In general, the resources listed here for the computational test will be somewhat helpful, but never as helpful as the materials covered in miRcore MVP meetings. We list most of the MVP meeting dates that cover each topic in hopes that you can refer to your notes/slides from those lectures.
Conceptual Test (multiple choice)
Immune system
Topics:
Common autoimmune diseases: Type 1 Diabetes, Multiple Sclerosis, Celiac Disease, Crohn’s Disease
Meetings:
Sep. 24, 2022: Groups
Oct. 29, 2022: Immune and autoimmune
Statistics
Topics:
P-values/logFC
t-tests
Enrichment
Meetings:
Nov. 5, 2022: Statistics
Genetics
Topics:
DNA and base pairing rules
DNA replication, transcription, translation
RNA processing (editing and splicing)
Central Dogma
Amino acids and codon relationships
Genetic crosses and Punnett squares
Basic knowledge of technologies measuring DNA sequences, RNA expression, and protein amount
Microarray analysis and electrophoresis
Meetings:
Oct. 8, 2022: DNA
Oct. 15, 2022: RNA
Other resources
Lecture slides from “Computational Biology Camp for High School Students”
DNA RNA Proteins on August 21, 2012
Gene Expressions on August 22, 2012
Additional lecture slides from the one-day camp on January 29, 2013
Computational Test (multiple choice + free response)
GEO2R About Page: Explanations on defining groups, volcano plots and boxplots, analyzing datasets with GEO2R
Meetings:
Oct. 22, 2022: Microarray and GEO
Nov. 5, 2022: Group definition and data validation
Nov. 5, 2022: T-test and GEO2R
String About Page: Explanations on creating String maps, interpreting String maps and enrichment analysis (GO, KEGG), navigating the platform. Goes a bit too in-depth though, would not recommend spending much time studying this.
Meetings:
Nov. 12, 2022: String-db
Nov. 19, 2022: Enriched testing and GO
Dec. 3, 2022: Enriched testing and GO
KEGG About Page: Explanations on KEGG sidebar functions and includes a great diagram of KEGG map notations. Would definitely at least have a look at the map notations.
Meetings:
Dec. 10, 2022: GO KEGG Pathways GeneCards
Meetings:
Oct. 8, 2022: DNA
Meetings:
Dec. 10, 2022: GO KEGG Pathways GeneCards
Meetings:
Oct. 8, 2022: DNA
Oct. 15, 2022: RNA
Examples of tasks for the computational test:
- Identify a gene related to the increased risk of developing late-onset Alzheimer’s with specific DNA sequences. This gene is on chromosome 19 and one of the four forms of this gene accounts for about 40 percent of all cases of late-onset Alzheimer’s. Write its general symbol, not differentiating the four forms.
- Identify the function of the gene (helpful sites: http://www.genecards.org, http://www.ncbi.nlm.nih.gov/gene)
- Find its genome position (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway, http://www.ncbi.nlm.nih.gov/gene)
- What is the total number of transcribed sequences?
- Find the mRNA sequences. No need to worry about U/T conversion or upper/lower cases. T will be considered as U (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway,http://www.ncbi.nlm.nih.gov/nuccore).
- Find only coding sequences among the mRNA sequences. No need to worry about U/T conversion or upper/lower cases. T will be considered as U (helpful sites: http://genome.ucsc.edu/cgi-bin/hgGateway: use “Genomic Sequence” rather than “mRNA” sequence for this task, http://www.ncbi.nlm.nih.gov/nuccore).
Other resources
UCSC Genome Browser Demo (prepared by a student)
Genes in general (from the One-day camp on January 29, 2013)
Using GEO2R to find biomarkers (from Saturday miRcore volunteer meetings)
Disease of focus: Autoimmune Diseases
General Topics
Symptoms
Treatment
Genes and Environments
Social impact