
Genomics, Proteomics and Interactomics
Code: 100947Credits: 6
| Degree programme | Type | Course |
|---|---|---|
| Biotechnology | OB | 3 |
Contact lecturer
- Name :
- Alicia Roque Cordova
- Email :
- alicia.roque@uab.cat
Teaching staff
- Marta Puig Font
Group languages
You can consult this information at the end of the document.
Prerequisites
Although no previous formal requirements have been set, basic knowledge is expected on Biochemistry and Molecular biology, Genetics, Microbiology, Cell biology, Methods on recombinant DNA and Statistics.
For certain activities a basic level of english reading comprehension ability is required.
Objectives
Genomics is the science dealing with the structure, content and evolution of genomes. Is a relatively novel science (we can say that it was born in 1995 with the sequencing of the first bacterial genomes) that developed explosively in the last years. The development of methods for automatic sequencing of nucleic acids has been a key factor about. In 2001 the first draft of the sequence of the human genome was presented, a historic milestone that opened the doors for the studies on comparative genomics and the evolution of the human species, on the biological clues of the human nature, on the genotype-phenotype association studies to find genes or regions of DNA related with diseases, etc.
After the sequencing of genomes appeared the so called "postgenomic" period. Among its tasks are the analyses of genes and genomes expression in a massive way (Transcriptomics and Functional Genomics), the identification and structural-functional analysis of proteins (Proteomics), and of their interactions (and with the other biomolecules) and formation of complexes (interactomics). Together with the identification and quantitation of all the metabolites present in a sample of an organism (Metabolomics), such knowledge provides the basis to try the integration of the whole conjoint and reach a global description of the biology of the cell (Systems biology).
The main formative goals of the subject are : the understanding of the diversity and complexity of genomes and proteomes; the study of the historic and evolutionary character of the genetic information as well as its nature, the meaning and consequences of the intraspecific and interspecific variability; and finally the potentiality of the applications that come from the genomic, transcriptomic and proteomic information. It is also part of the subject to know the experimental and computational methods that are used in the so-called "omic" sciences.
Learning outcomes
- CM25 (Work collaboratively in teams to solve problems in the field of systems biology.) Work collaboratively in teams to solve problems in the field of systems biology.
- KM25 (Describe the physical and chemical bases of the methodology and instrumentation used in genomic, transcriptomic, proteomic, interactomic and metabolomic analysis.) Describe the physical and chemical bases of the methodology and instrumentation used in genomic, transcriptomic, proteomic, interactomic and metabolomic analysis.
- SM23 (Use the fundamentals of mathematics, physics and chemistry necessary for the study of regulatory mechanisms at the molecular level in living beings.) Use the fundamentals of mathematics, physics and chemistry necessary for the study of regulatory mechanisms at the molecular level in living beings.
Contents
GENOMICS
Introduction to genomes
Sequencing, assembly and annotation of genomes
Study of gene expression: Transcriptomics
Genome evolution: Comparative genomics
Genomic variation
PROTEOMICS AND INTERACTOMICS
Introduction and basic concepts
Proteome diversity
Experimental methods in proteomics
Quantitative proteomics
Structural and functional proteomics
Interactomics
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Tutoring | 3 | 0.12 | KM25, SM23 |
| Theory sessions | 32 | 1.28 | KM25, SM23 |
| Seminars and Problems | 12 | 0.48 | CM25, KM25, SM23 |
| Recommended reading and problems | 40 | 1.6 | KM25, SM23 |
| Study | 42 | 1.68 | KM25, SM23 |
The subject consists of theoretical classes, seminars for the resolution of practical cases and scientific articles, problems and tutoring sessions. The following describes the organization and the teaching methodology that will be followed in these three types of training activities.
Theory:
The content of the theory program will be taught mainly by the teacher in the form of master classes with audiovisual support. Presentations used in class by the teacher will be previously available on the Virtual Campus of the subject. It is recommended that students print this material and take it to class, to use it as a support when taking notes. It is recommended that students regularly consult the books recommended in the Bibliography section of this teaching guide in order to consolidate and clarify, if necessary, the contents explained in class.
Seminars and problems:
The objective of the seminars and the problem sessions is to connect theory sessions with practical work, promoting active learning to develop the ability to analyze and synthesize, critical reasoning, and problem-solving ability. The seminars and problems are sessions with a small number of students (maximum 40 students). Their goal is to deepen or complete the knowledge exposed in the theory sessions by solving problems, discussing case studies and scientific literature. Students will receive periodic readings recommended in English, problems and cases to solve, web addresses to consult, bioinformatics tools, etc.
Tutoring:
There will be up to 3 tutoring sessions in small group with the teacher. In these sessions the doubts raised by the students about the theoretical program topics will be resolved, and they will facilitate the comprehension of specific aspects of the subject.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Joint project | 10% | 2.5 | 0.1 | CM25, KM25, SM23 |
| Partial test 2 | 35% | 7.5 | 0.3 | KM25, SM23 |
| Seminars and Problems | 20% | 3.5 | 0.14 | CM25, KM25, SM23 |
| Partial test 1 | 35% | 7.5 | 0.3 | KM25, SM23 |
The evaluation of the subject will be carried out through a series of activities of continuous assessment, a partial exam and a review of recovery, corresponding to each of the two parts of the subject: Genomics and Proteomics / Interactomics. The weight of each part of the subject is 50% on the final grade. When beginning the classes of each part of the subject, the corresponding professor will detail how he will carry out the continuous evaluation. Below is the weight of the different tests and activities:
- Genomic Partial test 35%
- Proteomic Partial test 35%
- Genomics problems 10%
- Proteomics seminars 10%
- Joint project 10%
- Optional bonus 10%
The partial exams will consist of questions of type test and of short answer or problems. These tests will be eliminatory of matter.
The joint project consists of a joint assignment where knowledge and tools corresponding to both parts of the subject must be applied to solve the proposed exercises.
It will only be average with those qualifications that are> = 4.0.
In each part of the course, you will have the option to complete an additional activity, either during the term or on the day of the corresponding midterm exam. This activity can add a bonus of up to 1 point to your final grade (0.5 for each part of the course). The bonus will be applied only if your overall grade for the course is 5 points or higher.
Retake exam
Those students who do not exceed the minimum qualification of one or both partial tests must present themselves to the retake exam, if they meet the following requirement: To participate in the recovery, the students must have been previously evaluated in a set of activities whose weight equals to a minimum of two thirds of the total grade of the subject or module. Therefore, students will obtain the \"Non-Valuable\" qualification when the assessment activities carried out have a weighting of less than 67% in the final grade.
Grade improvement
The retake exam will also be open to any student who, having passed the partial tests, wishes to improve the score obtained in one or both partial tests. In this case, the student will have to notify the corresponding professors of their interest in presenting themselves to the retake examenandwill have to renounce the grade previously obtained. The degree of difficulty of the test grade improvement may be higher than the partial assessments.
Qualification
The subject is considered approved if the final grade is equal or greater than 5.0 points.
For the purposes of qualification, the student will be considered as non-evaluable when the assessment activities carried out have a weighting of less than 67% in the final grade.
Single assessment
The single assessment consists of a single synthesis test that includes the entire theory program of the subject. It will be carried out on the day fixed in the calendar for the second partial test. The exam will consist of quiz questions, problems, short questions, and definitions. The grade obtained in this synthesis test will account for 70% of the final grade of the subject.
Students taking the single assessment can hand in all the evidence corresponding to the Genomics problems (from a collection specific for the single assessment students) on the day of the synthesis test. On the same day, the joint project done individually, or in a group where all students are accepted for the single assessment, will be delivered. The grade for the problems and the joint project will account for 20% of the final grade of the subject.
The evaluation of the proteomics seminars will follow the same process as the continuous evaluation. The grade obtained will account for 10% of the final grade of the subject.
The retake exam will be the same as that of students in the continuous assessment and will only incorporate theory content. The rest of the evaluations are not suitable for the retake.
The weight of each part of the subject and the criteria for passing it are the same as for students in the continuous assessment.
Use of AI
For this course, the use of Artificial Intelligence (AI) technologies is permitted exclusively for [support tasks, such as literature searches or information gathering, text editing, or translations or other activities approved by the teaching staff. Students must clearly identify which parts have been generated using this technology, specify the tools used, and include a critical reflection on how they influenced the process and the final result of the activity. Lack of transparency in the use of AI in this gradable activity will be considered a breach of academic honesty and may result in a partial or total grade penalty for the activity, or major sanctions in severe cases.
Irregularities during the assessment
Any irregularity in an assessment activity (academic fraud, plagiarism, or unauthorized use of AI, unless such use is explicitly permitted in the course syllabus) that may lead to a significant alteration of the grade will result in a mark of 0 for that assessment. If the course syllabus establishes a minimum grade in that assessment as a mandatory requirement to pass the course, or if multiple irregularities are committed in assessment activities for the same course, the final grade for the course will be 0. In addition, disciplinary proceedings may be initiated against any student involved in such irregularities.
Bibliography
Textbooks:
- Gibson, G. & S. V. Muse, 2009 (3rd edition). A Primer of Genome Science. Sinauer, Massachusetts. USA.
- Brown, T. A. 2017. Genomes 4 (4th edition). Garland Science, New York, USA.
- Lesk, A.M. 2017. Introduction to genomics (3rd edition). Oxford University Press, Oxford, UK.
- Twyman R. M., 2014 (2n edition). Principles of Proteomics. Garland Science, New York & London.
- Lovric J., 2011. Introducing Proteomics. Ed. John Wiley & Sons, Oxford, UK.
- Mirzaei, Hamid, Carrasco, Martin (Eds.) Modern Proteomics – Sample Preparation, Analysis and Practical Applications. Springer. 2016. Available in digital format
Links:
- Campus Virtual de la UAB: https://cv2008.uab.cat/
- Entrez Genome Database: http://www.ncbi.nlm.nih.gov/sites/genome
- Expasy Proteomics Server: http://expasy.org/sprot
Software
Databases and analysis tools used in this subject are listed below:
Databases:
- Animal Genome Size Database, http://www.genomesize.com/
- Ensembl Genome Browser, http://www.ensembl.org
- Flybase JBrowse, http://flybase.org/jbrowse/?data=data/json/dmel
- GOLD Genomes Online Database, https://gold.jgi.doe.gov/
- NCBI Genome, http://www.ncbi.nlm.nih.gov/genome
- PopHuman Genome Browser, https://pophuman.uab.cat
- UCSC Genome Browser, http://genome.ucsc.edu/cgi-bin/hgGateway
- Genome Reference Consortium, https://www.ncbi.nlm.nih.gov/grc/human
- RepeatMasker, http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
- BioGPS, http://biogps.org/
- ENCODE, http://genome.ucsc.edu/ENCODE/
- Expression Atlas, https://www.ebi.ac.uk/gxa/home
- GENCODE Human, https://www.gencodegenes.org/human/
- InterMine, http://intermine.org/
- RevTrans, http://www.cbs.dtu.dk/services/RevTrans-2.0/web/
- Synteny Portal, http://bioinfo.konkuk.ac.kr/synteny_portal/
- VISTA Genome Browser, http://genome.lbl.gov/vista/index.shtml
- International Cancer Genome Consortium, https://icgc.org/
- Open Targets, https://www.targetvalidation.org/
- The Cancer Genome Atlas, https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga
- Human protein Atlas, https://www.proteinatlas.org/
- Uniprot, https://www.uniprot.org/
- SWISS-2D, https://world-2dpage.expasy.org/swiss-2dpage/
- Phosphosite, http://www.phosphosite.org/
- String, https://string-db.org/
Analysis tools:
- ScanProsite, http://prosite.expasy.org/scanprosite/
- Transeq, http://www.ebi.ac.uk/Tools/st/emboss_transeq/
- GeneID, http://genome.crg.es/geneid.html
- MASCOT http://www.matrixscience.com/
- Protparam https://web.expasy.org/protparam/
- Swissmodel https://swissmodel.expasy.org/
- Provean http://provean.jcvi.org/index.php
- INPS-server https://inpsmd.biocomp.unibo.it/inpsSuite
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE
| Type of teaching | Group | Language | Semester | Shift |
|---|---|---|---|---|
| (TE) Theory | 43 | Catalan/Spanish | first semester | morning-mixed |
| (PAUL) Classroom practices | 431 | Catalan/Spanish | first semester | morning-mixed |
| (PAUL) Classroom practices | 432 | Catalan/Spanish | first semester | morning-mixed |