Communicated by Richard Cotton
Article first published online: 26 FEB 2007
This article is a U.S. Government work and is in the public domain in the U.S.A. Published in 2007 by Wiley-Liss, Inc.
Volume 28, Issue 6, pages 554–562, June 2007
How to Cite
Giardine, B., Riemer, C., Hefferon, T., Thomas, D., Hsu, F., Zielenski, J., Sang, Y., Elnitski, L., Cutting, G., Trumbower, H., Kern, A., Kuhn, R., Patrinos, G. P., Hughes, J., Higgs, D., Chui, D., Scriver, C., Phommarinh, M., Patnaik, S. K., Blumenfeld, O., Gottlieb, B., Vihinen, M., Väliaho, J., Kent, J., Miller, W. and Hardison, R. C. (2007), PhenCode: connecting ENCODE data with mutations and phenotype. Hum. Mutat., 28: 554–562. doi: 10.1002/humu.20484
This article is a US Government work and, as such, is in the public domain in the United States of America.
- Issue published online: 12 APR 2007
- Article first published online: 26 FEB 2007
- Manuscript Accepted: 18 DEC 2006
- Manuscript Received: 14 JUN 2006
- Intramural Program of the NIH
- Réseau de Médicine Génétique Appliquée/Fonds de la recherche en santé du Québec
- Canadian Cystic Fibrosis Foundation and Genome Canada
- NHGRI. Grant Numbers: HG002238, 1P41HG02371
- NIH. Grant Number: DK65806
- UCSC Genome Browser
PhenCode (Phenotypes for ENCODE; http://www.bx.psu.edu/phencode) is a collaborative, exploratory project to help understand phenotypes of human mutations in the context of sequence and functional data from genome projects. Currently, it connects human phenotype and clinical data in various locus-specific databases (LSDBs) with data on genome sequences, evolutionary history, and function from the ENCODE project and other resources in the UCSC Genome Browser. Initially, we focused on a few selected LSDBs covering genes encoding alpha- and beta-globins (HBA, HBB), phenylalanine hydroxylase (PAH), blood group antigens (various genes), androgen receptor (AR), cystic fibrosis transmembrane conductance regulator (CFTR), and Bruton's tyrosine kinase (BTK), but we plan to include additional loci of clinical importance, ultimately genomewide. We have also imported variant data and associated OMIM links from Swiss-Prot. Users can find interesting mutations in the UCSC Genome Browser (in a new Locus Variants track) and follow links back to the LSDBs for more detailed information. Alternatively, they can start with queries on mutations or phenotypes at an LSDB and then display the results at the Genome Browser to view complementary information such as functional data (e.g., chromatin modifications and protein binding from the ENCODE consortium), evolutionary constraint, regulatory potential, and/or any other tracks they choose. We present several examples illustrating the power of these connections for exploring phenotypes associated with functional elements, and for identifying genomic data that could help to explain clinical phenotypes. Hum Mutat 28(6), 554–562, 2007. Published 2007 Wiley-Liss, Inc.