Login

Join for Free!
118829 members
table of contents table of contents

Plant growth stages are identified as distinct morphological landmarks in a continuous …


Biology Articles » Botany » Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology » Tables

Tables
- Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

....................................................................................................


Table I. A summary of the number of synonyms integrated into the GSO from each species/family/source

The integration of synonyms for Soybean and Solanaceae is in progress.

Species/Source
No. of Synonyms
Arabidopsis 93
Rice 23
Maize 162
Wheat 65
Oat 65
Barley 65
Sorghum 13
BBCH and Zadok scales 381
Soybean 79
Solanaceae (mainly tomato) 51
All the species 997
Average no. of synonyms per GSO term
About 9

....................................................................................................


Table II. List of evidence codes for use in annotations to GSO

These are used in building the annotation inferences that indicate the type of experiment cited by the researcher whose data was used to determine the protein and/or transcript expression and phenotype of mutant(s) or quantitative trait loci.

Evidence Code
Name
IC Inferred by curator
IDA Inferred from direct assay
IEA Inferred from electronic annotation
IEP Inferred from expression pattern
IMP Inferred from mutant phenotype
IGI Inferred from genetic interaction
IPI Inferred from physical interaction
ISS Inferred from sequence or structural similarity
NAS Nontraceable author statement
TAS
Traceable author statement

....................................................................................................


Table III. Annotation of the three orthologous sets of flowering time pathway genes from Arabidopsis and rice

The GSO and PSO annotations for Arabidopsis GI, CO, and FT, and rice OsGI, Se1 (Hd1), and Hd3a genes were imported from the PO database. The annotations to GO (columns 4–6) were imported from TAIR and Gramene databases to give an overview on the functional characteristics of the orthologous genes. The curators assigned the ontology terms from the whole growth stage (GSO) and plant structure (PSO) aspect to suggest when and where in a plant these genes were expressed or phenotyped. Depending on the experiment type (evidence code) and citation evidence (references), the databases recorded information about the mutant/gene/gene product to GSO and PSO terms. The same procedure was used for GO annotations. Columns 2 to 6 provide information on the term names, ID, and the evidence code.

Genes
Plant Growth Stage (GSO)
Plant Structure (PSO)
GO: Cellular Component
GO: Molecular Function
GO: Biological Process
Arabidopsis
GI Whole plant (PO:0000003; TAS) Flower (PO:0009046; IMP) Nucleoplasm (GO:0005654; IDA) and nucleus (GO:0005634; IDA) Unknown Response to cold (GO:0009409; IMP), flower development (GO:0009908; TAS), regulation of circadian rhythm (GO:0042752; IMP), positive regulation of long-day photoperiodism, and flowering (GO:0048578; IMP)
CO Not available Flower (PO:0009046; IMP) Nucleus (GO:0005634; NAS) Transcription factor activity (GO:0003700; ISS) Regulation of flower development (GO:0009909; IMP)
FT Not available Leaf (PO:0009025; TAS) and shoot apex (PO:0000037; IDA) Unknown Phosphatidylethanolamine binding (GO:0008429; ISS) and protein binding (GO:0005515; IPI) Positive regulation of flower development (GO:0009911; IMP)
Rice
OsGi Inflorescence emergence from flag leaf sheath (PO:0000003; IMP) Inflorescence (PO:0009049; IMP) Nucleus (GO:0005634; IEP) Unknown Inflorescence development (GO:0010229; IMP)
Se1 (Hd1, Fl1) Inflorescence emergence from flag leaf sheath (PO:0007041; IGI, IMP), stem elongation (PO:0007089; IMP), and FR.04 fruit ripening complete (PO:0007038; IMP) Floret (sensu Poaceae; PO:0006318; IMP), inflorescence (PO:0009049; IGI, IMP), inflorescence meristem (PO:0000230; IMP), and seed (PO:0009010; IMP) Nucleus (GO:0005634; IEP) DNA binding (GO:0003677; ISS), transcription factor activity (GO:0003700; ISS), and zinc ion binding (GO:0008270; ISS) Inflorescence development (GO:0010229; IGI), long-day photoperiodism (GO:0048571; IEP, IGI), and short-day photoperiodism (GO:0048572; IEP, IGI)
Hd3a (Fl32a)
Inflorescence emergence from flag leaf sheath (PO:0007041; IMP), stem elongation (PO:0007089; IMP), and FR.04 fruit ripening complete (PO:0007038; IMP)
Floret (sensu Poaceae; PO:0006318; IMP), inflorescence (PO:0009049; IMP), inflorescence meristem (PO:0000230; IMP), seed (PO:0009010; IMP), and sporophyte (PO:0009003; IEP)
Unknown
Phosphatidylethanolamine binding (GO:0008429; ISS)
Inflorescence development (GO:0010229; IMP), short-day photoperiodism (GO:0048572; IMP), and regulation of timing of transition from vegetative to reproductive phase (GO:0048510; IMP)

....................................................................................................


Table III. Annotation of the three orthologous sets of flowering time pathway genes from Arabidopsis and rice

The GSO and PSO annotations for Arabidopsis GI, CO, and FT, and rice OsGI, Se1 (Hd1), and Hd3a genes were imported from the PO database. The annotations to GO (columns 4–6) were imported from TAIR and Gramene databases to give an overview on the functional characteristics of the orthologous genes. The curators assigned the ontology terms from the whole growth stage (GSO) and plant structure (PSO) aspect to suggest when and where in a plant these genes were expressed or phenotyped. Depending on the experiment type (evidence code) and citation evidence (references), the databases recorded information about the mutant/gene/gene product to GSO and PSO terms. The same procedure was used for GO annotations. Columns 2 to 6 provide information on the term names, ID, and the evidence code.

Genes
Plant Growth Stage (GSO)
Plant Structure (PSO)
GO: Cellular Component
GO: Molecular Function
GO: Biological Process
Arabidopsis
GI Whole plant (PO:0000003; TAS) Flower (PO:0009046; IMP) Nucleoplasm (GO:0005654; IDA) and nucleus (GO:0005634; IDA) Unknown Response to cold (GO:0009409; IMP), flower development (GO:0009908; TAS), regulation of circadian rhythm (GO:0042752; IMP), positive regulation of long-day photoperiodism, and flowering (GO:0048578; IMP)
CO Not available Flower (PO:0009046; IMP) Nucleus (GO:0005634; NAS) Transcription factor activity (GO:0003700; ISS) Regulation of flower development (GO:0009909; IMP)
FT Not available Leaf (PO:0009025; TAS) and shoot apex (PO:0000037; IDA) Unknown Phosphatidylethanolamine binding (GO:0008429; ISS) and protein binding (GO:0005515; IPI) Positive regulation of flower development (GO:0009911; IMP)
Rice
OsGi Inflorescence emergence from flag leaf sheath (PO:0000003; IMP) Inflorescence (PO:0009049; IMP) Nucleus (GO:0005634; IEP) Unknown Inflorescence development (GO:0010229; IMP)
Se1 (Hd1, Fl1) Inflorescence emergence from flag leaf sheath (PO:0007041; IGI, IMP), stem elongation (PO:0007089; IMP), and FR.04 fruit ripening complete (PO:0007038; IMP) Floret (sensu Poaceae; PO:0006318; IMP), inflorescence (PO:0009049; IGI, IMP), inflorescence meristem (PO:0000230; IMP), and seed (PO:0009010; IMP) Nucleus (GO:0005634; IEP) DNA binding (GO:0003677; ISS), transcription factor activity (GO:0003700; ISS), and zinc ion binding (GO:0008270; ISS) Inflorescence development (GO:0010229; IGI), long-day photoperiodism (GO:0048571; IEP, IGI), and short-day photoperiodism (GO:0048572; IEP, IGI)
Hd3a (Fl32a)
Inflorescence emergence from flag leaf sheath (PO:0007041; IMP), stem elongation (PO:0007089; IMP), and FR.04 fruit ripening complete (PO:0007038; IMP)
Floret (sensu Poaceae; PO:0006318; IMP), inflorescence (PO:0009049; IMP), inflorescence meristem (PO:0000230; IMP), seed (PO:0009010; IMP), and sporophyte (PO:0009003; IEP)
Unknown
Phosphatidylethanolamine binding (GO:0008429; ISS)
Inflorescence development (GO:0010229; IMP), short-day photoperiodism (GO:0048572; IMP), and regulation of timing of transition from vegetative to reproductive phase (GO:0048510; IMP)

....................................................................................................

 


rating: 1.60 from 5 votes | updated on: 17 Dec 2007 | views: 23333 |

Rate article:







excellent!bad…