Terms in the CoP database

CoP portal page

Additional option

• - spec : co-expression analysis using the experiments in which genes are specifically expressed

Functional description

This section presents the functional description of a gene. These data were obtained from the TAIR database.

Description

In the case of Arabidopsis thaliana, some descriptions are separated with semicolons/commas such as "F:...;P:...;C:...;MOBFPAV" according to the following format.

• - F: Gene Ontology molecular function
• - P: Gene Ontology biological process
• - C: Gene Ontology cellular component
• - the fourth data presents organism groups that include genes homologous to a gene of interest in descending order of the number of the BLAST hits. The groups are classified into the following seven categories.

• - A: Archae
• - B: Bacteria
• - M: Metazoa
• - F: Fungi
• - P: Plants
• - V: Viruses
• - O: Other eukaryotes

WoLF PSORT

The number [0-14] represents an index of the most possible prediction of subcellular localization. The higher number is the more responsible for the prediction.

• - chlo: chloroplast
• - cyto: cytosol
• - cysk: cytoskeleton
• - E.R.: endoplasmic reticulum
• - extr: extracellular
• - golg: Golgi apparatus
• - lyso: lysosome
• - mito: mitochondria
• - nucl: nuclear
• - pero: peroxisome
• - plas: plasma membrane
• - vacu: valuolar membrane

TargetP

The number [0-9] represents the integer of TargetP value multipled by 10. The higher number is the more responsible for the prediction.

• - C: chloroplast
• - M: mitochondrion
• - S: secretory
• - O: others

TMHMM

• - The value represents the number of trans-membrane domains.

Terminology for Confeito (co-expression) page

Network index

• - NF [0-1] (the Network F-measure index for a cluster of genes)

• - The higher NF represents the tighter network topology, i.e. the stronger co-expression.
• - NF (NC*) = 2 / ( 1 / NR + 1 / NP )
• - NR (ND*) [0-1]: Network Recall or Network Density
• - NP (NB*) [0-1]: Network Precision
• - That is, NF is a harmony mean of NR and NP.
• - NF is also calculated as the following equation.
• - NF = 2 x E / ( D + ( N x ( N - 1 ) / 2 )
• - E: the number of gene-to-gene links (edges) within a gene module
• - D: the number of gene-to-gene links of the module members to any genes (degree)
• - N: the number of module members
• - NR [0-1]: actual number of gene-to-gene links within a gene module ( E ) over potential number of gene-to-gene links within a gene module ( N x ( N - 1 ) / 2 )
• - NP [0-1]: E over D
• - The percentile values of NF [0-100] were calculated on the basis of those of all co-expression modules.

* defined in our paper (Ogata et al., Genome Informatics , 23:117-127, 2009; not yet available on line).

• - VF (VC*) [0-1] (the Vertex F-measure index for a gene)

• - The higher VF represents the stronger co-expression to a group of genes.
• - VF = 2 x E / ( D + N - 1 )
• - E: the number of gene-to-gene links (edges) of a gene to a gene cluster
• - D: the number of gene-to-gene links (degree) of a gene to any genes
• - N: the number of a gene cluster
• - The percentile values of VF [0-100] were calculated on the basis of those of genes/probes included in all co-expression modules.

* defined in our paper (Ogata et al., Genome Informatics , 23:117-127, 2009; not yet available on line).

• - TCC [0-1] (Threshold of Correlation Coefficient): a cutoff value for co-expression network

Node class in co-expression network

• - T: transcription factor, from AGRIS, DATF, RARTF
• - E: enzyme, from KaPPA-View 2, Aracyc, KEGG
• - B: binding protein, ncleic acid or protein binding, based on Gene Ontology annotation
• - M: transmembrane protein, obtained from the TAIR database
• - O: others, unknown or unclassified

Terminology for specifically-expressed experiment page

• - Std GX: gene expression values that were standardized within a microarray assay as follows.

• - Std GX is calculated as the square of the expression value of a gene multiplied by the number of microarray assays over the square sum of the expression values of all genes.
• - The values range over 0 and the value of 1 represents the average of the values.
• - Namely, a gene with the value over 1 is well expressed in the microarray assay, compared with the other genes.
• - Especially, a gene with the value over 5 is expected to be specifically expressed.
• - The percentile values of Std GX [0-100] were calculated on the basis of gene expression values within a microarray.

• - Std2 GX: gene expression values that were standardized within a microarray assay and then standardized for each gene between all assays, according to the procedure similar to that of Std GX.

• - Namely, a gene with the value over 1 is specifically expressed in the microarray assay, compared with in the other assays.
• - The percentile values of Std2 GX [0-100] were calculated on the basis of gene expression values for a gene through all microarray assays.

Terminology for homology page

• - HF [0-1] (the Homology F-measure index for a homologous gene)

• - The harmonic mean of mutual identity between a pair of genes.
• - HF = 2 / ( 1 / Ia + 1 / Ib )
• - Ia and Ib: the identities from gene A to gene B and from gene B to gene A, respectively.
• - Approximately, the same family gene is over 0.1 and the orthologous gene is over 0.4.

Terminology for Biological process (Gene Ontology) page

Evidence Code categories (ECC)

• - X (experimental): EXP, IDA, IPI, IMP, IGI, IEP
• - S (statement): TAS, IC


• - C (computational): ISS, ISO, ISA, ISM, IGC, RCA
• - L (electronic): IEA
• - N (not available): NAS, ND

Terminology for Pathway page

Index for KaPPA-View (metabolic pathway maps)

• - KF (F-measure for KaPPA-View)

• - KF = 2 * H / ( N + T )
• - H: the number of genes that are commonly included in a group of genes and a KaPPA-View map.
• - N: the number of genes included in a group of genes.
• - T: the number of genes included in a KaPPA-View map.

• - PF (F-measure for reference involved in a group of genes)

• - PF = 2 * H / ( N + T )
• - H: the number of genes that are commonly included in a group of genes and a paper.
• - N: the number of genes included in a group of genes.
• - T: the number of genes included in a paper.

Terms for comparison between gene groups

• - SF [0-1] (the similarity F-measure index for gene groups)

• - The similarity index between gene groups.

Other public databases for external links from CoP

• - TAIR: an integral database for Arabidopsis.
• - KEGG: an integral database, such as for metabolic pathways.
• - PlantTribes: an integral database.
• - Gramene: an integral database for crop species.
• - MPSS: a genome database for plants.
• - InParanoid: an ortholog database.
• - Plant RBP: an ortholog database.
• - SIGnAL: a T-DNA database for Arabidopsis.
• - PlantGDB: a genome database for plants.
• - Genevestigator: a gene expression database.
• - eFP Browser: a gene expression database for plants.
• - AVT: a gene expression database for Arabidopsis.
• - ATTED-II: a co-expression database for Arabidopsis.
• - AtcisDB: a cis-element database for Arabidopsis.
• - SUBA: a hydropathy database for Arabidopsis.
• - AtProteome: a proteome database for Arabidopsis.
• - Plant Proteome Database: a proteome database for plants.
• - PMN: a metabolic pathway database for plants.
• - KaPPA-View 4: a metabolic pathway webtool for plants.
• - RnR: an over-expression experiment database for Arabidopsis.
• - iHOP: an on-line information webtool.

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