This tutorial is intended to introduce basic principles and commonly used tools for the analysis of omics data (princioally proteomics and transcriptomics). For example:
How to use a mass spectrometry "search engine" to identify proteins from mass spectra in proteomics experiments
How to identify differentially expressed genes from transcriptomic studies in the Gene Expression Omnibus
Using online tools to analyze gene or protein sets in terms of their underlying functional networks
How to do basic gene set enrichment analysis
The tutorial is centred around using proteomic and transcriptomic case studies, taken from the scientific literature. Data are provided for each case study and a synopsis or link to the associated paper.
Overview and getting started
Proteomics
Read through the case studies, and select one for analysis
To search the mass-spectra against a sequence database:
Download the peak list files provided for each case study. See here for guidance on peak list file formats
Use the Mascot or Tandem search engine to identify proteins. See here for guidance
Run the search and extract the proteins from the output file
Transcriptomics
Read through the case studies, and select one for analysis
Follow the guide on using analyzing gene-expression datasets within GEO here
Functional analysis of gene or protein sets
To identify enriched Gene Ontology categories, analyze the genes or proteins in GOrilla (See here)
Perform gene network analysis by analyzing the genes or proteins in STRING (See here)
This resource was developed with financial support to Professor Rob Ewing from The University Center for Innovation in Teaching and Education (UCITE), Case Western Reserve University, Cleveland, Ohio
