Statistical Bioinformatics
Statistics 5570/6570, Spring 2014
Instructor: John R. Stevens

Course Documents and Announcements

• Course Syllabus
• Homework 1 --- GSE36149 Data
• Homework 2
• Homework 3
• Projects: Discussions and 6570 Tutorials
• Homework 4
• Homework 5 --- hw5.fasta --- cheung.csv --- cheungGender.csv
• Final Exam --- GSE37516 Data
  --- Alternate Final Exam

Unit 1: Gene Expression Analysis - Technology and Preprocessing

• 1.0: Initial Case Study --- 4up
• 1.1: Intro. to Microarray Technology --- 4up --- structure cartoon --- function cartoon --- Forbes story
• 1.2: Installing and Using R --- code
• 1.3: Getting Started with Bioconductor --- code
• 1.4: Intro. to Preprocessing --- 4up --- code

Unit 2: Gene Expression Analysis - Visualization

• 2.1: Quality Checks --- 4up --- code
• 2.2: Distance Measures --- 4up --- code
• 2.3: Clustering --- 4up --- code
• 2.4: Visualization and PCA --- 4up --- code

Unit 3: Gene Expression Analysis - Inference (Identifying Candidate Genes)

• 3.1: Multiple Testing --- 4up --- code
• 3.2: Filtering --- 4up --- code
• 3.3: Differential Expression (pt. 1) --- 4up --- code
• 3.4: Differential Expression (pt. 2) --- 4up --- code
• 3.5: Random Forests --- 4up --- code
• 3.6: Case Study (pt. 1)

Unit 4: Gene Expression Analysis - Annotation (Characterizing Candidate Genes)

• 4.1: Gene Ontology and KEGG Databases --- 4up --- code
• 4.2: Interactive Reports --- 4up --- code
• 4.3: Gene Set Testing --- 4up --- code
• 4.4: Gene Set Graphs --- 4up --- code

Unit 5: Mass Spectrometry Analysis - Technology and Preprocessing

Unit 6: Sequence Analysis and Next-Generation Sequencing Technology

• 6.1: Intro. to Sequence Analysis --- 4up --- code
• 6.2: Intro. to BLAST --- 4up
• 6.3: Intro. to Next-Gen Sequencing --- 4up --- code
• 6.4: Analysis of Sequence Count Data --- 4up --- code

Unit 7: Discussion Topics

• Possible Discussion Topics
• mvGST (4/7 class)
• FWER in GO Graph (4/11 class)
• 6570 tutorial presentations
  • MRPP
  • KEGGgraph
  • GSEA
  • MHT in Global Test

Miscellaneous

• Good R resources:
  • R: The R Project
  • CRAN: The Comprehensive R Archive Network
  • Introduction to R: A good resource for most uses of R
  • Bioconductor Project: Free R packages for the analysis of genomic data
  • R reference card: Tom Short's ''cheat sheet'' for R commands