Analysis of regulatory sequences (UNAM LCG BE-II)

This site contains the support for the courses 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
• Final report
• Resources
• Support or Contact

Access

• Web site
• Download ZIP File
• Download TARBall
• View On GitHub

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 gene regulation based on Next Generation Sequencing data.

Keywords

• Regulatory Sequence Analysis Tools (RSAT)
• Bioinformatics
• Statistics
• Genomics
• Next Generation Sequencing (NGS)
• ChIP-seq

Authors and Contributors

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

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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]
Exercises: scaning sequences with a reference motif	[html] [Rmd]
Solutions scaning sequences with a reference motif	[html] [Rmd]

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]

Final report

• The final report will consist in finishing the practical on ChIP-seq analysis.

• Reports must be submitted on the LCG BEII Web site before Feb 9.

• A template is provided in .docx and Rmd formats. Read carefully the instructions before starting the work.

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/
ChIP-seq tutorial	Tutorial on chip-seq analysis written by Morgane Thomas-Chollier, from which I used the FNR dataset used in this course http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/
Stats4bioinfo	Supporting site for an introductory course about statistics for bioingormatics http://pedagogix-tagc.univ-mrs.fr/courses/statistics_bioinformatics/
AVIESAN NGS ChIP-seq course	http://jvanheld.github.io/EBA15_stats_RStudio/
Classification performance indicators	Confusion matrix, Sensitivity and specificity
JASPAR	Open-access database for eukaryotic transcription factor binding profiles: https://jaspar.genereg.net

Support or Contact

Jacques.van-Helden@univ-amu.fr

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