Resources
| Information | GO Consortium |
Home page for the GO consortium (GOC) |
| GOA statistics |
View the current annotation statistics for UniProt GO |
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| GO Evidence Codes | Guide to GO evidence codes | |
| Annotation Tutorial | Tutorial describing how electronic and manual annotations are made | |
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For information on how the CV gene list was generated, and information on workshops and other projects that BHF-UCL is involved in |
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| Outreach |
GOC
cardiovascular project |
Further details about the CV gene annotation project and GO annotation |
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Feedback form |
Users can supply us with the PubMed identifier of a key experimental publication for curation or provide more detailed information or commentary, such as pointing out any experimental data that might be controversial. Information regarding genes in any species is welcome. | |
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Cardiovascular Gene List |
A searchable list of 4000+ cardiovascular associated human genes |
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| SourceForge Request Tracker | Request ontology amendments with the GO editorial office | |
| GO browsers | QuickGO | Find GO terms or terms associated with specific UniProt accessions |
| AmiGO | Find GO terms, filters for species, datasource or evidence codes available | |
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Gene browsers |
Sequence Retrieval Service (SRS) | EBI search tool to find UniProt accession IDs |
| Integr8 | Features include ability to search for sequences associated with a particular GO:ID | |
| NCBI Gene | NCBI search tool to find gene record with wide range of annotations and links | |
| Blast searches | AmiGO Blast | BLAST search shows the associated GO terms for each hit. Useful for finding GO terms associated with homologues |
| MPsrch | BLAST search which returns UniProt accession IDs | |
| NCBI BLASTP | Protein BLAST with options for SwissProt or NCBI database search | |
| Annotation tools | CitExplore | Literature search and text mining tool. Can highlight abstracts to show potential GO terms |
| Whatizit | Can paste in any text for highlighting with potential GO terms | |
| iHOP | Links together protein information. Search using gene symbol or accession ID | |
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GoPubMed |
Literature search tool that categorises results by GO terms mentioned in abstract |
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GO analysis tools |
Tutorial |
This powerpoint presentation introduces the basic features of four third-party GO analysis tools; Blast2GO, FatiGO, Onto-Express, and Ontologizer. |
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Practical proteomics |
This article provides an overview of the Gene Ontology, its uses and the software available for the analysis of high-throughput data. We recommend that you analyse your data with a variety of functional analysis tools, as there will be differences in the date the annotation dataset was uploaded into the tool and the statistical packages used. The tools listed below are easy to use and generally update their datasets regularly |
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AmiGO tool |
GOC tool, provides a table of enriched terms, and associated sample frequency and genes. For human analysis either input your own background dataset or leave this section blank, the tool will then use the one available with the 'select the database filter' option 'UniProtKB' |
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Bableomics |
Provides a range of functional analysis tools, e.g. FatiGO and ‘gene set analysis’ |
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Blast2GO |
Displays a wide range of outputs and graphical views |
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| gprofiler | Displays a table of genes associated with an ontology tree of the enriched GO terms, and enables alignment of multiple data analyses | |
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Onto-express |
Displays the enriched GO terms within the ontology structure or as a table, can be more difficult to get to work due to pop-ups |
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Ontologizer |
Requires local installation. Displays a table of results related to the term and a list of all genes annotated to the term in the study set, as well as an integrated graphical display |
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VLAD |
MGI tool which provides a table of enriched terms, and the associated genes, as well as a graph of the enriched terms. For human analysis choose ‘Annotation Set: goa_human [date]’ option from dropdown menu |
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| Cardiovascular databases |
CADgene |
Contains more than 300 Coronary artery disease (CAD) related genes and their detailed information associated with CAD from about 2000 publications |
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Cardiogenomics |
Contains 148 genes, selected from published genetic pathways and murine transcriptional profiling experiments, considered to be important in left ventricular hypertrophy and congestive heart failure. | |
| CardMoc | Contains published inherited arrhythmogenic diseases and cardiac ion channels genetic variations. | |
| CVCGD | Contains more than 250 CAD related genes | |
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Other human GO annotation groups |
GOA database |
Comprehensively annotating disease-related human proteins as part of the broader GOC Reference Genome Annotation project and responsible for the integration and release of GO annotations to the human proteome. In addition GOA assists in the curation of another 120,000 species. Funded by EMBL, NHGRI, BBSRC. |
| Renal Gene Ontology Annotation Initiative |
Part of the GOA database, providing high-quality, detailed functional GO annotation for mammalian gene products implicated in renal development and disease. Funded by Kidney Research UK to April 2012. |
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Human protein interaction data |
IntAct |
Provides a database and analysis tools for molecular interaction data |
Page last modified on 20 dec 12 08:03
The work of the Cardiovascular Gene Annotation group is supported by British Heart Foundation grant RG/13/5/30112his
