Part I Resources for Systems Genetics
1. Resources for Systems Genetics
Robert W. Williams and Evan G. Williams
2. Heterogeneous Stock Populations for Analysis of Complex Traits
Leah Solberg Woods and Richard Mott
Part II Tools for Analysis and Integration in Systems Genetics
3. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research
Janan T. Eppig, Cynthia L. Smith, Judith A. Blake, Martin Ringwald, James A. Kadin, Joel E. Richardson, and Carol J. Bult 4. GeneNetwork: A Toolbox for Systems Genetics
Megan K. Mulligan, Khyobeni Mozhui, Pjotr Prins, and Robert W. Williams
5. Complex Trait Analyses of the Collaborative Cross: Tools and Databases
Ramesh Ram and Grant Morahan
6. Integrative Functional Genomics for Systems Genetics in GeneWeaver.org
Jason A. Bubier, Michael A. Langston, Erich J. Baker, and Elissa J. Chesler
7. A Suite of Tools for Biologists that Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel
Christoph D. Rau, Mete Civelek, Calvin Pan, and Aldons J. Lusis
8. Expression QTLs Mapping and Analysis: A Bayesian Perspective
Martha Imprialou, Leonardo Bottolo, and Enrico Petretto
9. Epigenetics and Control of RNAs
Henrike Maatz, Sebastiaan van Heesch, Allison Faber, Franziska Kreuchwig, Eleonora Adami, Norbert Hubner, and Matthias Heinig
10. Integrating Multidimensional Data Sources to Identify Genes Regulating Complex Phenotypes
Rupert W. Overall
11. RNA-Seq in the Collaborative Cross
Richard Green, Courtney Wilkins, Martin T. Ferris, and Michael Gale, Jr.
12. QTL Mapping and Identification of Candidate Genes in DO Mice: A Use Case Model Derived from a Benzene Toxicity Experiment
Dan Gatti, John E. French, and Klaus Schughart
13. Visualization of Results from System Genetics Studies in Chromosomal Context
Karen Y. Oróstica and Ricardo A. Verdugo
Part III Systems Genetics Use Cases: Mapping and Combining Multiple Phenotypic Traits in Mouse Genetic Reference Populations
Organ Systems
14. Genomic Control of Retinal Cell Number: Challenges, Protocols, and Results
Patrick W. Keeley, Irene E. Whitney, and Benjamin E. Reese
15. Systems Genetics Analysis to Identify the Genetic Modulation of a Glaucoma-Associated Gene
Sumana R. Chintalapudi and Monica M. Jablonski 16. Genetic Dissection of Variation in Hippocampal Intra-and Infrapyramidal Mossy Fibers in the Mouse
Anna Delprato and Wim E. Crusio
17. Complex Genetics of Cardiovascular Traits in Mice: F2-Mapping of QTLs and their Underlying Genes
Svitlana Podliesna, Connie R. Bezzina, and Elisabeth M. Lodder
18. Systems Genetics of Live Fibrosis
Rabea A. Hall and Frank Lammert
Metabolism
19. Systems Genetic Analysis of Iron and its Regulation in Brain and Periphery
Byron C. Jones and Leslie C. Jellen
20. Systems Genetics of Obesity
Sebastian Heise, Danny Arends, Ayca Dogan, and Gudrun A. Brockmann
Behavior
21. Social Interactions and Indirect Genetic Effects on Complex Juvenile and Adult Traits
David G. Ashbrook and Reinmar Hager
22. Complex Genetics of Behaior: BXDs in the Automated Home-Cage
Maarten Loos, NeuroBsik Mouse Phenomics Consortium, Matth
