Yeast “adopt an ORFan gene” project

Informatics and wet lab modules are available on this page

Informatics Lab Modules:

The modules provide introductory explanations and directions for implementation of bioinformatics algorithms, including multiple sequence alignment, conserved domain identification, signal sequence prediction, and cellular localization, to determining the function of yeast ORFans. The modules, which direct students in interpretation of algorithm results, result in a final product of student generated hypotheses of gene function.

The modules below are original or updated version of the modules as published in Bowling, Schultheis, and Strome at Northern Kentucky University (Bowling et al., 2015).  The original modules  available for  through SGD (http://yeastgenome.org/) at http://wiki.yeastgenome.org/index.php/Educational_Resources.  

Informatics Modules Overview  ppt: Informatics Modules Overview

NOTE: If worksheet (docx) links don’t work, right click, copy link address and paste in a new tab to download

Module 1. Introduction to Saccharomyces cerevisiae
This module provides an introduction to the SGD site, and the sequence tools available at SGD. A video walk through of this module can be viewed at https://youtu.be/yAxCT6U9IRQ

Module 1 Worksheet (PDF)

Module 1 worksheet (docx)

Module 1 guide (rev 6-2022)

Module 2: Structure-Based Evidence Part 1
This module guides students through finding functional predictions, based on homology to protein motifs and families, using the online tools Pfam, and PDB. (Note: TIGRfam has been incorporated into NCBI and has been removed from the module) A video walk through of this module can be viewed at https://youtu.be/jstz4JBbYvM

Module 2 worksheet-PDF (rev 6.6.20220)

Module 2 Worksheet docx (rev 6.6.2022)

Module 2 Guide (rev 6.6.2022)

Module 3: Structure-Based Evidence Part 2
This module is a continuation of the previous module. Like Module 2, Module 3 guides students through finding functional predictions, based on homology to protein motifs and families, using databases and tools such as SUPERFAMILY, SMART, GENE3D, and PANTHER. A video walk through of this module can be viewed at https://youtu.be/YmqqtWBrFLg

Module 3 Worksheet-PDF

Module 3 Worksheet (docx)

Module 3 Guide (rev 6.6.2022)

Module 4: Multiple Sequence Alignment
This module guides students through using protein sequence alignment tools, such as T-COFFEE and WEB LOGO, to view amino acid conservation and mutations. (Note: SGD no longer has synteny viewer; it has been removed from the module) A video walk through of this module can be viewed at https://youtu.be/qnFDN7BuFOo

Module 4 Worksheet -PDF (revised 6-6-2022)

Module 4 Worksheet docx (rev 6.6.2022)

Module 4 Guide (rev 6.6.2022)

Module 5: Cellular Localization Data Part 1
This module guides students through a number of algorithms used to predict protein membrane topology and cellular localization. The tools and algorithms use in this modules are: Transmembrane Helices Hidden Markov Models (TMHMM), TargetP (predicts the subcellular location of eukaryotic proteins), Phobius (a tool that combines data from TMHMM and TargetP to form a graphical output), and SignalP (predicts presence of a signal peptide). A video walk through of this module can be viewed at https://www.youtube.com/watch?v=xMj-5Q5t_68&feature=youtu.be

Module 5 Worksheet (PDF)

Module 5 Worksheet (docx)

Module 5 Guide (rev 6.6.2022)

Module 6: Cellular Localization Data Part 2
This module is a continuation of the previous module; it continues to guide students through a number of algorithms used to predict protein membrane topology and cellular localization. The tools and algorithms use in this modules are: Philius (an alternative algorithm for transmembrane topology), TargetP (predicts the subcellular location of eukaryotic proteins), NucPred (analyzes a eukaryotic protein sequence for nuclear localization signals), and the Yeast Protein Localization Database (YPL), a compilation of GFP-fusion data. A video walk through of this module can be viewed at https://youtu.be/udR-XBArox0

Module 6 Worksheet (PDF)

Module 6 Worksheet (docx)

Module 6 Guide (rev 6.6.2022)

Module 7: Gene Deletion Phenotypes
This module guides students through tools that summarize the phenotypic data available for each ORF deletion. PROPHECY provides quantitative information about phenotypes for the complete collection of deletion strains. The fitness database provides observed phenotypes when a given ORF deletion strain is exposed to a panel of drugs and chemicals. The yeast phenotype and publication summaries on SGD(http://yeastgenome.org/) are also covered in this module. (NOTE: SCMD and prophecy  have been discontinued; the guide and worksheets have been edited to remove these). A video walk through of this module can be viewed at https://youtu.be/Q75O6pwkhTc

Module 7 Worksheet PDF (rev 6.6.2022)

Module 7 Worksheet docx (rev 6.6.2022)

Module 7 Guide (rev 6.6.2022)

Module 8: Genetic and Physical Interactors and Expression Data
This module explains the bioinformatics tools available for investigating physical and genetic interactions and co-expression data with a selected ORF. Specifically, the module directs students through the use of GeneMania, which looks for correlations or associations amongst large sets of functional data and SPELL (Serial Pattern of Expression Levels Locator), which looks for correlations in microarray expression data. A video walk through of this module can be viewed at https://youtu.be/AS01Gp97H8M

Module 8 Worksheet (PDF)

Module 8 Worksheet (docx)

Module 8 Guide

Wet lab Modules:

The wet lab modules provide instructions for constructing gene deletions and testing for phenotypes. The modules are published here:

CURE on yeast genes of unknown function increases students’ bioinformatics proficiency and research confidence

The wet lab modules are in the supplementary materials.