Analysis of regulatory sequences (UNAM LCG BE-II)

This site contains the support for the course taught by Jacques van Helden to 2nd year students of the Licenciatura en Ciencias Genomicas de la Universidad Nacional Autonoma de Mexico, in the module “Bioinformatica & Estadistica II”.

Contents

• Access
• Scope of the course
• Keywords
• Authors and contributors
• Teaching material
• Resources
• Support or Contact

Access

• Web site
• Code repository

Scope of the course

This Web site contains the teaching material for a 1-week course taught by Jacques van Helden to 2nd year's students of the Licenciatura en Ciencias Genomicas (LCG) of the Universidad Nacional Autonoma de Mexico (UNAM).

The goal of the course is to introduce bioinformatics and statistical methods to analyse cis-regulatory elements in non-coding DNA sequences.

Keywords

• Regulatory Sequence Analysis Tools (RSAT)
• Transcription factor
• Transcription factor binding site (TFBS)
• Transcription factor binding motif (TFBM)
• Bioinformatics
• Statistics
• Genomics
• Next Generation Sequencing (NGS)
• ChIP-seq

Authors and Contributors

• Jacques van Helden (ORCID 0000-0002-8799-8584)

• Alfredo Hernandez (UNAM, Cuernavaca, Mexico) : deployment of the RSAT server on the LCG server; RSAT containerisation on Singularity.

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Teaching material

The slides presented in this course are a subset of a general course on Regulatory Sequence Analysis, available on github.

• Web site on gitlab
• gitlab repository

From TF binding sites to motifs and back (days 1-2)

Topics	Supports
Transcriptional regulation	[slides]
Position-specific scoring matrices (PSSM)	[slides]
Sequence models (Bernoulli, Markov chains)	[slides]
Matrix-based pattern matching	[slides]

Motif discovery (day 3)

Topics	Supports
Introduction to motif discovery	[slides]
String-based pattern discovery	[slides]
Tutorial: motif discovery in promoters of yeast regulons	[tutorial]
Exercise: discovering a motif discovery algorithm	[html] [pdf] [Rmd]

ChIP-seq analysis (day 4)

Topics	Supports
Slides: ChIP-seq technology + motif discovery	[pdf]
Practical: analyzing ChIP-seq peaks	[html] [Rmd]

Resources

Name	Description + URL
RSAT	Regulatory sequence analysis tools: http://rsat.eu/
RegulonDB	Transcription factor database: http://regulondb.ccg.unam.mx/
RSAT course	Teaching material about the analysis of regulatory sequences http://rsa-tools.github.io/course/
JASPAR	Open-access database for eukaryotic transcription factor binding profiles: https://jaspar.genereg.net
ReMap	Catalogues of TF binding peaks obtained with high-throughput methods (ChIP-seq, ChIP-exo, DAP-seq) for Homo sapiens, Mus musculus and Drosophila melanogaster: https://remap.univ-amu.fr/
Classification performance indicators	Confusion matrix, Sensitivity and specificity

Support and contact

Jacques.van-Helden@univ-amu.fr

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