_____________ next generation sequencing
NGS
What is the primary goal of NGS
Capture expression levels
_______________ align across intron where splicing occurs. Thus RNA sequencing is key for determining alternative splicing
Reads align to exon junctions in Next generation sequencing
_____________ is very prevalent. We can figure out using RNA sequencing we can understand how many human genes are alternatively spliced
Alternative splicing (AS)
using RNA sequencing we can understand how may genes are __________________
alternatively spliced
Alternatively splicing allows multiple ____________ to be produced from one gene. This allows for incredible diversity.
mRNA
The more reads you take the more genes with _______
______________
alternative splicing.
technological advancement has shown _____________________
alternative splicing events
_____________________ what we want to count from RNA sequencing
Expression level
Simply count the number of reads to exon or genes this is proportional to _______________________
expression levels
______________ we need to normalize the sequence length.
simply count the number of reads to exon or genes. This is proportional to expression levels
__________________ Now we have a long list of genes and exons and their expression levels (number of reads or spot intensity)
post processing of transcriptome data
Post processing of Transcriptome data:
- differential gene expression
- Data Clustering
- Biological network and function
_______________________:
- microarray values are used as age axis labels
- each blue dot represents a gene
- The x and y axis: Cy5 or Cy3 of normal tissue
- The x and y axis of normal vs tumor tissue didn’t show correlation
Differential gene expression
_____________________________
- diagonal lines are the fold change lines
- To measure the difference in gene expression
- The distance of the data point from the diagonal line (label 1)
Data Clustering
________ is a measure describing how much a quantity changes between an original and a subsequent measurement
Fold change
Statistical Treating of differential expression
T test of single gene
What is the purpose of a T test
- we want to know if its expression level changed between sample sample A and B
- Null: assumption no change
- obtained the expression level of the Gennes in two Samples, A and B in multiple experiments.
- Calculate X and X the mean levels in duplicated A and B samples
- Goal: to determine if the mean values are different
What is the goal of a T test
the average values of A and B different
- Requires independent experimental duplication
- assumes the data are normally distributed
Statitical T testing
