Curated plant transcriptomic data

GENEVESTIGATOR® Plants


IMPORTANT NOTE TO ALL PLANT USERS

In July 2021, Nebion AG, the company developing GENEVESTIGATOR®, was acquired by Immunai Inc., a biotech company focusing on developing immunomodulatory drugs using a combination of single-cell multiomics technologies with machine learning. As a result, the future development of GENEVESTIGATOR® will focus on biopharma data, while the curation of the plant data is being phased out. To continue supporting the plant community, however, Immunai is maintaining the current plant version of GENEVESTIGATOR® on a separate server for 2023. Please take note of the following:

  • Users who have an active GENEVESTIGATOR® license for plant data will continue to have access to all tools and plant data through the new app until the end of their current licensing period.
  • NEBION will not register any new plant users after the 31st of January 2023.
  • For any questions please contact sales@nebion.com



Overview of curated plant data

At NEBION, we have curated and integrate data from different plant species. In 2020, we have added sunflower and watermelon while we also increased the content for other crop species and for Arabidopsis. The below figure shows the number of samples (microarray and RNA-Seq datasets) per species.

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Typical GENEVESTIGATOR® use cases


Characterize the regulation of a gene of interest by visualising its

  • expression across tissues and cell types
  • expression across developmental stages
  • response to biotic and abiotic stresses
  • comparative expression in different genotypes


Find genes specifically expressed in

  • tissues or cell types of interest
  • stages of development
  • response to biotic and abiotic tresses
  • comparisons of genotypes


Analyse an experiment of interest

  • expression of a gene of interest across samples from a chose experiment
  • genes differentially expressed in conditions from our curated database
  • genes differentially expressed in conditions from your own experiment
  • quality control: see how samples group by their expression profiles
  • check which factors cause the main difference between samples


Compare your results with curated public data

  • find experimental conditions causing a similar result


Compare results across species

  • check the regulation of a gene and its orthologs from up to 10 other plant species


Find pathways associated with a gene list

  • overrepresentation analysis against Reactome pathways and GO terms
  • Venn diagram of up to four lists / pathways


Find genes having most similar expression across

  • tissues and cell types
  • stages of development
  • experimental conditions
  • samples


Compare the expression of two genes of interest across

  • tissues and cell types
  • stages of development
  • experimental conditions
  • samples


Find and compare reference genes for RT-qPCR

  • most stable in a chosen tissue
  • compare with frequently used, unspecific reference genes


Find functional gene orthologs from other species

  • based on protein and phylogenic information (based on OMA)
  • based on similar tissue expression (based on GENEVESTIGATOR®)


Example analyses & screenshots


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Differential expression analysis of the effect of an M. oryzae isolate in a rice experiment (GSE95394). Volcano plot showing significantly up- and downregulated genes, with a shortlist of highly significant genes marked and selected for comparing with other experimental conditions (see figure below).


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Comparing results obtained from the above differential expression analysis against a compendium of other rice data. A number of biotic and genetic perturbations cause a similar response. By extension, the signature can be translated to another species using our orthologs feature or tool, and the signature matched to experimental conditions found in these other compendia. This allows a better understanding of the list of genes obtained in our original analysis.


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Venn diagram of genes regulated in response to cold, salt and osmotic stress from experiment AT-00814, as well as enrichment analysis against Reactome pathways.


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Identification of genes specifically expressed in wheat endosperm, as calculated from 55 anatomical categories aggregated from 2332 samples.


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Clustering of endosperm-specific genes identified in the previous example. Two main clusters appear, one including genes that are also expressed in the aleuron layer.


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2-gene plot comparing the expression of LTP3 and LTP4 across 1727 Arabidopsis RNA-Seq samples.


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Identification of candidate reference genes having a stable expression in adult Arabidopsis leaves, as measured from 1006 samples. Known reference genes as examples are shown in the upper part of the plot by comparison, showing that alternative genes exist having a higher expression stability in adult leaves.