Previous project and useful links

Website that we built:

1. 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.

2. Hi-C 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.

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