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 @ dannyarends.nl/bioinformatik/
Programming Assignments and Answers @ dannyarends.nl/bioinfo/
Playlist: • Bioinformatics for Pla...
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 @ / dannyarends
This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see creativecommons.org/licenses/b...
#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

[@fs7463]

Thank you professor, it is extremely helpful and clear. I really appreciate the composition and structure of the slides. Actually, the best thing is even the small detail, which is usage of each slide titles very effectively. It makes everything very understandable.

[@DannyArends]

Thank you for the kind words, and awesome to hear you found it helpful. Enjoy the lectures

[@HeLiAn5]

Thank you for making this content available for everyone, you made everything really clear!! Can I ask for the pdf of these slides, lecture 12 is not included in the attached link.

[@DannyArends]

Sure, just drop me an email and I can send them. My email is on the about page of the channel.

[@MrEgol]

Thank you very much, awesome content!

[@DannyArends]

Glad you liked it! Thanks for leaving a comment