Change Log

last update; Mar. 05. 2010
COXPRESdb version Date contents
ver. 4.0 2010.03.05 Draw "Tool" tab is renamed "Draw" tab.
2010.02.10 Search The function to making unified coexpressed gene list from multiple genes were previously provided as a part of [Tool > NetworkDrawer]. This funct\ ion is newly supplied as [Search > CoexSearch].
2009.08.25 Coexpression datal Coexpression data for Rno (Rattus norvegicus) was updated;
Rno ver. c1.1 (11912 genes, 632 GeneChips) → ver. c2.0 (13751 genes, 3526 GeneChips for 146 Experiments)
Coexpression datal Coexpression data for the following 4 species was made available; [example]
Gga (Gallus gallus) ver. c1.0, 13757 genes, 352 GeneChips (22 Experiments)
Dre (Danio rerio) ver. c1.0, 10112 genes, 590 GeneChips (41 Experiments)
Dme (Drosophila melanogaster) ver. c1.0, 12626 genes, 1102 GeneChips (52 Experiments)
Cel (Caenorhabditis elegans) ver. c1.0, 17256 genes, 514 GeneChips (35 Experiments)
ver. 3.3 2009.07.25 Tool The search box next to the title logo in the top page was renewed.
Tool CoexViewer was renewed. [Tool > CoexViewer]
2009.06.14 Tool A tool to draw hierarchical structures of Gene Ontology terms was made available. [Tool > GOPathDrawer]
2009.05.20 Search A tool to obtain tissue-specific expression data for human was made available. The data of GSE3526 was used as the tissue-specific expression data in COXPRESdb. Replicate experiments were averaged.[Tool > TissueDataExtractor]
2009.04.13 Tool Hierarchical clustering for query genes was made available. [Tool > HCluster]
2008.12.12 Download Protein subcellular localization predicted by WoLF PSORT was made downloadable. [Download > WoLF]
data update Public annotations were updated. [more]
ver. 3.2 2008.10.31 others Introducing new version numbering system.
COXPERSdb has two types of important versions: version for COXPRESdb and version for coexpression data.
  • To prevent confusions between the two types of versions, we added extra "c" for coexpression version.
  • To ensure consistency with COXPRESdb version, coexpression versions were renamed as follows;
    • Human;
      • (old) → (new)
      • ver.1 → ver.c1.0
      • ver.2 → ver.c2.0
      • ver.4 → ver.c3.0
      • ver.6 → ver.c3.1 (current version!)
    • Mouse;
      • ver.1 → ver.c1.0
      • ver.2 → ver.c2.0
      • ver.3 → ver.c2.1 (current version!)
    • Rat;
      • ver.2 → ver.c1.0
      • ver.4 → ver.c1.1
2008.09.22 Network Annotations for KEGG pathways are added above the gene names on the coexpressed gene networks. For each gene network, up to five KEGG pathways with larger numbers of genes are selected.
2008.07.30 bug fix The tool to extract coexpressions for input genes had a bug that this tool only returned the Entrez Gene IDs with five digits. The bug is fixed.
2008.05.29 representation Coexpressed gene networks are developed easy to recognize the relationships of PPIs and conserved coxpressions.
  • PPIs are presented as red dotted edges independently of the existence of gene coexpression.
  • Genes commonly appeared in the coexpressed gene networks for the corresponding orthologs are marked by orange.
data update Public annotations were updated. [more]
ver. 3.1 2008.05.10 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 Tool "PPI search" was available in "Search" tab. It returns a PPI list between query genes and any genes. The sources of PPI data used in COXPRESdb are HPRD and IntAct.
representationFollowing 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.
  • PPI data in the coexpressed gene network drawn for user query genes are available in the tab-delimitated text file.
    • Data source; HPRD_binary, HPRD_complex, IntAct
    • Number of publication
    • Experiment type; H (yeast two hibrid), T (in vitro), V (in vivo)
    • Example; HPRD_binary(2;T)
      • According to HPRD, this binary PPI was supported by two publications, which were based on in vitro experiments.
2008.04.08 data update Coexpression data is updated as follows (except Google Map coexpression network which is now preparing).
  • Human; ver.4 → ver.6 ver.c3.0 → ver.c3.1
  • Mouse; ver.2 → ver.3 ver.c2.0 → ver.c2.1
  • Rat; ver.2 → ver.4 ver.c1.0 → ver.c1.1
These update is a minor bug fix in the calculation of gene coexpression.
representation PPI representation in coexpressed gene network was changed as follows.
  • PPI without coexpression is shown as Red dotted edges.
  • PPI with coexpression is shown as "PPI" in letters.
ver. 3.0 2008.03.26 representation In GO networks or network-drawing CGI, annotations of additional nodes by calculation was also displayed. (example)
bug fix Red (PPI) and orenge (conserced coexpression) edges in coexpressed gene networks in "gene pages" are mistaken for each other at the latest update (Mar, 17, 2008). This bug was fixed.
2008.03.17 coexpressed gene network Network drawing rule was changed for gene pages.
  • OLD;
    • Node; Top 20 Cor genes
    • Edge; MR < 50
  • NEW;
    • Edge; Top 3 MR genes.
    • Node; 20 genes selected by path length and MR.
coexpressed gene list Score for coexpressed gene list was changed to MR from Correlation value.
new data Rat data were added.
data update Public annotations and coexpressed gene table were updated. [more]
ver. 2.0 2008.02.29 ToolGoogle Maps representation of coexpressed gene network can be marked for multiple genes. Focus is set on first gene. (example)
2008.01.16 ToolInterface of Drawing gene networks and searching coexpressed genes was updated.
2007.09.25 PublicationAdded
2007.07.31 Toolco-expression viewer: This tool makes graphs of sample contribution for co-expression between two genes.
Toolexpression viewer: This tool makes graphs of gene expression pattern for every probes for one genes.
2007.06.30 graphGraph of tissue-specific expression was changed for each gene. (Previously it was for each probe.)
2007.06.22 officially openedCOXPRESdb was officially opened.
data updateCoexpressed gene data for Human and Mouse were updated to ver.2ver.c2.0. [more]
data updatePublic annotations were updated. [more]
graphTissue specific expressions on probe level were represented in gene pages.
graphReported protein-protein interactions were overlayed on co-expressed gene network.
ver. 1.1 2007.05.21 ToolSearch from Affymetrix probe ID was provided in "Search tab".
Bug fixNetwork drawing tool for Human genes included a bug in the representation of gene symbol. It was fixed.
Data DownloadRMA-normalized expression data used in COXPRESdb were downloadable in "Source of GeneChip data" in the help tab.
2007.05.01ToolThe restriction of the maximum number of genes to draw co-expressed gene networks was relaxed from 20 to 300.
2007.03.22ToolDrawing co-expressed gene network for query genes was available in "Search Tab".
2007.01.26new dataHuman data were released. [more]
ver. 1.0 2007.01.17new formblast search form in Search Tab.
2007.01.08newly openedopened as β version.
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