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 2022 plant version of GENEVESTIGATOR^® on a separate server during 2023.

Please take note of the following:

• IT IS NO LONGER POSSIBLE TO REGISTER NEW USERS. The platform is made available to existing users to give them time to finish their running projects. At some point, it will be shut down.
• 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.
• To access the plant data with your existing user account, please uninstall the former version (which no longer has plant data) and install the specific plant version that is available here.
• User support is no longer provided for the plant server, it is provided “as is”.

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.

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

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).

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.

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.

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

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.

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

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.