Changelog
TomExpress v21.0.0 (Current)
Release Date: Dec-2021
Database changes:
-
All samples have been remapped against 2 long reads reference genomes :
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Use PANTHER (Protein ANalysis THrough Evolutionary Relationships) GO slim subset for gene annotation (3336 total terms)
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New data
- 8 new Projects (46 in total)
- 57 new Conditions (477 in total)
- 136 new Samples (1352 in total)
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Clear low quality samples
- 68 removed Samples (without losing conditions)
Features changes:
- Unconnected access to whole website with gene number restriction in order to test the platform functionalities
- Add interactive documentation
- Consolidation of private project management
- New search mode category : search by tissue
- New advanced search mode : search by project
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Redesign of database statistics
- One page with global statistics (Samples, Projects, Conditions, Cultivars ...)
- One page per genome reference (on which the RNAseq data are aligned) to sum up both gene-transcript mapping information and normalization quality of each sample
- All interactive and dynamic graphs by combining all strength of Highcharts.js and Stimulus.js
- New on-click access for conditions metadata in search dataTable
- Add legend sidebar to give information about conditions when statTools are active
- Add new layout about TomExpress, team members and citations
StatTool changes:
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In the expression chart:
- The tooltips now display information for each condition
- The logarithmic scale has been swapped from base 2 to base 10
- Interactive heatmap using InChLib
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The Coexpression tool has been split into 2 tools :
- Select one gene to search its most correlated counterparts under a given threshold
- Select multiple genes to compute the correlation network
- Use of D3js to display interactive networks
TomExpress v18.0.0
Release Date: Dec-2018
Database changes:
- Mapping on the new MicroTom tomato genome assembled using Long Read Sequencing
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New data
- 8 new Projects, 1 of which private (38 in total)
- 211 new Conditions, 38 of which private (420 in total)
- 452 new Samples (1201 in total)
- Several database fixes
Features changes:
- New page with database statistics
TomExpress v17.0.1
Release Date: Dec-2017
Features changes:
- fix
TomExpress v17.0.0
Release Date: May-2017
Features changes:
- Hudge design & performance rework
- One page UI
- workspace size increase
- User Account management with queries history
- Simple/Advanced mode Search
- Svg outputs for plots
- in Planta, new version coming soon
TomExpress v16.5.0
Release Date: July-2016
Database changes:
- 13 RNA-Seq projects (29 total)
- 98 unique global conditions (222 total)
- 300 sequence files (749 total)
TomExpress v16.0.0
Release Date: Jan-2016
Database changes:
- Added Gene name/symbol when available & Uniprot ID for each gene
- Lots of fixes and improvements in samples annotation
- Several databases fixes
Features changes:
- Overal theme & user interface rewrite
- Added Search by "Gene Name/Symbol"
- Added Gene Name/Symbol display to the result table
- Added UniProt card link for each gene
- Added filtering options in result entries
- Added the possibility to search for a fixed number of correlated genes in the Co-Expression visualization
- Added online documentation
- Removed Search by "MapMan description"
TomExpress v15.0.0 (First Release)
Release Date: Dec-2014
Database:
- 16 RNA-seq projects
- 124 unique global conditions
- 449 sequence files
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Search for gene expression using :
- gene Locus ID
- iTAG description
- MapMan description
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4 visualizations options:
- Expression in Planta
- Gene Expression
- Expression Heatmap
- Co Expression
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Export of :
- expression data
- plots
- pictures
Version naming convention : X.Y.Z
- X => Major Update : Year of release
- Y => Minor Features, major bugs fixe
- Z => Minor bugs fixe