Transcript CGDN-Poster-final-postrevised

Mining Brain-Related Transcription FactorDisease Relationships for Novel Linkages
Warren
1,3,4
Cheung ,
BF Francis
2,3
Ouellette ,
Wyeth W
2,4
Wasserman
1
Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada.
E-mail: [email protected]
2 Department of Medical Genetics, University of British Columbia.
3 University of British Columbia Bioinformatics Centre.
4 Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute.
TF-Cat 4
•Annotated
transcription
factor
database
PAZAR 4
•database of gene
regulatory elements
NCBI Entrez Gene
•Gene Reference into Function annotations
•Gene Ontology annotations
PAZAR
TF Cat
NLM Medical Subject Heading
•controlled vocabulary thesaurus
Entrez
Gene
Specialised Databases
Discovering
Links Between
Genes and Disease
Atlas Data Warehouse
Medical Subject
Headings
(MeSH)
NLM UMLS
Metathesaurus
Unified Medical
•database of
Language System (UMLS) medical
terminologies
UniProt
RefSeq
Gene Ontology
(GO) Terms
ICD 9/10
HPRD
Genes
GenBank
BIND
Diseases
Gene
Ontology
Annotation
Validation
Atlas Data Warehouse 3
•unified access to nucleotide, protein,
interactions and ontology annotations
Evidence
PubMed
Design
MeSH
Annotations
•Freeze database contents
(Online) at a cut-off date and
Mendelian compare against more
Inheritance recent discoveries.
•Withhold and verify using
in Man
the Mendelian Inheritance in
Man (MIM) Database
Goals
Selected TF Gene Associations
to Brain Diseases
•Open Access
•Integrated, Unified Repository
•Efficient Programmatic Framework
•Exploration of Gene-Disease
Relationships
Gene
TP53
Entrez
Gene
Entrez Gene ID
Locus name
Statistics
Related
Articles
PMID
Related_PMID
Score
MeSH
Term
Tree_number
Entrez Gene
2 631 524
Total Genes
38 624
Human Genes
1 192
Human Transcription Factor (TF) Genes
Gene Reference Into Function
(GeneRIFs)
Genes with GeneRIFs
Human TF Genes with GeneRIFs
33 216
914
GeneRIF
Entrez Gene ID
PMID
Heading
Description
PubMed
PMID
Title
PubMed
MeSH
Annotations
PMID
MeSH Term
MeSH Qualifier
Major Topic?
Medical Subject Headings
MeSH terms
Unique MeSH terms
MeSH terms under “Brain Diseases”
47 143
24 355
312
Results
Brain Diseases by Number of Genes
PubMed / MEDLINE
PubMed Articles
PubMed Articles with MeSH annotation
Brain Disease (MeSH) PubMed Articles
PubMed Articles referenced by
Human TF GeneRIFs
PubMed Articles marked with MeSH Brain
Disease terms, linked by Human TF GeneRIFs
Human TF Genes with GeneRIFs to
Brain Disease PubMed Articles
SnoMed
CT
16 120 074
15 806 221
660 538
15 741
351
146
Brain Disease (MeSH Term) Human TF Genes
146
Brain Diseases
68
Dementia
54
Brain Neoplasms
39
Alzheimer Disease
31
Basal Ganglia Diseases
…
93 MeSH terms have a human TF gene reference
Brain Disease
Papers
43
Brain Diseases
27
Brain Neoplasms
6
Ataxia Telangiectasia
27
TNF
Brain Diseases
5
Alzheimer Disease
13
ESR1
Brain Diseases
7
Alzheimer Disease
12
PPARG
Brain Diseases
4
Brain Neoplasms
11
POU1F1
Brain Diseases
4
Pituitary Neoplasms
4
Hypopituitarism
9
NR4A2
Brain Diseases
9
Parkinson Disease
7
CTNNB1
Brain Disease
7
Alzheimer Disease
9
TBP
Brain Diseases
6
Spinocerebellar
Ataxias
6
ARX
Spasms, Infantile
5
HIF1A
Brain Neoplasms
…
780 Total Gene-Brain Disease pairs
OMIM verified
PubMed verified
Future Work
•Statistical Evaluation of Support
•Secondary and Tertiary Relationships