Log In Instructions¶

Log In Instructions for NEW Genboree Users (if you have previously created a Genboree account, your user name and password will not change)

• http://genboree.org/theCommons/attachments/2291/login_directions.docx

Canned Output Data From Use Cases¶

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

• Group
  • Epigenome Informatics Demo Output Data
• Database
  • Epigenome_Informatics_Demo_Db_hg19
• Project page
  • http://genboree.org/java-bin/project.jsp?projectName=Use_Case_01-project
  • http://genboree.org/java-bin/project.jsp?projectName=Use_Case_02-project
  • http://genboree.org/java-bin/project.jsp?projectName=Use_Case_05-project
  • http://genboree.org/java-bin/project.jsp?projectName=Use_Case_13-project

Introduction¶

• http://genboree.org/theCommons/attachments/2275/6th_workshop_Matt_intro_030413.pdf

Aleks' Talks¶

• http://genboree.org/theCommons/attachments/2297/Intro-to-Epigenomics-and-Genboree-AM-Aleks.pdf
• http://genboree.org/theCommons/attachments/2295/Intro-to-Genboree-Network-PM-Aleks.pdf

Alan's Talk - 450K¶

• http://genboree.org/theCommons/attachments/2296/raharris.Illumina_Infinium_450K_Array.pdf

Karin Michels Talk (October 2012 Workshop)¶

• http://genboree.org/theCommons/attachments/2292/Michels_Epigenome_Informatics_workshop_Oct_2012.pdf

Kim Siegmund Talk (October 2012 Workshop)¶

• http://genboree.org/theCommons/attachments/2293/Siegmund_Epigenome_Informatics_workshop_Oct_2012.pdf

Use cases¶

Use Case #1 - Genomewide Patterns of Methylation Distinguishes Blood, Cerebellum, and Cortex¶

• http://genboree.org/theCommons/attachments/2277/UseCase-1-Clustering_of_Blood_Cerebellum_Cortex_030113.pdf
• 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://genboree.org/theCommons/attachments/2274/Weber_Prom_Methyl_Nat_Gen_2007.pdf
• The Davies paper describing tissue specific epigenomic variation
  • Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood
    • http://genboree.org/theCommons/attachments/2280/Davies_Brain_Methylome_Gen_Biol_2012.pdf

Use Case #2 - Clustering of Breast Cell Types (via Epigenome Atlas)¶

• http://genboree.org/theCommons/attachments/2282/UseCase-2-Clustering_of_Breast_Cell_Types_030113.pdf

Use Case #5 - Methylation of Specific Regions Discriminate Tissues Types Better Than Others¶

• http://genboree.org/theCommons/attachments/2278/UseCase-5-Clustering_of_Blood_Cerebellum_Cortex_High_CpG_030113.pdf

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

• http://genboree.org/theCommons/attachments/2283/UseCase-9-Epigenomic_Marks_Across_Tissue_Types_030113.pdf
  • http://genboree.org/theCommons/attachments/2276/UseCase9-EpigenomeWorkshop-matrix_work-HCP-promoters.xls
  • http://genboree.org/theCommons/attachments/2281/UseCase9-EpigenomeWorkshop-matrix_work-HCP-promoters-1k-subset.xls

Use Case #13 - Analysis of Epigenomic Variation in Breast Tumors¶

• http://genboree.org/theCommons/attachments/2279/UseCase-13-Epigenomic_Variation_in_Breast_Tumors_030313.pdf
  • Please see the FAQ that takes a published publicly available 450k data set from beginning to end on the Genboree Workbench:
    • http://genboree.org/theCommons/ezfaq/show/epigenome-workshop?faq_id=474

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

• http://genboree.org/theCommons/attachments/2284/Use_Case_14_ChipSeq_MACS_030313.pdf
  • Addendum
    • http://genboree.org/theCommons/attachments/2299/Usse_Case_14_Addendum_peak-calls-50epi.pdf

Use Case #15 - Spark tool for epigenomic data exploration¶

• http://genboree.org/theCommons/attachments/2286/Usecase15_SPARK_030113.pdf
  • ENCODE ChIP-Seq Data Experimental Description
    • encode_ChIP-Seq_exp_description
  • Optional Spark Analysis
    • http://genboree.org/theCommons/attachments/2287/Usecase15_OPTIONAL_SPARK_030113.pdf

Use Case #16 - Differential Expression Analysis of Two Breast Cancer Cell Lines Using Cuffdiff¶

• http://genboree.org/theCommons/attachments/2290/Use_Case_16_RNASeq_Cuffdiff_030313.pdf

Use Case #17 - RNA-Seq with TopHat and Cufflinks¶

• http://genboree.org/theCommons/attachments/2298/UseCase-17_mRNA-Seq_Cufflinks_TopHat_030313.pdf

Other Useful Information¶

FAQs relating to the Epigenomics Toolset

• http://genboree.org/theCommons/ezfaq/index/epigenome-workshop