Terms in ATTED-II

last update; Oct. 31. 2017

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Terms in ATTED-II

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AGRIS

Annotation of transcription factor used in ATTED-II is downloaded from AGRIS.
AraCyc

AraCyc was developed by TAIR for the annotation of biochemical pathways in Arabidopsis thaliana.
AtGenExpress

Gene expression data used in ATTED-II are collected by AtGenExpress consortium, and are download from TAIR.

Coexpression calculation methods

Abbr	Description
C	Combat
CB	Combat & Bagging
Q	Quantile
CQ	Combat & Quantile
QCQ	Quantile, Combat & Quantile
CQB	Combat & Quantile & Bagging

Condition-specific coexpression
Five AtGenExpress subgroups were used to construct condition-specific coexpression. [more].
- Tissue (237)
- Abiotic stress (534)
- Biotic stress (200)
- Hormone (200)
- Light (48)
cis elements

Computationally predicted cis elements were used in ATTED-II. From all heptamer from AAAAAAA to TTTTTTT, 304 heptamers were used in ATTED-II. Extraction of cis elements was considered\ with gene expression and a position of appearance in promoter region. [more].
ExSim

Expression similarity (ExSim) is the degree of similarity of gene expression pattern. It is calculated as pearson's correlation coefficient between 2 genes.

MR^* Edge

MR < 5 Bold edge

MR < 30 Normal edge

MR > 30 Thin edge
External Link

External links on locus page are added up on request.
In addition, a bookmarklet for Arabidopsis research is useful. You can move any Arabidopsis database to another databse. [Arabimarklet]
Function

Annotation released by TAIR.

MR^*	Edge
MR < 5	Bold edge
MR < 30	Normal edge
MR > 30	Thin edge

Gene Ontology (GO)

Gene Ontology released by TAIR was used.
Prefix of original IDs of GO were changed in ATTED-II according to those type (BP, CC and MF).

Prefix	Type
BP	Biological Process
CC	Cellular Component
MF	Molecular Function

Evidence code [www.geneontology.org];

Code	Description
IC	inferred by curator
IDA	inferred from direct assay
IEA	inferred from electronic annotation
IEP	inferred from expression pattern
IGI	inferred from genetic interation
IMP	inferred from mutant phenotype
IPI	inferred from physical interaction
ISS	inferred from sequence or structural similarity
NAS	non-traceable author statement
ND	no biological data available
TAS	traceable author statemen

Loose hieralchy of the code;
[TAS/IDA] > [IMP/IGI/IPI] > [ISS/IEP] > [NAS] > [IEA]

Graph in gene page
- Click to enlarge.
- Colors in tissue-specific expression graph in gene page indicate probesets corresponding to the gene.
Kappa-view

KaPPA-View (The Kazusa Plant Pathway Viewer) was developed by Kazusa DNA Res. Inst.. Annotation of\ biochemical pathways were used in ATTED-II.
KEGG

KEGG (Kyoto Encyclopedia of Genes and Genemes) was developed by Genomenet. Annotation of biochemical pathways were used in ATTED-II.

Locus

Loci defined by TAIR were used in ATTED-II.

	Number	Example	Comments
Total loci	31,128	At1g01010 ... At5g67640	Nucleus-encoded genes with 1000-bp upstream sequence accroding to At_upstream_1000_20051108 of TAIR.
Total loci with Affy. expression data	22,263	At1g01010 ... At5g67630	conversion of probe to locus is done according to MaxPlanck-released expression data.
Total loci with protein sequence	26,544	At1g01010 ... At5g67640	according to ATH1_pep_20051108 of TAIR.

Murual rank (MR)

Mutual rank is calculated for edge strength of coexpressed gene network. [more]

MR^* Edge

MR < 5 Bold edge

MR < 30 Normal edge

MR > 30 Thin edge
Reported cis elements

Predicted cis elements by CEG method^* was compared with reported cis elements. The information of reported cis elements was downloa\ \ ded from PLACE (A Database of Plant Cis-acting Regulatory DNA Elements) web site.
Sample contribution score
Sample contribution score is calculated as a product of z-scored expression values. Avarage of the score is pearsons correlation coefficient.
Stability
Stability of coexpression (S) is roughly corresponding to the number of samples which support the focused gene-to-gene correlation.

Example of stability
Coexpression stability is difined for a pair of genes.
- The coexpression is supported by few samples or only tissue deferences. [exapmle]
- The coexpression is supported by many samples. [exapmle]
Coexpression stability (S) is introduced to distinguish these two situations.
Definition of stability

where cor_i is the correlation without the first i PCs, cormax is their maximum value (i=N), and N = 10 was used in this study. The numerator and denominator correspond to the area under the curve and that between cormax and 0.0, which is the ratio of the yellow area to the total of the blue and yellow areas i\ n the example of stability. Therefore, the S-values will change from 0.0 to 1.0, and the larger S-values indicate stable correlations or small changes of correlations, while smaller S-values mean fragile coexpre\ ssion, or imply that the cor0 was determined from a small number of experiments.

Reference

Kinoshita K, Obayashi T. (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics., 25. 2677-84. [PubMed] [PDF]

MR^*	Edge
MR < 5	Bold edge
MR < 30	Normal edge
MR > 30	Thin edge

Target

Two tools are used to predict localizations of proteins; TargetP and WoLF PSORT. In t\ ables in ATTED-II, long target names pop up when the mouse is over the abbrevations.

TargetP results were released by TAIR. c:m:s:o scores represent reliabilities for chlor\ oplast, mitochondoria, scretory, and others.

Abbr	Name
C	chloroplast
M	mitochondoria
S	scretory
O	others

Stand alone program of WoLF PSORT is provided by Dr. Paul Horton in Computational Biology Research Center, AIST, Japan.

Abbr		Name
C	chlo	chloroplast
E	E.R.	E.R.
G	golg	golgi body
K	cysk	cytoskeletal
L	lyso	lysosome
M	mito	mitochondria
N	nucl	nuclear
P	plas	plasma membrane
S	extr	extracellular
V	vacu	vacuole
X	pero	peroxisome
Y	cyto	cytoplast

Localization names joining two abbreviated names with "_", such as "cyto_nucl", indicate dual localization.

TargetP

Result of TargetP released by TAIR
c:m:s:o scores represent reliabilities for chloroplast, mitochondoria, scretory, and others.

WoLF PSORT

Result of WoLF PSORT calculated by Dr. Paul Horton in Computational Biology Research Center, AIST, Japan.

Abbr		Name
C	chlo	chloroplast
E	E.R.	E.R.
G	golg	golgi bod
K	cysk	cytoskeletal
L	lyso	lysosome
M	mito	mitochondria
N	nucl	nuclear
P	plas	plasma membrane
S	extr	extracellular
V	vacu	vacuole
X	pero	peroxisome
Y	cyto	cytoplast

Localization names joining two abbreviated names with "_", such as "cyto_nucl", indicate dual localization.

Terms in ATTED-II

Example of stability

Definition of stability

Reference