Bioinformatics Lecture 4

Question 1

transcriptomics

Answer 1

all RNA in a cell

Question 2

advantage transcriptomics

Answer 2

better measurable than proteins

higher test retest reliability

Question 3

low throughput transcriptomics

Answer 3

qPCR

mRNA FISH

Question 4

qPCR

Answer 4

one piece of RNA gets amplified

used for covid tests

Question 5

mRNA FISH

Answer 5

visualizes RNA molecules

fluorescent molecules stick to them

Question 6

high throughput transcriptomics

Answer 6

RNA-seq

older: micro arrays

Question 7

RNA-seq

Answer 7

turns RNA into DNA
replicates DNA
maps and counts genes

Question 8

biases in RNA-seq

Answer 8

leading to higher count
longer genes
bigger libraries
position and length in genome

Question 9

what RNA-seq can and cannot

Answer 9

can NOT compare counts of two genes

CAN compare the same gene between samples

Question 10

cell lines

Answer 10

derived from tutors

grown in petri dish

Question 11

measure of drug effectiveness

Answer 11

IC50

how much you need to kill 50% of cells

Question 12

dimensionality reduction methods

Answer 12

MDS - multidimensional scaling
PCA - principal component analysis
UMAP

Question 13

MDS

Answer 13

organisms with similar genes are plotted closer together

ideally, control and experimental are far apart

Question 14

effect size measure transcriptomics

Answer 14

log-fold changed

log2(expression A / expression B)