Cis-regulation 2015 - Course content

Web site for this course

http://jvanheld.github.io/cisreg_course/

Teachers

Abbrev	Name
JCM	Jaime Castro Mondragon
DP	Denis Puthier
JvH	Jacques van Helden

Resources

Resource	Link
Glossary	concept definitions
Regulatory Sequence Analysis Tools (RSAT)	http://rsat.eu/
RSAT teaching material	http://rsa-tools.github.io/teaching/
RSAT course (slides)	http://rsa-tools.github.io/course/
footprintDB	http://floresta.eead.csic.es/footprintdb/
MEME suite	http://meme-suite.org/

Content table

Date	From	To	Subject	Teacher	Practicals
Mon 17/10	09:00	10:30	Characterizing and representing TF-DNA interactions (from sites to motifs)	JvH	[01.2_regulatory_sequences_intro] [RSAT] [tutorial from sites to motifs]
Mon 17/10	11:00	12:30	Introduction to motif database	JvH	[footprintDB] [JASPAR] [HOCOMOCO] [RegulonDB]
Mon 17/10	14:00	15:30	ChIP-seq analysis	DP	[slides] [tutorial mapping]
Wed 21/10	16:00	17:30	ChIP-seq analysis	DP	[tutorial peak annotation] [tutorial peak-motifs]
Tue 18/10	09:00	10:30	Scanning sequences to predict binding sites (from motifs to sites)	JvH	[01.4.PSSM_theory] [02.3.pattern_matching_matrices] [01.3.sequence_models] [RSAT] dna-pattern, matrix-scan, permute-matrix, random-seq [tutorial E.coli promoter scanning]
Tue 18/10	15:10	16:55	ENCODE	JvH	[tutorial: ENCODE ChIP-seq peaks]
Wed 19/10	14:00	15:30	Discovering motifs in regulatory sequences (from sequences to motifs)	JvH	[03.2.1.pattern_discovery_strings] [03.3.pattern_discovery_matrices] [RSAT] oligo-analysis, dyad-analysis, position-analysis, random-genes [MEME]
Wed 19/10	16:00	17:30	Motif comparison and clustering	JvH + JCM	[RSAT] matrix-clustering [slides] [tutorial matrix-clustering]

Travaux personnels

Description des travaux personnels

White/green board pictures

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