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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

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

Teaching material

Day 1: from TF binding sites to motifs and back

Topics Supports
Introduction to the course [slides]
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]

Day 2: motif discovery

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

Day 3: ChIP-seq analysis

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://rsat-doc.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/

Support or Contact

Jacques.van-Helden@univ-amu.fr