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)
Motif discovery
	Introduction: motif discovery
	String-based motif discovery
	K-mer count statistics
	Matrix-based motif discovery
	Genome-scale motif discovery
Evaluation of discoverd motifs
	Motif comparisons
	Evaluating pattern matching and motif discovery results
Classifying gene promoters (upstream non-coding sequences) based on motif counts
Analysis of tanscriptomic data
	Introduction to DNA chips
	Analysis of regulatory regions from clusters of co-expressed genes
Comparative genomics
	Phylogenetic footprints (intro)
	Discovering phylogenetic footprints in bacterial genomes
Inferring groups of functionally related genes
Hgh-throughput sequencing
	peak-motifs: detecting motifs in large sets of ChIP-seq peak sequences
Acknowledgements
Short presentation