Previous project and useful links

Website that we built:

1. 3D Genome Browser : users can visualize the recenlty published Hi-C data in different species, different assembly and different resolution. A cool feature of the website is that you can generate a virtual 4C figure, where you can hypothesize the potential interactions between enhancers and promoters. This website has been visited by users from all over the world for over 700,000 times.

2. ENCODE element browser : the main purpose of this website is to help users easily query the gene expresssion file and genomic annotations generated by the ENCODE consortium. We have used this website extensively in many ENCODE workshops.

3. Download the candiate cis-elements in 19 mouse tissue/cell types and some intermediate files used in (Shen and Yue, et al, Nature 2012) link

Useful links:

UCSC Genome Browser

ENCODE

Roadmap Epigenome Project

RegulomeDB

HaploReg

Slides for class:

A tutorial slides I made on how to use UCSC genome browser and ENCODE website link