Help

Ontology Tree View

Select an organism

Genes of different organisms can be visualized by checking their respective checkboxes.

  • Arabidopsis: TAIR9
  • Rice: MSU_v7 (Rice Genome Annotation Project, Release 7)
  • Potato: stNIB-v1 (combining PGSC Gene Model v3.4, ITAG Potato Gene Model v.1, POCI and StGIv13)
  • Tomato: ITAG Tomato Gene Models (v2.3), assembly SL2.40, annotation ITAG2.3

Select ortholog type

Select ortholog grouping based on two ortholog groupings:

  • PGSCorthoMCL: clustering of proteins of 12 plant species with the orthoMCL algorithm (PGSC, 2011)
  • ITAG RSD: clustering of proteins of 4 plant species with the RSD method (kindly provided by ITAG)

Browse bins

Open sub-bins by clicking on the selected bin. Opened bins are shown as opened and closed as closed folders (see Legend below). Ortholog groups are presented by a white icon, and genes by green (those belonging to orthologs) or red icons (those not belonging to orthologs).

  • Ortholog group name
  • Gene within ortholog group
  • Gene without ortholog group
  • Ontology bin - opened
  • Ontology bin - closed

Mouseover a gene name will show its annotation. Select an ortholog or gene by clicking on it and Gene/Ortholog Details view will open.

Gene Details View

In this view information on the individual gene including annotations and links to other sources are listed.

  • Identifier, with link to the primary database
  • Plant: plant species (with link to respective NCBI taxa page)
  • Description: description of the selected gene
  • Synonym, Short Name
  • Genomic Context: position of the gene in the genome (if available)
  • Source of the gene model
  • Last modified: date of last modification of the gene

Ontology annotations: bin(s) that the gene belongs to; click to view the bin in the ontology tree

Orthologs: Orthologous groups that gene belongs to; clicking on one group will open Ortholog Details View

Microarray features: microarray feature ID, description and microarray source are shown.
Annotations: Various gene annotations with links to external databases: NCBI Entrez gene, Gene Ontology (GO), Plant Ontology (PO), PubMed citations linked to the respective gene, KEGG pathways and protein related information from different databases (EC, Gene3D, HAMAP, InterPro, PANTHER, PFAM, PIR, ProDom, PROSITE, SMART, SPRINT, SUPERFAMILY, TIGRFAM).

Ortholog Details View

Identifier of the ortholog group

  • Type: source of the ortholog grouping
  • Last modified: date of last modification of the ortholog
  • Ontology annotations: bin(s) that ortholog group belongs to; click to view the bin in the ontology tree.
  • Ortholog genes: List of genes belonging to the ortholog group that we include in the database, grouped by species. Clicking on gene ID of the species will return you Gene Details view.
  • Annotations: List of genes belonging to the ortholog group of species, that we don’t include in the database. When applicable, the identifiers connect with EnsemblPlants database.

Search

Search is enabled for identifiers (gene, ortholog groups and microarray features), their descriptions and short names (where possible). Search can be limited to selected species only and/or identifier type.

Exports

Exports of gene identifiers and microarray features for individual species are available for import to BioMine (http://biomine.cs.helsinki.fi/search/), GSEA (http://www.broadinstitute.org/gsea/index.jsp), MapMan (http://mapman.gabipd.org/web/guest/mapman) and SEGS (http://kt.ijs.si/software/SEGS/). Date of the last export creation is shown.

Log in

Gene position editing is reserved for collaborators only. Minor changes can be implemented upon request.
For username requests, write to us at gomapman@nib.si, specifying your scientific background and motivation for curation.