCR and micro-arrays. With applied examples in the R language for statistical computing. Lectures @ https://dannyarends.nl/bioinformatik/ Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/ Playlist: https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl Chapters: 00:00 Gene Expression Analysis, Question we want to solve 02:07 Real Time qPCR compared to genomic PCR, The delta delta CT method 05:58 Macro and microarrays to measure thousands of probes at the same time 07:30 Real Time qPCR and microarray workflow 08:30 Probe hybridisation due to complementary base pairing 10:15 One color versus Two-Color microarrays 12:04 Comparative Genomics, Expression Profiling, SNP Genotyping, ChIP-on-chip epigenetics 15:13 Microarray workflow: the Cy3 and Cy5 dyes 20:34 Into the data - Normalization 23:12 Microarrays, what could go wrong ? (and does) 25:52 Background correction of microarrays 27:58 Spatial normalization of microarrays 29:20 Bioconductor packages: RMA, GC-RMA, MAS 5, LOESS 30:26 After preprocessing: Expression matrix data overview 31:33 Processing the signal intensity data into Log2 Ratio 34:47 Dye bias is related to their Dynamic Range 35:57 Normalization as a concept, two goals and definitions 39:11 Quantile Normalization via preprocessCore, risks 42:50 Differentially expressed genes 44:25 T-test, average, standard deviations, T-statistics, Significance table 47:09 Analysis of Variance, multiple groups, covariates 50:29 ANOVA table, Two mouse strains and their offspring This is a live-stream recording of the MSc and PhD lecture series: #Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends. Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on Twitch @ https://www.twitch.tv/dannyarends This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/by/3.0/legalcode #bioinformatics #computationalbiology #lectureseries #programming #playlist #molecularbiology #science #englishstream #msc #phd #livestream #assignments #academicyoutube #academia #geneexpression #qpcr #rtqpcr #epigenetics #normalization #genes #microarray #significance #pvalue #dyebias #anova #covariates #log2 #ratios #hybridisation #RMA #GCRMA #MAS5 #LOESS #standardeviation #expressionprofiling #snps #chiponchip