PhenCode: connecting ENCODE data with mutations and phenotype.
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.
Giardine
Belinda
B
Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Riemer
Cathy
C
Hefferon
Tim
T
Thomas
Daryl
D
Hsu
Fan
F
Zielenski
Julian
J
Sang
Yunhua
Y
Elnitski
Laura
L
Cutting
Garry
G
Trumbower
Heather
H
Kern
Andrew
A
Kuhn
Robert
R
Patrinos
George P
GP
Hughes
Jim
J
Higgs
Doug
D
Chui
David
D
Scriver
Charles
C
Phommarinh
Manyphong
M
Patnaik
Santosh K
SK
Blumenfeld
Olga
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Gottlieb
Bruce
B
Vihinen
Mauno
M
Väliaho
Jouni
J
Kent
Jim
J
Miller
Webb
W
Hardison
Ross C
RC
D000077329:Agammaglobulinaemia Tyrosine Kinase; D001789:Blood Group Antigens / Q000235:genetics; D003299:Cooperative Behavior; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D030541:Databases, Genetic / Q000592:standards; D005838:Genotype; D005914:Globins / Q000235:genetics; D006801:Humans; D020407:Internet; D009154:Mutation; D010641:Phenotype; D010651:Phenylalanine Hydroxylase / Q000235:genetics; D011505:Protein-Tyrosine Kinases / Q000235:genetics; D011944:Receptors, Androgen / Q000235:genetics; D012985:Software Design; D018511:Systems Integration
D001789:Blood Group Antigens; D011944:Receptors, Androgen; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D005914:Globins; D010651:Phenylalanine Hydroxylase; D011505:Protein-Tyrosine Kinases; D000077329:Agammaglobulinaemia Tyrosine Kinase; C000625949:BTK protein, human