Warnings: this version is still in Beta


TomExpress v21.0.0 (Current)

Release Date: Dec-2021

Database changes:

  • dna-icon All samples have been remapped against 2 long reads reference genomes :
    • MicroTom (SLMIC V1.0 Assembly, SLMIC1.1 annotation)
    • Heinz (SL4.0 Assembly, ITAG4.1 annotation)

  • panther-icon Use PANTHER (Protein ANalysis THrough Evolutionary Relationships) GO slim subset for gene annotation (3336 total terms)

  • New data
    • 8 new Projects (46 in total)
    • 57 new Conditions (477 in total)
    • 136 new Samples (1352 in total)

  • 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
  • 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:

  • 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
  • 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
    • Structural annotation using EuGene-EP (Includes correspondences with ITAG genes)
    • Functional annotation using BLAST2GO
  • 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"


  • 16 RNA-seq projects
  • 124 unique global conditions
  • 449 sequence files
  • Search for gene expression using :
    • gene Locus ID
    • iTAG description
    • MapMan description
  • 4 visualizations options:
    • Expression in Planta
    • Gene Expression
    • Expression Heatmap
    • Co Expression
  • 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