Viewing Ensembl Regulation & ENCODE Using the Matrix

submitted by: gspudich
This tutorial demonstrates how to view sequences potentially involved in gene regulation. These sequences are analysed by Ensembl Regulation based mostly on ENCODE data, along with Roadmap Epigenomics data for human. The end of this tutorial shows how to add the full ENCODE data set to a genome display in Ensembl. The Region in Detail in the Ensembl browser will be explored. You may be interested in: Ensembl Regulation docs: http://www.ensembl.org/info/docs/func ... Region in Detail...

Demo: Old genome coordinates to new

submitted by: gspudich
Genome sequences are updated with time. Your data might be on an older version of the genome, for example the human genome assembly NCBI36 (also known as hg18 by UCSC). In 2009, this assembly was updated to GRCh37 (named hg19 by UCSC). You can use the Ensembl archive site to view the older genome: http://may2009.archive.ensembl.org . To convert your coordinates to the newest genome sequence, use the Ensembl assembly converter (demonstrated in this video.)

Demo: Structural variation for a region

submitted by: gspudich

Large structural variations like CNVs (copy number variation) are explored for a region of the human genome. We use the Ensembl genome browser at www.ensembl.org

Demo: Variation for the ZAP70 gene with Ensembl

submitted by: gspudich

We use the Ensembl genome browser at www.ensembl.org to view small scale sequence variants such as SNPs (single nucleotide polymorphims) along with larger structural variations like CNVs (copy number variation) for the human ZAP70 gene.

Ensembl Overview (given at ErasmusMC, Sept 2011)

submitted by: gspudich

This is an overview of the data available in the Ensembl Genome Browser with a focus on the gene set and sequence variation. Four demos follow this presentation, using www.ensembl.org.