last update; Oct. 16. 2024
| ATTED-II version | Date | Contents | |
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| ver 12.0 | 2024.09.27 | New Functionality | To improve understanding of individual coexpression relationships, we’ve added a new page called "PC View" that displays the Principal Components (PCs) of gene expression data, which can be interpreted as meta-samples. This page shows, for each PC, 10 studies (SRPs) with six representative samples (the three with the highest and three with the lowest loading values). It highlights how sample annotations typically distinguish between the highest and lowest values. Additionally, the top 100 up- and down-regulated genes for each PC are displayed. |
| NetworkDrawer | Paralogous genes based on KEGG Orthology can be highlighted by color. This function facilitates coexpression relationships among multiple gene families. | ||
| Enhanced Integration | Hyperlinks to Plant GARDEN and its GBrowse are now available from the Arabidopsis gene pages. Plant GARDEN includes genome information for non-model species, complementing ATTED-II’s focus on model species. | ||
| Updated Data | NA-seq coexpression data have been updated for all species (Xxx-r). New coexpression data for wheat and barley have been added. Additionally, the Ath-r data set has been decomposed into Ath-e, which specifically focuses on Arabidopsis ecotype comparisons. The new Ath-r data set no longer includes experiments comparing ecotypes. | ||
| 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.
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| 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.
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| 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.
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| 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. |
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| 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. |
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| 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.
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| 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
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| 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.
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| 2008.04.07 | data update | Coexpression data was updated to version
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| 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.
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| 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. |
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| 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 |
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