NEWS

Translational analysis of gene lists across species

(6 June 2017)
To facilitate the work transition between organisms it is now possible to translate a gene selection from one species to another using a mapping by OMA. To create a new selection with orthologs from another species, simply right click on the gene selection of interest, go on "Create Orthologs" and select the desired organism. As a result, a new gene selection containing the corresponding gene orthologs is made.




Creation and export of gene signatures

(6 June 2017)
From most of the GENEVESTIGATOR tools it is now possible to export a gene "signature". A "signature" consists of a list of genes and their corresponding expression values for a selected category (eg an anatomical part, a cancer type, a perturbation). To create such a "signature", select a category from a condition of interest (Anatomy, Cell lines, Cancers, or Perturbations), and click in the toolbar on the Signature: "Copy" "New" or "Add" buttons. The "signature" will appear in the Gene Selection panel with a "S" tag. A "signature" can be opened directly in the Signature tool and compared against results from other studies.




Release of Gene Set Enrichment tool

(1 December 2016)
To complement the existing GENEVESTIGATOR tools for the interpretation of gene lists, a new tool called Gene Set Enrichment has been released. It allows you to upload a list of genes and to check which pathways or biological processes are enriched in this list. In its initial version, the enrichment analysis is performed against Gene Ontology categories or Reactome pathways. Other collections of gene sets will be added in the future. Enterprise customers can also include proprietary gene set collections as references.
A short video is available explaining this tool:





New classification of tissues and cell types

(13 June 2016)
All organs, tissues and cell types have been restructured using the recently released CALOHA ontology developed by the CALIPHO Group at the Swiss Institute of Bioinformatics in Geneva. CALOHA represents a major improvement over existing anatomical ontologies, since many tissues and cell types were rigorously curated and structured. While originally developed for human, we adapted it also to mouse and rat.
See also the corresponding Technical Note about CALOHA classification.


New video tutorial for the Perturbations tool

(5 June 2016)
The Perturbations tool (from CONDITION SEARCH toolset) allows you to rapidly and effectively screen for experimental conditions that regulate your genes of interest. A new video tutorial explains how to use this tool:




Cross-platform capability for gene lists

(8 March 2016)
The visualization of gene lists across multiple platforms has been significantly facilitated. Instead of having to choose a representative probe or gene identifier per platform, and switching between them, GENEVESTIGATOR now allows entering a list of genes only once for all platforms. The corresponding probes or gene identifiers are automatically selected, making it very easy to check the expression of this list across different compendia of curated studies.


Completely redesigned Data Selection dialogs

(18 November 2015)
With the implementation of a brand new classification of experiments by therapeutic area, study type and experimental design, it has now become much easier to search and select experiments of interest. With the new dialogs, you can select any set of experiments in a very refined way. For example, you can easily find diabetes-related experiments done in vivo on a particular mouse model with a dietary study design.




Release of RNA-seq datasets for plants

(28 August 2015)
We are pleased to announce that a first batch of curated Arabidopsis and Maize RNA-seq data is available in GENEVESTIGATOR. All your favorite tools and features can run the same way, irrespective of whether you choose RNA-seq or microarray data.
  • 402 RNA-seq datasets from Arabidopsis samples
  • 217 RNA-seq datasets from Maize samples

Release of Medicago truncatula as a new organism

(30 June 2015)
Medicago trunculata was added as new organism with 653 curated samples covering:
  • 246 Perturbations (mainly for biotic response, drought and salt stresses, various genetic backgrounds)
  • 35 Anatomical parts (including roots, nodules, seeds, leaves, flowers, stem)
  • 8 Developmental stages
All the samples are from the Affymetrix Medicago Genome Array platform. !


Release of Orthologs Search tool

(27 March 2015)
Thanks to the Orthologs Search tool you can quickly and easily find gene orthologs in other organisms, starting with a gene of interest from one species. The uniqueness of this tool lies in the fact that it uses both sequence and expression data to predict the most likely functional orthologs!


Release of Genevisible

(2 December 2014)
We announce the release of Genevisible, a new free resource for biologists. You can simply enter a gene of interest and Genevisible will show you the top five tissues, cell lines, cancers or perturbations in which it has highest expression or response. Genevisible is powered by GENEVESTIGATOR and runs on desktop computers and mobile devices. Whether you sit at your office, are traveling or listening to a conference speaker, Genevisible allows you to quickly verify the most relevant conditions for a gene of interest.


Cell Lines ontology is extended

(23 October 2014)
The Cell Lines tool has been revisited and now allows users to search the results by trivial names of cell lines (e.g. HeLa). Over 1400 different cell lines can be screened to find genes specifically expressed in a chosen cell line, or to find cell lines in which a target gene is strongly expressed (or non-expressed).


New Cell Lines tools

(23 July 2014)
Two new tools with an identical layout as the Anatomy and Cancers tool are available to explore gene expression across cell lines. With little effort, you can easily identify those cell lines in which your genes of interest are strongly expressed, or identify genes specifically expressed in selected cell lines. Additionally, you can blend into the plot expression data across normal tissues for comparison. Different types of cell lines are available:
  • Non-neoplastic cell lines
  • Neoplastic cell lines


New video tutorial for the Signature tool

(12 June 2014)
The Signature tool allows you to compare your own gene expression results with thousands of curated experiments. A new video tutorial explains how to use this tool:




Release of Diff-Expression tool

(26 May 2014)
The new Diff-Expression tool is a very easy to use, but powerful tool to run differential expression analysis between two groups of samples. The user only needs to choose an experiment from GENEVESTIGATOR, define which samples belong to each group, and run the analysis. As algorithm, LIMMA with multiple testing correction (Benjamini-Hochberg) is performed. Lists of differentially expressed genes can directly be stored into a sample selection and interpreted using other GENEVESTIGATOR tools. See also the video tutorial:




Complete reorganization of oncology data according to ICD-10 and ICD-O-3

(23 May 2014)
The previous classification of cancer data according to site of origin and histology resulted in extremely refined categories of cancer types often with few samples and was therefore hampering analyses in GENEVESTIGATOR. To be compliant with international standards and provide a better summary of expression across cancers, the complete set of cancer data was mapped and re-annotated according to ICD-10 and ICD-O-3 resulting in less but better populated categories (in the Cancers tool). Moreover, to facilitate the comparison, primary tumors, metastasis and xenografts are now displayed alongside each other and normal tissues can easily be added as reference.


Release of pig data

(12 May 2014)
Pig has been set up as a new organism in GENEVESTIGATOR. 26 experiments containing 741 samples were manually curated and integrated into the database for analysis and visualization with the GENEVESTIGATOR tools. All data is from the Affymetrix Porcine Genome array platform. The released experiments come primarily from the fields of cardiovascular, diet/obesity, infection (Salmonella), and cover a variety of tissues and other experimental conditions. The pig data is available from the Pharma/Biomedical page.


Partnership with Qlucore

(14 March 2014)
With GENEVESTIGATOR you can easily identify experiments or conditions that are relevant for your genes of interest. Each of these conditions is described in detail and the source of the original data is indicated (e.g. link to Gene Expression Omnibus), from where the raw data can be downloaded. To help you further explore these experiments in detail, we recommend you to use Qlucore Omics Explorer. It's a visual, intuitive and extremely fast bioinformatics software to explore omics datasets. No in-depth statistical expertise is required to find differentially expressed genes, compare groups of samples and interpret your results using GSEA or GO enrichment analysis. Vice-versa, lists of genes obtained in Qlucore can easily be imported into GENEVESTIGATOR to visualize their expression across a wide variety of biological contexts. To learn more about Qlucore Omics Explorer or request a trial, please visit the Qlucore website.


New human data on IBD, atherosclerosis and diabetes have been released

(4 March 2014)
Six studies comprising in total 291 samples have been released to complement the current compendia for Crohn's disease, atherosclerosis and diabetes.


Arabidopsis reaches 10,000 samples!

(1 March 2014)
A few Arabidopsis ATH1 array experiments have just been released, bringing the total number of samples to 10,000! This compendium includes 1,536 experimental conditions, 995 genotypes, and 105 different tissue types.


Application Notes

(23 January 2014)
Summary documents called Application Notes are now available online. They provide overviews of curated expression data for selected disease areas. See DATABASE section for more details.


See older news releases