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Ontology Tree View

Select an organism

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

  • Arabidopsis: Araport11 (Araport11 official release from Arabidopsis Information Portal (2016))
  • Beet: RefBeet1.1 (The genome of the recently domesticated crop plant sugar beet. Nature 505, 546-549 (2014).)
  • Cacao tree: Phytozome9.1 (The genome of Theobroma cacao. Nature genetics 43, 101-108 (2011).)
  • Potato: stNIB-v1 (combining PGSC Gene Model v3.4, ITAG Potato Gene Model v.1, POCI and StGIv13)
  • Rice: MSU_v7 (Rice Genome Annotation Project, Release 7)
  • Tobacco: ntaUG17 (NCBI's Unigene set for Nicotiana tabacum, version 17 (2011)
  • Tomato: ITAG Tomato Gene Models (v2.3), assembly SL2.40, annotation ITAG2.3

Select ortholog type

Several orthologue groupings are available for selection:

  • PLAZA_dicots_sub: PLAZA 3.0 dicot subfamilies (PLAZA dicot subfamilies)
  • PLAZA_monocots_sub: PLAZA 3.0 monocot subfamilies (PLAZA monocot subfamilies)
  • ITAG_orthoMCL: OrthoMCL orthologous groups by the Tomato Sequencing Consortium (ITAG, 2012)
  • ITAG RSD: Reciprocal Shortest Distance (RSD) orthologous groups; 4 plant species (kindly provided by Stephane Rombauts; 2012-10-19)
  • PGSC_orthoMCL: OrthoMCL orthologous groups by the Potato Genome Sequencing Consortium; 12 plant species (PGSC, 2011)
  • PLAZA_dicots: PLAZA 3.0 dicot families (PLAZA dicot families)
  • PLAZA_monocots: PLAZA 3.0 monocot families (PLAZA monocot families)

Due to the variation of orthologue relationship predictions (different algorithms, evolutionary distance between plants used in predictions, etc.) we also create the so-called weak components from various combinations with Pajek:

  • WC_Pajek: ITAG_RSD + ITAG_orthoMCL + PGSC_orthoMCL (2014-03-31)
  • OCD_PLAZAiTAG: ITAG_RSD + ITAG_orthoMCL + PLAZA_dicots_sub (2016-08-23)
  • OCD_all: ITAG_RSD + ITAG_orthoMCL + PLAZA_dicots_sub (2016-08-23)
  • OCD_PLAZA: PLAZA_dicots_sub + PLAZA_monocots_sub (2016-08-23)

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 purple 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
  • Short Name
  • Synonym
  • 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:

There are also generic exports available, generally linking one identifier to another.
Archive of previous export files is available in the exports section.

Curation

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.