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PhenCode: connecting ENCODE data with mutations and phenotype.

På svenska

Author

  • Belinda Giardine
  • Cathy Riemer
  • Tim Hefferon
  • Daryl Thomas
  • Fan Hsu
  • Julian Zielenski
  • Yunhua Sang
  • Laura Elnitski
  • Garry Cutting
  • Heather Trumbower
  • Andrew Kern
  • Robert Kuhn
  • George P Patrinos
  • Jim Hughes
  • Doug Higgs
  • David Chui
  • Charles Scriver
  • Manyphong Phommarinh
  • Santosh K Patnaik
  • Olga Blumenfeld
  • Bruce Gottlieb
  • Mauno Vihinen
  • Jouni Väliaho
  • Jim Kent
  • Webb Miller
  • Ross C Hardison
Show all

Summary, in English

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.

Publishing year

2007

Language

English

Pages

554-562

Publication/Series

Human Mutation

Volume

28

Issue

6

Document type

Journal article

Publisher

John Wiley & Sons Inc.

Topic

  • Medical Genetics

Keywords

  • Globins: genetics
  • Phenylalanine Hydroxylase: genetics
  • Genetic: standards
  • Databases
  • Blood Group Antigens: genetics
  • Cystic Fibrosis Transmembrane Conductance Regulator: genetics
  • Protein-Tyrosine Kinases: genetics
  • Receptors
  • Androgen: genetics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1059-7794