66569 - DNA/RNA DYNAMICS

Scheda insegnamento

SDGs

L'insegnamento contribuisce al perseguimento degli Obiettivi di Sviluppo Sostenibile dell'Agenda 2030 dell'ONU.

Parità di genere

Anno Accademico 2021/2022

Conoscenze e abilità da conseguire

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.

Contenuti

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 tests of statistical analysis such as t student test, Wilcoxon signed-rank test, ANOVA, Mann-Whitney test, GLM •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. 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

Testi/Bibliografia

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

Metodi didattici

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).

Modalità di verifica e valutazione dell'apprendimento

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.

Strumenti a supporto della didattica

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.

Orario di ricevimento

Consulta il sito web di Miriam Capri

Consulta il sito web di Maria Giulia Bacalini