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Resources

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
  NCBI Gene Find gene record with wide range of annotations and links
  UniProt
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
  PubMed
NCBI literature search tool with multiple filter options
  iHOP Links together protein information. Search using gene symbol or accession ID
  GoPubMed
Literature search tool that categorises results by GO terms mentioned in abstract
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'
  Bableomics
Provides a range of functional analysis tools, e.g. FatiGO and ‘gene set analysis’
  Blast2GO
Displays a wide range of outputs and graphical views
  gprofiler Displays a table of genes associated with an ontology tree of the enriched GO terms, and enables alignment of multiple data analyses
  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
  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
  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
  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
  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 Coronary artery disease related genes

Page last modified on 13 mar 14 08:21



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.