Database Detectives: Exploring Public Genomic Databases

Overview

This activity guides students through using publicly-available genomics databases. Students start with four Drosophila genes and learn how to find information about these genes, as well as information about homologous genes in mice, zebrafish, and humans. Finally, they use human disease databases to identify the human health consequences of mutations to the Drosophila homologs.

This activity is loosely based on the game Clue. Students need to match four Drosophila genes to the correct experimental data and background research.

Duration: 1-3 hours (help us improve this estimate!)

Learning Objectives

  1. Explore commonly-used public genomic databases to become familiar with the biological information on them.

  2. Identify genomic information for four different Drosophila genes.

  3. Compare how gene location and expression differs between species for homologous genes.

  4. Determine the associations between Drosophila gene homologs and human diseases.

Prerequisites

Students will benefit from some awareness of chromosome and genome organization and model organisms, as well as having a solid understanding of the Central Dogma. We suggest this activity could accompany lectures that discuss these topics.

Evaluation

GEMs is an NIH-funded program. Part of our mission is understanding the impact of our materials. Please take the time to review our program as an instructor after this activity. We also appreciate you distributing our survey to students before and after they participate in GEMs content.

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Instructor survey

Student pre-activity survey

Student post-activity survey

You can view our IRB approval here. Feel free to contact the GEMs team with any questions (gems at fredhutch dot org).

Materials

Student Activity

You can use this module in several formats. Feel free to adapt to your needs!

Students will need a device that accesses the internet.

WarningThis content contains URLs

We suggest confirming links are still active prior to running this activity.

Students will use these websites: FlyBase, Mouse Genome Informatics, ZFIN (Zebrafish Information Network), GeneCards, OMIM, and MalaCards

Instructor Materials

A Google Slides presentation is available for borrowing images here.

An answer key is available here. Please message Ava Hoffman (ahoffma2 at fredhutch dot org) to get access.

Scientific Topics

In addition to working with public genomic databases, students are exposed to the following concepts:

  • Curated Databases: databases where information is screened, validated, and organized by experts to ensure the data are accurate and reliable. Information from these databases is typically standardized and organized in a consistent way so it is easily accessible and searchable.

  • Homologs and Orthologs: genes or proteins across species that are similar to each other due to having a common evolutionary origin. An ortholog is a special type of homolog, in which both genes also have similar functions within different species.

  • Model Organisms: species used by researchers to study specific biological processes and diseases in an effort to understand how how the processes and diseases work in humans.

  • Gene Ontology: a bioinformatics initiative focused on standardizing the vocabulary and annotations researchers use to describe genes, proteins, and data about gene and protein function.

  • Genome Assembly: a version of the genome map.

Outline

  • Part 1: Using FlyBase

  • Part 2: Identifying Homologs; Using Mouse Genome Informations, ZFIN, and GeneCards

  • Part 3: Using OMIM and MalaCards

  • Part 4: Solving the Data Mystery