last update; Jun. 03. 2022

Change Log

ATTED-II version Date Contents
ver 11.1 2022.06.03 New data The calculation of the union version of the coexpression data (Xxx-u) has been revised. Xxx-u is determined as the mean value between Xxx-r and Xxx-m. For the gene pairs with only Xxx-r, linear regression from Xxx-r to Xxx-u was used in the previous versions, whereas the Xxx-r value is directly scaled to obtain the Xxx-u value in the current version in the following equation. Xxx-u(g1,g2) = (1/2)^alpha * Xxx-r(g1,g2). Based on the function score of Xxx-u, alpha=0.2 was commonly used for all species.
Tool The global view of coexpression data is newly released, which is the UMAP representation of coexpression relationships in species.
ver 11.0 2021.02.23 New Index The coexpression index, LS (Logit Score), is newly provided as a z-score. The original LS values can have a large range of values depending on the parameters in a calculation step. This makes it difficult to compare different versions of coexpression data. By converting to Z-values, the range of values is aligned and the intercomparability of coexpression values is greatly improved.
New data The following two factors improve the performance of coexpression data; (1) optimizing the calculation parameters and (2) to increased number of RNAseq data.
ver 10.1 2020.10.01 NetworkDrawer In the version 10.0, there was a bug in the network drawing function (NetworkDrawer and gene network in the gene pages etc). In ATTED-II, the network edge is supposed to be drawn from each gene to the three most (namely, first, second and third) strongly co-expressed genes. However, ATTED-II v10.0, the most strongly co-expressed genes was mistakenly skipped and edges were drawn on the second, third and fourth most strongly co-expressed genes. This bug has been resolved in ATTED-II v10.1. We sincerely apologize for the inconvenience this may have caused.
ver.10.0 2020.07.31 NetworkDrawer For simple representation, a functionality to represent the conserved coexpression in orange is disabled, because the union-version coexpression data includes reproducibility between microarray and RNAseq data.
2020.06.24 New Index LS (Logit Score) is introduced. Larger LS indicates stronger coexpression, and LS=0 indicates no coexpression. LS is a monotonic transformation (negative logit) of MR index. To easily understand this transformation, these two indices can be changed with a radio button in coexpressed gene list pages.
New Data New coexpression data are available for 17 data sets of 9 species. In addition to the microarray-based (Xxx-m) and RNAseq-based (Xxx-r) coexpression data, ATTED-II now provides a unified version of coexpression for each species (Xxx-u), which is calculated by linear regression of Xxx-m and Xxx-r coexpression data in each species
ver 9.2 2017.10.31 New data New coexpression data are available for 16 data sets of 9 species.
ver.9.1 2017.12.13 Publication New ATTED-II publication available. Obayashi et al. (2018) "ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of Statistical Property of the Mutual Rank Index". (Publication)
2017.10.31 New data New coexpression data are available for 16 data sets of 9 species.
ver.9.0 2017.09.08 New data New coexpression data are available for 15 data sets of 9 species.
Tool Most of the tools are workable for the all species.
ver.8.0 2016.01.13 Publication New ATTED-II publication available. Aoki et al (2016): "ATTED-II in 2016: a plant coexpression database towards lineage-specific coexpression" (Publication)
2015.09.01 New data New coexpression data is available for 14 platforms (nine microarrays and five RNAseqs) of nine species (seven dicots and two monocots).
Draw NetworkDrawer is renewed to automatically detect biologically meaningful subnetworks.
ver.7.1 2013.08.17 New data New coexpression data is available for Arabidopsis which is constructed from 328 RNAseq data.
ver.7.0 2013.05.20 New data New 5 species (soybean, maize, grape, medicago and poplar) are added as reference species in the coexpressed gene list for Arabidopsis.
ver.6.0 2010.09.28 New external links External links for the 32 Arabidopsis databases are available in locus page. Based on the click log, the following five databases are given as the database icons: TAIR, MIPS, SALK, BAR and SALAD.
New data Five types of condition-specific gene coexpressions for Arabidopsis were made available. The conditions are defined in AtGenExpress: Tissue, Abiotic, Biotic, Hormone and Light.
ver.5.5 2010.05.20 Draw "NetworkDrawer" is renewed to draw larger gene networks.
  • New options to collect additional coexpressed genes.
    • [Add no genes]
    • [Add genes directly connected with query genes] This is the previous setting. Additional genes with at least 2 query genes are selected.
    • [Add genes indirectly conneted with query genes] Up to 20 coexpressed genes in "gene page" for each of query genes are selected. Genes only connected with single gene is omitted.
  • New function is available to refine the obtained figure.
    After obtaining the gene network, user can refine the figure by following ways.
    1. Enlarge or shrink the figure.
    2. Set exact position of genes.
    3. Using spline edge.
      Before this renewal, the spline edge was always ON. We apply it OFF as default to draw larger gene network.
2010.03.05 Draw "Tool" tab is renamed "Draw" tab.
Search The function to making unified coexpressed gene list from multiple genes were previously provided as a part of [Tool > NetworkDrawer]. This function is newly supplied as [Search > CoexSearch].
2009.07.08 Tool Search box on the top page was renewed. As the default, this tool searches loci and GO terms.
  • Locus search; AGI code (perfect matching), aliases, short descriptions, TAIR curator summaries
  • GO search; GO ID (perfect matching) and GO titles
Locus page New external link for SALAD DB was made available. This link can be used to compare domain structures of Arabidopsis and rice homologs.
public data update Publicly available data for TAIR9 as well as GO and KEGG annotations was made updated. [History of data version] Please note that probe-locus correspondence was not updated this time. ATTED-II still use the TAIR7-base probe-locus correspondence. The coexpression data will be updated in this August or September.
ver.5.4 2009.07.01 New data Rice coexpression data (Osa ver. c1.0) was made available. The coexpression data was calculated using 208 GeneChip data downloaded from ArrayExpress
ver.5.3 2009.06.14 Tool A tool to draw hierarchical structures of Gene Ontology terms was made available. [Tool > GOPathDrawer]
2009.05.27 Locus page New external link for TileViz was made available.
TileViz in At-TAX shows tiling array data with ATH1 array data (Laubinger et al., 2008). User can use this tool to estimate the effect of crosshybridization of ATH1 probes, when the gene of interest is cross-hybridized on ATH1 array.
public data update Publicly available data for Gene alias, GO, KEGG and AraCyc was updated. [History of data version]
ver.5.2 2009.04.13 Tool Hierarchical clustering for query genes was made available. [Tool > HCluster]
2009.01.15 Tool Coexpression viewer was changed to provide new analysis method to investigate gene coexpression of a focused gene pair. [Tool]
Stability of coexpression is roughly corresponding to the number of samples which support the focused gene-to-gene correlation.
2008.10.27 Publication ATTED-II official reference was renewed. (Publication)
2008.09.10 Version numbering ATTED-II has two types of important versions: version for ATTED-II and version for coexpression data.
  • To prevent confusions between the two types of versions, we added extra "c" for coexpression version (e.g. version c4.0).
  • To ensure consistency with ATTED-II version, present coexpression version (ver. 5) was renamed as ver. c4.1, and ver. c5.0 becomes a missing version.
2008.09.05 Google Map Networks for six subcellular locations were updated with PPI and KEGG pathway information. (Browsing > Coexpressed gene network for subcellular locations)
2008.09.05 new data Coexpression data from non-tissue samples is searchable as ver. c6.0 coexpression data. It possibly provides another functional relationships. (Search)
2008.09.05 others Database version of ATTED-II was added in the bottom region of most pages to prevent confusions of data update. Major version number is mainly responded to coexpression data version, while minor version number is from public data update. Version histories can be checked from [Logs > History of data version].
2008.07.31 tool The previous versions of gene coexpression data are available from "Search" tab, which may be required for user's publication. (Search)
2008.07.19 representation Following points were changed for coexpressed gene network
  • PPI is always drawn as red dotted edge irrespective of the existence of gene coexpression.
  • Annotations for KEGG pathways are added above the gene names on the coexpressed gene networks. Representation of this KEGG pathway information is limited to 5 pathways.
2008.07.19 public data update All data except of Google Map and probe-locus correspondences were constructed based on TAIR8.
ver.5.1 2008.05.08 tool New search tool are available to extract gene coexpression data for query gene pairs. (Search)
2008.04.15 Page Access logs are available. (Access log)
2008.04.14 representation Following three points were changed for drawing tool of coexpressed gene network.
  • An option was added for drawing singlet query nodes.
  • The default selection for making coexpressed gene list is changed to "Not execute".
    The function of making coexpressed gene list from multiple query genes assumes that the query genes are coexpressed well. This assumption is sometimes not fulfilled with the use of drawing coexpressed gene networks for grouping purposes of query genes.
2008.04.07 data update Coexpression data was updated to version 5 c4.1 (except Google Map coexpression network). The following two points were changed from version c4.0.
  • Minor bug fix of calculation program of gene-to-gene correlation.
  • The ME00330 sample was divided into the shoot and the root.
2008.04.07 public data update  
ver.5.0 2008.03.26 representation In GO networks or network-drawing CGI, annotations of nodes added by ATTED-II was displayed as same way as query nodes.
2008.03.18 representation Network drawing rule was changed for gene page.
  • OLD;
    • Node; Top 20 Cor genes
    • Edge; MR < 50
  • NEW;
    • Edge; Top 3 MR genes.
    • Node; 20 genes selected by path length and MR.
2008.03.18 representation Score for coexpressed gene list was changed to MR from Correlation value.
2008.03.18 representation Coexpressed gene list was changed to include possibly cross-hybridized probes.
2008.03.18 public data update  
ver.4.4 2008.02.29 tool Google Maps representation of coexpressed gene network can be marked for multiple genes. (example)
2007.12.20 data update PPI information includes PPIs for orthologs in other species. This PPI information is derived from NCBI.
2007.12.17 representation Network drawing tool was moved into 'Tool' tab from 'Search' tab.
2007.12.13 representation Gene-to-gene relationships (Red: PPI, Green: common pathways, Orange: conserved coexpression) were added to coexpressed gene networks.
2007.10.16 public data update  
ver.4.3 2007.09.23 representation Coexpressed gene network in subcellular location is available. [list]
2007.09.23 Tool Coexpression viewer was available.
2007.09.12 representation Network representation was updated, which is now clickable to move corresponding locus page. TF genes are represented as a octagon-shape node. The other genes are represented as a circle node.
2007.09.12 public data update  
ver.4.2 2007.05.01 tool The restriction of the maximum number of genes to draw coexpressed gene networks was relaxed from 20 to 300.
2006.09.25 data update predicted TF to bind cis element. The prediction is now based on 1388 GeneChip data.
2006.08.19 renewal browsing pages for functional categories and predicted cis elements.
2006.07.24 renewal cis page (correspondence with reported cis elements in PLACE)
ver.4.1 2006.07.22 renewal home page and locus page
2006.07.20 renewal coexpressed gene network for functional categories and coexpressed genes.
2006.06.06 renewal locus (a graph for correlation decay)
form for coexpressed TFs.
2006.06.03 data update WoLF to proteins (ATH1_pep.20051108)
2006.06.03 public data update  
ver.4.0 2006.03.25 renewal A local coexpressed gene network is prepared in the pages for coexpressed gene list.
2006.03.25 data update coexpressed gene table (ver. c3.0)
2006.03.25 public data update  
ver.3.4 2006.02.16 minor update form for coexpressed gene list; adding TF annotation to the list from that of AGRIS TFDB.
2006.02.02 new page How to make in-lab DB, LabATTED (Sorry, Japanese only).
2005.12.29 minor update form for coexpressed gene list; printing table of query loci as well as coexpressed gene list.
2005.12.02 new form new form for coexpressed gene list.
2005.08.29 public data update  
ver.3.3 2005.08.21 renewal Changing subcellular localization prediction tool; iPSORT -> WoLF PSORT.
2005.08.15 newly opened! Name: ATTED -> ATTED-II [more]
cis element predictions and these statistical tests for gene lists.
WoLF PSORT results in locus pages