Information GO Consortium Home page for the GO consortium (GOC)
  GOA statistics View the current annotation statistics for UniProt GO
  GO Evidence Codes Guide to GO evidence codes
  Annotation Tutorial Tutorial describing how electronic and manual annotations are made
  Cardiovascular Gene List
A searchable list of 4000+ cardiovascular associated human genes
  Whatizit Can paste in any text for highlighting with potential GO terms
  Dimmer et al., 2008 (pdf)
 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
  Tutorial (pdf) This powerpoint presentation introduces the basic features of four third-party GO analysis tools; Blast2GO, FatiGO, Onto-Express, and Ontologizer.
Browsers QuickGO Find GO terms or terms associated with specific UniProt accessions
  AmiGO Find GO terms, filters for species, datasource or evidence codes available
  IntAct Provides a database and analysis tools for molecular interaction data
  IntAct Complex Portal
Provides manually curated macromolecular complexes from a number of key model organisms.

New! provides computational access to molecular-interaction data including protein-protein interaction (PPI) resources. Now includes access to both the non-IMEX PPI data set called EBI-GOA-nonIntAct and the IMEX-curated PPI data set provided by IntAct (which includes IntAct, BHF-UCL, MINT, UniProt, MatrixDB, I2D-IMEx, InnateDB-IMEx, Molecular Connections, MPIDB, and MBInfo, all of which are in IntAct and DIP which is not). The two data sets are readily accessible and easily merged via the Cytoscape molecular interaction network tool.

For more details, read our web page dedicated to PSCIQUIC.

  NCBI Gene Find gene record with wide range of annotations and links
Find protein record with wide range of annotations and links
Literature search engines
CitExplore Literature search and text mining tool. Can highlight abstracts to show potential GO terms
NCBI literature search tool with multiple filter options
  iHOP Links together protein information. Search using gene symbol or accession ID
Literature search tool that categorises results by GO terms mentioned in abstract
  OnTheFly Automatically annotates files and extracts biological information, including text-mining for GO annotation terms 
Functional analysis tools GO Consortium term enrichment 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'
Provides a range of functional analysis tools, e.g. FatiGO and ‘gene set analysis’
Displays a wide range of outputs and graphical views
  gprofiler performs statistical enrichment analysis to find over-representation of information like Gene Ontology terms. Its output is tabular graphic where ontology tree relationships of enriched terms are shown. Other output formats are available and can be used as input for other software such as EnrichmentMap via Cytoscape software.
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
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
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
  GeneMANIA  Overlays enriched GO terms on a protein 'network'. Online version can only analyse short gene lists (50 genes), for longer lists use this tool as a plugin with Cytoscape. Be selective in the networks tab to avoid error prone text mined data.
Disease specific databases HGVS
Contains links to locus specific mutation databases
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.
  CVCGD Contains more than 250 Coronary artery disease related genes
  PDMap The Parkinson's Disease map is a knowledge repository established to describe mechanisms of PD by means of molecular networks to grasp complex relationships between the genetic and environmental risk factors.

Page last modified on 06 aug 15 14:07

The work of the Cardiovascular Gene Annotation group is supported by British Heart Foundation grant RG/13/5/30112. The work of the Neurological Gene Annotation group is supported by Parkinson's UK grant G-1307. The Functional Gene Annotation team is supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre.