In silico cis-analysispromoter analysis

- Promoters and cis-elements

- Searching for patterns

- Searching redundant patterns

What is a promoter?and why care about it?

CDS

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

A little about thesecis-elements

- Transcription Factors (TF) often bind to them

- They are normally from 5-10 bp long

- They are often placed in the region from TSS and upstream

- Often they come in clusters i.e. must be placed in some ‘syntax’ to be functional

- We assume, they are shared by the promoters in a regulon

- They are not always conserved 100%

Sound hard to find?it is hard

Some tricksmakes it possible

Regulon (cluster)

Comparing promoters from a regulon to all other promotersi.e. using a negative set (all other promoters in species X)

This allows us to use hypergeometric statistics

Ranked list of genes

The distribution of sequences with a given pattern along a ranki.e. is the pattern overrepresented in promoters with low (or high)

p-values in a microarray experiment

This allows us to use Kolmogorov-Smirnov

Hypergeometric Statistic

10x5x

Takeout 6 balls

1x5x p=0.04

Kolmogorov-Smirnov, here test for deviations from a uniform distribution of patterns along a sorted list og promoters

Patte

rnO

ccurre

nce

Promoters ranked by e.g. p-value

A cis-elementas it might be seen by a TF

So, the elements maynot always be 100% conserved

If we only had a weight matrice to describe our pattern we could find less conserved patterns

With a Gibbs sampler we can work backwards• We give it promoters and it builds a weight matrix

Motif model (residue frequency x 100):POS A C G T Info1 89 . . . 1.02 . . 92 . 2.03 . . . 94 1.24 . 92 . . 2.05 94 . . . 1.26 94 . . . 1.2

weight matrix

Try it!Find the exercise on the course page

Exercise: in silico cis-analysis

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mRNAs OVEREXPRESSED IN mpk4 MUTANT

Gibbs sample evaluation

TTGACT

Gibbs sampling on 1000 random sampled sets of 17 Arabidopsis promoters, evaluated by information content.

monte carlo

GACTTTTC

Gibbs sample evaluation

Gibbs sampling on 1000 random sampled sets of 17 Arabidopsis promoters, evaluated by information content.

monte carlo

Here for 8bp patterns

Lebel et al. 1998Arabidopsis PR1 promoter