ATTED-II   version 5.5

ATTED-II; Arabidopsis thaliana trans-factor and cis-element prediction database



(last update) 2010.03.05

Search:

  • <GeneTable>
    Making gene function table
    • This form simply adds information about gene function and predicted subcellular localization for query genes.
    • Gene functions are based on TAIR annotation.
    • Subcellular localizations are predicted by TargetP and WoLF PSORT.

  • <CoexSearch>
    Unified coexpressed gene list from multiple query genes



    Coexpression masure:
    .
    .
    • This form returns unified coexpressed gene list from a couple of query genes (usually less than 10) that strongly coexpress with each other.
    • To construct unified coexpressed gene list:
      1. ATTED-II first makes coexpressed genes list for each of query genes.
      2. Then the MR of each gene list is averaged.
      3. Finally, coexpressed genes are sorted along with the averaged MR.

  • <EdgeAnnotation>
    Extracting coexpression data for query gene pairs


    • This form returns coexpression data with following information;
      • PPIs described in TAIR and IntAct.
      • Conserved coexpression with mammals (Human, Mouse or Rat in COXPRESdb).
      • Common pathways defined by KEGG, AraCyc or KaPPA-View.

  • <CoexVersion>
    Retrieving previously released coexpression data


    gene:
    version of coexpression*1 Release date Details Predictive performance
    of gene function*2
    #samples GeneChip summarization probe-loci annotation #genes coexpression measure remarks
    ver. c6.0 2008.09.05 1151 RMA TAIR7 20906 MR The 237 tissue data (ME00319) in ver. c4.1 was omitted.
    Although the overall performance is slighly worse than ver. c4-1, this data focused on stress or hormone responces, and may provide another functional relationships.    		 (0.781)
    ver. c4.1
    (previously called as ver.5)     		2008.04.08 1388 RMA TAIR7 20906 MR Current version
    Minor calculation bug fix of ver. c4.0.    		 0.792
    ver. c4.0 2008.03.18 1388 RMA TAIR7 20906 MR Using MR as a coexpression measure.
    Possible cross-hybridizing probes were included only for coexpressed gene list.    		 0.790
    ver. c3.1 2007.09.12 1388 RMA CSB.DB & TAIR7 20703 weighted PCC Omitting possible cross-hybridizing probes from ver. c3.0 using TAIR annotation file. 0.756
    ver. c3.0 2006.05.25 1388 RMA CSB.DB 22263 weighted PCC GeneChip normalization became improved.
    After RMA summarization, some experiments are divided for organs or genetic background.    		 0.756
    ver. c1.0 2005.08.15 771 MAS5 (for RIKEN data)
    GCRMA (for MaxPlanck data)    		 CSB.DB 22591 weighted PCC Output restriction; PCC > 0.6
    To combine RIKEN and MaxPlanck data, expression values for each GeneChip are transformed to z-score.    		 could not assessed
    by data limitation
    Output format:


    *1; "c" in version number indicates versions for coexpression, preventing confusion with ATTED-II version.
    *2; Predictive performance is calculated as AUC of ROC curves to prediction GO terms of genes using coexpression data. (1; perfect prediction, 0.5; random prediction)