Gene Ontology Project geneontology

Gene OntologyProject

http://www.geneontology.org/

Clark et al., 2005

part_of

is_a

Clark et al., 2005

Who uses GO?

1. National Institute on Alcohol Abuse and Alcoholism (NIAAA)

2. National Institute on Aging (NIA)3. National Institute of Allergy and

Infectious Diseases (NIAID)4. National Institute of Arthritis and

Musculoskeletal and Skin Diseases (NIAMS)

5. National Center for Complementary and Alternative Medicine (NCCAM)

6. National Cancer Institute (NCI)7. National Institute on Drug Abuse

(NIDA)8. National Institute on Deafness and

Other Communication Disorders (NIDCD)

9. National Institute of Dental & Craniofacial Research (NIDCR)

10. National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

11. National Institute of Biomedical Imaging and Bioengineering (NIBIB)

12. National Institute of Environmental Health Sciences (NIEHS)

13. National Eye Institute (NEI)

14. National Institute of General Medical Sciences (NIGMS)

15. National Institute of Child Health and Human Development (NICHD)

16. National Human Genome Research Institute (NHGRI)

17. National Heart, Lung and Blood Institute (NHLBI)

18. National Library of Medicine (NLM)

19. National Center on Minority Health and Health Disparities (NCMHD)

20. National Institute of Mental Health (NIMH)

21. National Institute of Nursing Research (NINR)

22. National Institute of Neurological Disorders and Stroke (NINDS)

23. National Center for Research Resources (NCRR)

24. Fogarty International Center (FIC)

Sample of 77 research papers, both intra-mural & extra-mural research.

NIH funded experimental research that uses the GO

Companies

• NLP & Ontology Products BioWisdom, IBM

• Array Products and data analysis Affymetrix, Spotfire

• Products that use GO Clontech, Inpharmatica

• Reagents & services Sigma, Abnova• Big Pharmas AstraZeneca

Publications

• Published articles

mentioning GO = 1063, in 284 journals

• Google Scholar• ‘gene ontology, tool for unification of biology’

1291 citations

25th September 2006

http://www.geneontology.org/cgi-bin/biblio.cgi

0 50 100 150 200 250 300 350 400 450 500

overviews of GO

Network modeling and analysis

Supporting predictions

Comparative genomics and evolutionary analysis

GO annotations

Genome Annotation

GO Consortium

Protein Annotation

Proteomics studies

EST annotation

OBO Ontologies

Data and Text mining

GO Annotation Predictions

Biological Databases

GO Tools

Other

Clinical applications

Gene Expression studies

450

1063 publications

over 284 Journals

Who is citing GO?

Mitochondrial P450 (CC24 PR01238; MITP450CC24)

Annotation

GO cellular component term:mitochondrial inner membrane ; GO:0005743

Where is it?

Mitochondrial p450

GO molecular function term:monooxygenase activity ; GO:0004497

What does it do?

substrate + O2 = CO2 +H20 product

http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

GO biological process term:electron transport ; GO:0006118

Which process is this?

monooxygenase activity ; GO:0004497

Other gene products:

MGI monooxygenase, DBH-like 1MGI prostaglandin I2 (prostacyclin) synthaseMGI splicing factor 3b, subunit 2SGD    flavin-containing monooxygenaseTAIR   FERULATE-5-HYDROXYLASE 1

Cell type ontology

Whole genome analysis(J. D. Munkvold et al., 2004)

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

attacked

time

control

Puparial adhesionMolting cyclehemocyanin

Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes

Immune responseToll regulated genes

Amino acid catabolismLipid metobolism

Peptidase activityProtein catabloismImmune response

Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...

Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)

Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

…analysis of high-throughput data according to GOMicroArray data analysis