| ATTED-II version |
Date |
Contents |
| ver.5.5 |
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 |
