gene ontology: go

http://www.ugr.es/~oliver/ José L. Oliver

Gene Ontology: GO


• …los bioquímicos caracterizan las proteínas por su actividad y concentración

• …los genéticos caracterizan los genes por sus fenotipos y sus mutaciones

• …todos los biólogos reconocen ahora que probablemente existe un universo limitado de genes y proteínas, conservado en la mayor parte de las formas de vida

Esto ha promovido la gran unificación de la biología; la información acerca de los genes y proteínas compartidos contribuye a comprender mejor las diversas formas de vida

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics, 25(1), 25-9. doi: 10.1038/75556.

Regulatory elements

miRNA

CisRed

Transcription Factor Binding Sites

Biocarta pathways

InterPro Motifs

Bioentities from literature:

Diseases terms Chemical terms

Gene Expression in tissues

Keywords Swissprot

Biological databases

Arabidopsis thaliana

Homo sapiens

Mus musculus

Rattus norvegicus

Drosophila melanogaster

Caenorhabditis elegans

Saccharmoyces cerevisae

Gallus gallus

Danio rerio

HGNC symbol

EMBL acc

RefSeq

PDB

Protein Id

IPI….

Genes IDs

Gene Ontology

Biological Process Molecular Function Cellular Component

UniProt/Swiss-Prot

UniProtKB/TrEMBL

Ensembl IDs

EntrezGene

Affymetrix

Agilent

KEGG pathways

http://www.ensembl.org/Homo_sapiens/

http://www.ensembl.org/Mus_musculus/

http://www.ensembl.org/Rattus_norvegicus/

http://www.ensembl.org/Drosophila_melanogaster/

http://www.ensembl.org/Caenorhabditis_elegans/

http://www.ensembl.org/Saccharomyces_cerevisiae/

http://arabidopsis.info/

http://www.ensembl.org/Gallus_gallus/

Gene Ontology CONSORTIUM

http://www.geneontology.org

• The objective of GO is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products

• These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them

• The controlled vocabularies of terms are structured


http://www.geneontology.org/

The three categories of GO

Molecular Function

the tasks performed by individual gene products; examples are transcription factor and DNA helicase

Biological Process

broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions

Cellular Component

subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex



Biological process ontology


Molecular function ontology


Cellular component ontology


So what does a Gene Ontology do?

• A Gene Ontology takes a gene product (protein) and gives it a cellular context

• For each of the three ontology's, gene products can be placed where they belong, and various terms can be looked up to find the associated gene products


Go Term

• A decriptive term that is used to give a gene product a cellular, molecular, or biological context

• Terms are standardized across all databases and use synonyms to bridge gaps in spelling or similar function

• Older terms can become obsolete


Example of gene product data

• Look up gene “Q59J86”

• Gives:

• Name(s) “DNA polymerase”

• Type “protein”

• Species “Gallus gallus (chicken)”

• Synonyms “IPI00588123”

• Sequence

• References

• Term associations

http://amigo.geneontology.org/cgi-bin/amigo/gp-details.cgi?gp=UniProtKB:Q59J86&session_id=2294amigo1235363544

http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9031

GO tree structure



Types of Relationships

• Is_a [i]

• Part_of [p]

• Regulates/ positively_regulates / negatively_regulates [r]

GO:0010467 : gene expression [r] GO:0010468 : regulation of gene expression ---[i] GO:0045449 : regulation of transcription [p] GO:0006350 : transcription ---[r] GO:0045449 : regulation of transcription


Example

Solid lines are Is_a relationships

Dotted Lines are Part_of relationships


Graph structure

• The ontologies are structured as directed acyclic graphs (DAG), which are graphs that do not cycle or repeat

• These are similar to hierarchies but differ in that a more specialized term (child) can be related to more than one less specialized term (parent)

• This allows annotations to one GO term to be also annotated to related GO terms connected in the graph structure


GO Directed Acyclic Graph


Database structure

• All 3 Gene Ontologies, Annotations, and Gene products are stored in one relational database.

• The Database is written in MySQL and is updated with various daily, weekly, and monthly builds in addition to various mirrors and stored previous builds

• The database can be accessed by AmiGO or queried remotely by various methods, or even downloaded

• The Ontology data is in OBO file format (Open Biomedical Ontologies)


http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?session_id=1830amigo1294836292


http://www.ebi.ac.uk/QuickGO/

gene ontology: go

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