66569 - Dna/Rna Dynamics

Course Unit Page

  • Teacher Miriam Capri

  • Learning modules Miriam Capri (Modulo 1)
    Maria Giulia Bacalini (Modulo 2)

  • Credits 6

  • SSD MED/04

  • Language English

  • Campus of Bologna

  • Degree Programme Second cycle degree programme (LM) in Bioinformatics (cod. 8020)

SDGs

This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.

Gender equality

Academic Year 2021/2022

Learning outcomes

At the end of the course, the student has the basic knowledge that gene transcription is intrinsically a dynamic process based on chromatin remodeling and a complex RNAs pool mediating the transcript regulation. In particular, the student will be acquainted with the most up-dated high throughput technologies (microarrays and deep sequencing) from two points of view such as biological and statistics. Data mining and cluster analyses will be acquired by the student.

Course contents

Module I and II classes' frequency IS MANDATORY.

- Main Topics of Module I:

•DNA and RNA dynamics: the meaning •Microarrays: origin and history and next generation sequencing •Stanford University Method - Competitive method •Affymetrix Method - Non Competitive method •Illumina Method- Non Competitive •Next Generation Sequencing: basic concepts including ChIP-sequencing and DNA methylation sequencing•Analysis and discussion of published articles

-Elements of basic statistics in Module I:

•Normalization methods; •description of the main parametric and non-parametric statistical tests such as t Student test, Wilcoxon signed-rank test, ANOVA, Mann-Whitney test; •main methods for multiple test correction (FDR, Bonferroni, Benjamini-Hochberg). •Unsupervised data analyses •pathways reconstruction and mapping of expression values onto known pathways and ontologies embedded in databases (GeneOntology).

-Practical application of data mining in R environment in Module II. In particular, an overview of the bioinformatic tools currently available to explore and analyse genome-wide and sequencing data, with a particular focus on DNA methylation microarrays. Through the use of example-oriented exercises, the student will learn how to use R environment and Bioconductor packages to manage genomic data and answer biological questions •

  • A practical application of ChIP-Sequencing will be performed with a special guest

Readings/Bibliography

Statistical ANALYSIS OF NEXT GENERATION SEQUENCING DATA

Somna Datt, Dan Nettleton Editors- Springer 2014

MICROARRAY BIOINFORMATICS- DOV STEKEL – Cambrige University

press- reprinted in 2005

Statistics (The Easier Way) with R: an informal text on applied statistics by Nicole M. Radziwil, 2015

Teaching methods

Module I and II lessons will be tightly interrelated being theoretical the former and applicative the latter.

However, due to CoViD-emergency the lessons will be given following the rules decided by the Rector, including the possibility to attend all the course by the online platform TEAMS.

During the lessons take home messages will be highlighted and discussed. Published papers will be shown and discussed during the lessons.  

At the end of Module I, a verification test will be proposed to evaluate the level of acquired knowledge and the effectiveness of lessons. Those students able to achieve high score (> 15/20) will be allowed to keep the score as DRD module I evaluation, which will be added to DRD module II score (see you below).

 

 

 

Assessment methods

Exam consists of two parts:

1. Module I exam, for the theoretical part, will be a written test based on 4 program-related and open questions (5 scores each; 20+ is the maximum level considering the highest performance).

No restriction of characters are foreseen for each open question, but 8-12 lines are suggested.

For each relevant mistake (related to the basic knowledge to be acquired) -1 score will be subtracted, while for a small mistake (typically due to an incomplete definition) -0.5 score will be subtracted

A scanty answer will be judged with severity, until the loss of all the scores available for each question.

The time for the exam will be 45 minutes.

 

2. Module II exam, for the practical part, will be a home-made report focused on a data set of DNA methylation at genome-wide CpG levels). Data processing and analysis are expected to be performed and described as well as learned during the module II lessons (10+ is the maximum level considering the highest performance).

Final DRD mark will be the DRD module I score plus module II score. Laude will be added in the case of excellent performance.

The online platform used in case of persistent CoViD-emergency will be EOL-ZOOM.

 

Teaching tools

The teacher will use personal laptop, projector and slides.

Students will be provided with slides related to each lessons and papers/reviews obtained by up-dated scientific literature.

 

The online platform is TEAMS.

 

Office hours

See the website of Miriam Capri

See the website of Maria Giulia Bacalini