Lecture 4 - Transcriptomics

Hidden Markov Model
=> It is the method that calculate a frequency of the degree of different nucleotide in the part which you want to analyze.
cf SNP = Single Nucleotide Polymorphism
Calculate a frequency of the degree of the only one different nucleptide in the part you want to analyze

Expression is up and down of gene product
Transcriptomics : RNA seq, microarray
RNA is the first of life machinaries of biochemistry

Transcription : copy of them -> one to one
Translation : make different one based on original things -> one to another one 

RNA - It has an oxygen on 2`site of sugar, It is the single stranded nucleic acid => unstable - very short half life
DNA - It has no oxygen on 2`site of sugar, It is the double stranded nucleic acid => stable

There are many RNA types : noncoding RNA (miRNA, siRNA), spliceosome, ribosome...
The number of RNA species : 10 millions

Question: Is it possible to calculate the case of combination in the different order(ex - ABC, BCA)?

Homework
There are about 8 exons in one gene. What is the possible combination by the alternative splicing or How can we restirct the number of possible exons.

I think that it must exist the both ends of the exons because those parts are required to the UTR(UnTranslated Region), therefore we should calculate the number of the possible exons in only 6 exons.

We can also select or exclude each exon about the 6 exons -> possible case is 2(select or not) x 2 x 2 x 2 x 2 x 2 = 32

File:Select or not.png
 
We can restirct the possible cases if we consider the part which must exsit because it is an essential for survival or connected parts which must exist together for one function(This is Incheon`s idea).

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