Introduction

Welcome to the Homepage of the Functional Genomics Resource Center at the Beckman Institute at the California Institute of Technology

Integration and visualization of many genome-wide chromatin datasets from multiple cell types using self-organizing maps (SOM). The schematic (prepared by Iain Dunham) illustrates the first use of SOMs for large-scale functional genomics integration and associated data mining. This method was developed by Ali Mortazavi (Caltech Beckman Fellow and currently Asst. Professor, UC Irvine) and Shirley Pepke (CACR and Wold Lab Cell Center Project). From: "An Integrated Encyclopedia of DNA Elements in the Human Genome". Nature (in press; 2012) The ENCODE Consortium. The resulting SOM for human ENCODE data can be interactively viewed and mined using a web SOMviewer developed by Mortazavi, Camden Jansen (UCI) and Diane Trout (BIFGRC).

The Functional Genomics Resource Center develops and disseminates experimental and computational methods for functional genomics. These include RNA transcript expression (RNA-seq) from traditional samples, small pools of cells and single cells, genome-wide transcription regulatory protein occupancy (ChIP-seq of all kinds), long distance chromosomal interactions, and various assays of regulatory elements. Our objective is to develop useful and well-controlled protocols and standards and to help Caltech labs adapt and use these tools in their own systems. We work in close collaboration with the Jacobs Genetics and Genomics Lab (Igor Antoshechkin director - http://mmjggl.caltech.edu) The analysis and integration of RNA-seq and ChIP-seq datasets is a rapidly evolving computationally intensive area. Our wet bench and computational staff work together to develop, import, refine and benchmark analysis tools.