The Analysis of Regulatory Sequences

This web site contains support material for the course on the Analysis of Regulatory Sequences.

Jacques van Helden
ORCID 0000-0002-8799-8584
jacques.van-helden@univ-amu.fr

Pre-print version of a book chapter for a course given in Les Houches (2004).

Transcriptional regulation
Sequence models
Position-specific scoring matrices
Transcription factor databases
Pattern matching
	Introduction
	String-based pattern matching
	Matrix-based pattern matching
	Probability distributions of matrix scores (matrix-distrib)
	Empirical distributions of matrix scores (matrix-quality).
	Detection of cis-regulatory modules (CRMs)
Pattern discovery
	Introduction
	String-based pattern discovery
	Word count statistics
	Matrix-based pattern discovery
	Genome-scale pattern discovery
Evaluation of pattern predictions
	Motif comparisons
	Evaluating pattern matching and pattern discovery results
Gene classification on the basis of upstream motifs
Analysis of gene expression data
	Introduction to DNA chips
	Analysis of regulatory regions from DNA chip clusters
Comparative genomics
	Phylogenetic footprints (intro)
	Discovering phylogenetic footprints in bacterial genomes
Inference of clusters of functionally related genes
Hgh-throughput sequencing
	peak-motifs: detecting motifs in large sets of ChIP-seq peak sequences
Acknowledgements
Short presentation