Answers S4 and Protein lecture overview (Bioinformatics S5E1)
Channel: Danny Arends
Date: 26/11/2021

Answers to assignments 4 and overview of the protein lecture as well as a short history of proteins. During the first part, we'll investigate the RNA structure of the COVID19 spike protein, as well as using microarray expression data to perform differential gene expression analysis.

Lectures @ https://dannyarends.nl/bioinformatik/
Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/
Playlist: https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl

Chapters:
0:00 Welcome
0:30 Overview for today
1:30 Answers to the previous assignments
1:57 Downloading the COVID-19 spike RNA
4:25 Predicting the secondary RNA structure using #RNAfold
4:53 Loading micro array data into R
7:25 Determine the number of probes and samples
9:08 Explaining the read.table parameters
15:13 Creating box plots and histograms to visualize probe expressions
17:49 Use the apply function to log2 transform micro array data
20:14 Quality control on transformed expression data
24:12 Normalizing expression data using quantile normalization
32:33 Investigating groups by computing distances between samples
36:02 An alternative to statistics, looking at highly variable genes
42:28 Making a heat map of highly variable genes
46:48 Results of the  COVID-19 spike RNA folding
49:46 Start of the lecture - Quick history of proteins

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.

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This work is licensed under version 3.0 of the Creative Commons CC-BY license. 
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