ATTED-II

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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.


  • 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).
    PrefixType
    BPBiological Process
    CCCellular Component
    MFMolecular Function

    Evidence code [www.geneontology.org];

    CodeDescription
    ICinferred by curator
    IDAinferred from direct assay
    IEAinferred from electronic annotation
    IEPinferred from expression pattern
    IGIinferred from genetic interation
    IMPinferred from mutant phenotype
    IPIinferred from physical interaction
    ISSinferred from sequence or structural similarity
    NASnon-traceable author statement
    NDno biological data available
    TAStraceable 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.
    NumberExampleComments
    Total loci31,128At1g01010
    ...
    At5g67640
    Nucleus-encoded genes with 1000-bp upstream sequence accroding to At_upstream_1000_20051108 of TAIR.
    Total loci with Affy. expression data22,263At1g01010
    ...
    At5g67630
    conversion of probe to locus is done according to MaxPlanck-released expression data.
    Total loci with protein sequence26,544At1g01010
    ...
    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 cori 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]



  • 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.
    AbbrName
    Cchloroplast
    Mmitochondoria
    Sscretory
    Oothers
    Stand alone program of WoLF PSORT is provided by Dr. Paul Horton in Computational Biology Research Center, AIST, Japan.
    AbbrName
    Cchlochloroplast
    EE.R.E.R.
    Ggolggolgi body
    Kcyskcytoskeletal
    Llysolysosome
    Mmitomitochondria
    Nnuclnuclear
    Pplasplasma membrane
    Sextrextracellular
    Vvacuvacuole
    Xperoperoxisome
    Ycytocytoplast
    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.
    AbbrName
    Cchlochloroplast
    EE.R.E.R.
    Ggolggolgi bod
    Kcyskcytoskeletal
    Llysolysosome
    Mmitomitochondria
    Nnuclnuclear
    Pplasplasma membrane
    Sextrextracellular
    Vvacuvacuole
    Xperoperoxisome
    Ycytocytoplast
    Localization names joining two abbreviated names with "_", such as "cyto_nucl", indicate dual localization.