The Analysis of Regulatory Sequences
Warning
This web site contains support material for the course on the Analysis of Regulatory Sequences.
Site
http://rsa-tools.github.io/course/
source repository
Author
Jacques van Helden
ORCID 0000-0002-8799-8584
jacques.van-helden@univ-amu.fr
Book chapter
Pre-print version of a book chapter for a course given in Les Houches (2004).
The Analysis of Regulatory Sequences
Slides
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