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Small RNA Analysis
Small single stranded RNAs (~21-25 nucleotides)
but derived from larger precursors (double
stranded RNAs)
Non-coding sequences
Form imperfect stem-loop structures (hairpin)
Negative regulators of gene expression
(Postranscriptional and Translational regulation )
The journey that led to the discovery of miRNAs
began in 1993 with the humble nematode worm
...
After some remarkable
detective work, they decided
that this RNA did not code for
any protein, but the actual role
seemed somewhat obscure
Differential expression
SmallRNA characterization
More the 1 sample, study the
up and down regulated
smallRNA expression
...
Read characterization by
mapping to a reference genome
sequence, known RNA families (e
...
,
Rfam), and known microRNA
sequences (e
...
, miRBase)
smRNA-seq
Analysis
Target gene prediction and
pathway analysis
Expression count (mature
mirRNA)
Predict the genes target and
their pathway (GO)
Novel microRNA prediction
Secondary structure criteria
and MFEI calculation
Data preparation
Prepare and check the sequence quality
Basic Analysis
Trim sequence adapters and low quality
sequence reads
Merge the read and count
Annotate by mirBase
Produce Annotated and Un-annotated result
http://articles
...
com/sites/articles/archive/2012/02/18/eating-wrong-plants-can-mess-dnaexpression
...
Annotated result
Un-Annotated result
Formula
Information need
1
...
Number of G and C in pre-miRNA
3
...
P
...
A=17 , C=10 , G=11, T=26
Prediction of potential target of miRNAs
Software - http://omictools
...
noble
...
genetics
...
cn/psRobot/
MAGI
http://elgar
...
edu/software/magi/index
...
ym
...
tw/ym500/index
...
cs
...
ca/~blanchem/mirdup/
CleaveLand http://axtell-lab-psu
...
com/cleaveland
...
cmp
...
ac