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
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
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
- - 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.