Canned Data¶

All data from these use cases has been run in the following:

• Group
  • Epigenome Informatics Workshop (May 2012)
• Database
  • Epigenome Informatics Workshop db Hg19 (May 2012)
• Project page
  • http://www.genboree.org/java-bin/project.jsp?projectName=Use_Case_01
  • http://www.genboree.org/java-bin/project.jsp?projectName=Use_Case_02
  • http://www.genboree.org/java-bin/project.jsp?projectName=Use_Case_05
  • http://www.genboree.org/java-bin/project.jsp?projectName=Use_Case_12
  • http://www.genboree.org/java-bin/project.jsp?projectName=Use_Case_13

Introduction¶

• http://genboree.org/theCommons/attachments/1760/4th_Workshop_Introduction_May_2012.pdf

Use cases¶

Use Case #1¶

• http://genboree.org/theCommons/attachments/1761/UseCase-1-Clustering_of_Blood_Cerebellum_Cortex_May_2012.pdf

Use Case #2¶

• http://genboree.org/theCommons/attachments/1762/UseCase-2-Clustering_of_Breast_Cell_Types_May_2012.pdf

Use Case #5¶

• http://genboree.org/theCommons/attachments/1763/UseCase-5-Clustering_of_Blood_Cerebellum_Cortex_High_CpG_May_2012.pdf

Use Case #9 - Coordinated Changes of Epigenomic Marks Across Tissue Types¶

• http://genboree.org/theCommons/attachments/1764/UseCase-9-Epigenomic_Marks_Across_Tissue_Types_May_2012.pdf
  • http://genboree.org/theCommons/attachments/1748/UseCase9-EpigenomeWorkshopMay2012-matrix_work-HCP-promoters.xls
  • http://genboree.org/theCommons/attachments/1749/UseCase9-EpigenomeWorkshopMay2012-matrix_work-HCP-promoters-1k-subset.xls

Use Case #12¶

• http://genboree.org/theCommons/attachments/1757/UseCase-12-Breast_Cancer_Cell_Type_of_Origin_May_2012.pdf

Use Case #13¶

• http://genboree.org/theCommons/attachments/1758/UseCase-13-Epigenomic_Variation_in_Breast_Tumors_May_2012.pdf

Use Case #14 - ChIP-Seq and mRNA-Seq Data Analysisvia the Genboree Workench¶

• http://genboree.org/theCommons/attachments/1759/UseCase-14-ChIP-Seq_mRNA-Seq_Analysis_May_2012.pdf

Other Useful Information¶

The Weber paper describing the HPC, LCP, and ICP regions of interests:

• Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
  • http://www.ncbi.nlm.nih.gov/pubmed/17334365