OLDER NEWS RELEASES

11 May 2013. Major database update & new tool features


New content:
  • Human: Data from 4967 microarrays have been added, with a particular focus on experiments from toxicology and neurology. Users can now instantly explore a highly standardized and well annotated compendium of over 35000 Affymetrix Human133 Plus 2 arrays to identify significant conditions or genes.
  • Rat: Data from toxicogenomic experiments (8124 microarrays) with more than 130 chemicals, primarily medicinal compounds, tested at multiple concentrations and timepoints in vivo have been added.
  • Arabidopsis: Data from 527 microarrays have been added, covering a wide variety of experimental conditions. Arabidopsis now contains 8,600 samples with an impressive coverage of over 100 tissue types and over 2100 experimental conditions.
  • Rice: Data from 144 microarrays have been added, with experiments dealing mainly with biotic - and abiotic stress responses.
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New tool features:
  • Detailed view panel: A detailed view option has been added to the Anatomy, Neoplasms and Perturbations tools. For each category of tissue, cancer or perturbation, you can view how your gene of interest is expressed across all samples composing that category. The indication of experimental and patient characteristics allows a better interpretation of gene expression in that category.
  • Box plots: For the Anatomy and Neoplasms tools, box plots have been added to visualize expression of single genes across tissues or cancers. This provides a richer visualization than previously.
  • Sorting: In the Anatomy and Neoplasms tools, by default the categories are sorted from highest to lowest average expression level. This helps you quickly identify those tissues or cancers in which your gene of interest has a high expression level.


14 March 2013. Overall feature improvements

A new version of Genevestigator has been released with lots of improvements, including better graphics, easier handling of gene lists, and the introduction of boxplots for better single-gene analysis in the Anatomy and Neoplasms tools. Furthermore, in those two tools a detailed view is now available to view sample-level expression for each anatomical or neoplasm category. This helps understanding the cause of expression variation observed in a given tissue or cancer type.

  

12 February 2013. Workflows.

Genevestigator is not primarily a set of tools that are used individually. On the contrary, workflows through different tools offer unique ways of extracting biological information.
We have just released a new video tutorial showing you how to efficiently identify genes that are co-regulated with your gene of interest. This workflow represents a significant improvement over existing co-expression databases. Try it out now, you will be surprised!

See Workflow video for finding co-regulated genes.

  

10 December 2012. New: Signature tool

For most scientists, it is highly interesting to know if anybody else has found similar results. With the new Signature tool, you can easily screen the complete Genevestigator database to identify conditions in which a given expression signature occurs. Simply enter an expression signature from your own RT-qPCR, microarray or RNAseq experiment (genes and the corresponding expression values) and run the search.

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19 October 2012. New function to filter samples by patient or clinical parameters

A new feature has been added to filter an existing selection of samples by patient and clinical parameters. It is built as a negative filter, i.e. you can remove samples associated with a given parameter. For example, you can remove all samples that are from patients aged 60 or more, male and who are smokers.

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21 September 2012. Improved search by keyword or gene symbol

The search for individual genes has been significantly improved. You can now enter gene symbols (e.g. "KRT2") or keywords (e.g. "keratin"), and Genevestigator will propose a number of genes and probe sets.

In addition, a direct entry into Genevestigator was created by adding a search field on the website that launches Genevestigator and displays results for the queried gene.

Finally, the CONDITION SEARCH Cancers tool is now OPEN ACCESS for everyone, without login.

  

20 August 2012. Addition of clinical data information and tools

The CONDITION SEARCH Perturbations tool has been complemented with a detailed view showing gene expression in the samples from the chosen perturbation and clinical parameters for each sample. This allows you to check the composition of data within such a perturbation and remove individual samples if needed.

Several improvement in the analysis tool have been released, including a feature to create a new selection of samples based on results obtained from a given tool such as Perturbations. This allows you to create a group of samples that are relevant for your particular gene of interest and work in a more targeted way in other tools, such as the Co-Expression tool.

  

20 July 2012. Video tutorial for RefGenes tool.

A new video tutorial has just been released for the RefGenes tool. This and other videos are posted here.

  

2 May 2012. Release of new Co-Expression tool / online videos.

The goal of the Co-Expression tool is to allow you to find genes that are expressed in the same tissues, at the same time, or respond to the same set of conditions as your target gene. It runs on a powerful engine that processes results on-the-fly based on any dataset that you compose from the Genevestigator database. You can choose to correlate against selected meta-profiles such as anatomy, neoplasms, perturbations or development, or you can create a custom selection of samples based on annotations (e.g. all arrays related to a disease) or on individual experiments. The Co-Expression tool identifies the genes best correlated to your target and shows you the mutual correlation structure between these genes.

The Genevestigator Team has created a few short video tutorials to help you getting started or to learn how to use individual tools more in detail. The videos are posted here.

  

28 February 2012. Release of Genevestigator 4.

Genevestigator 4 has recently been released. Here are the main novelties and improvements:

  • Workflow: same as in previous versions, so you can immediately start using it
  • Entry page with overview of all tools
  • Gene search function: simply enter a gene ID and see results instantly
  • Keyword search function: identify conditions or gene names in the results
  • Selection of data by biological context (disease, drug, tissue, etc.) made better
  • Identification of conditions that are relevant for a target gene using new filters
  • Improved mappings of probesets to gene symbols or gene models
  • New "Perturbations" tool includes genetic modifications, diseases and external perturbations. It replaces the previous "Conditions" and "Genotypes" tools and is now part of the ADVANCED Edition.

  

5 October 2011. RefGenes becomes OPEN ACCESS. Release of RefGenes website.

After being available for some time only in the BASIC and ADVANCED versions, RefGenes has now become fully open access. Additionally, we now offer better support for our RefGenes users with an online step-by-step manual, an example analysis and live tutorials that are available on the RefGenes website.

  

11 May 2011. New normalization, data updates and new organisms.

This is one of the most significant releases during the past 12 months:
a) the complete database has been re-normalized with RMA and an inter-experiment correction. This change in data processing significantly improves the results from weakly expressed genes, especially in tools displaying relative values such as Conditions and Genotypes (experimental versus control samples). More information about the new normalization scheme can be found in the User Manual .
b) more than 7000 newly curated microarray data samples have been added for several mammalian and plant species, including human (5164), Arabidopsis (567), rice (747), maize (355), barley (101), wheat (12), soybean (116) and Drosophila (30).
c) Tomato and tobacco, two solanaceous species, have been added to Genevestigator. The tomato dataset contains 334 samples from 18 experiments and covers a variety of experimental conditions, whereas the tobacco dataset is a baseline experiment on tobacco development, with different tissue types and growth stages (100 arrays).

  

25 March 2011. Publication of RefGenes.

Although the RefGenes tool has been available for some time already, we have now published our analysis about reference genes in BMC Genomics. This paper revokes the idea of "general purpose" reference genes and calls for the use of context specific reference genes. A tool called RefGenes is available in Genevestigator to look for genes that are stable under chosen conditions, such as tissue types.
[Abstract]

  

8 December 2010. Rice mapping error fixed; release of new rice data.

If you have recently worked with rice data in Genevestigator and have used MSU Locus IDs to select probesets you might have been affected by a problem in the gene alias mapping. There was an error in the mapping of MSU Locus IDs to Affymetrix probesets. The problem is now fixed. If you have important results for rice data based on using MSU Locus IDs we suggest that you check them in the current version. All other types of gene aliases were not affected. We sincerely apologize for this problem. If you have any further questions please contact us at support@genevestigator.com.
A new set of 17 rice experiments including 158 arrays has been released. 40 new response comparisons have thereby been added (12 in "Stimulus" and 28 in "Mutation").

  

16 November 2010. New data from more than 5500 tumor samples.

A dataset of more than 5500 human cancer microarrays was manually curated and released, covering a variety of different tumor types, with special focus on lung cancer, lymphomas and leukemia.

  

14 September 2010. Release of wheat as a new organism.

Wheat has been added as a new plant species in Genevestigator. This dataset of 860 samples nicely complements the existing set of crop species and adds several specific experimental conditions that are not found in the other crop species.

  

30 August 2010. Release of Drosophila expression data.

Drosophila was added as a new model organism in Genevestigator. In total, data from more than 2300 samples is available, covering a wide variety of tissues, developmental stages, perturbations and genetic backgrounds.

  

12 August 2010. Major release of new data.

We have released major data and software updates for all existing organisms (16,460 arrays in total). Drosophila is soon to be released as a new organism in Genevestigator with 2300 arrays. We are also happy to announce the redesign of our website, with more detailed content describing Genevestigator.

  

27 July 2010. Upgraded Genevestigator link feature and faster Genevestigator analyses through better caching

Genevestigator links directly link into Genevestigator results showing expression profiles in one click. Links now accept several additional arguments. Please contact us if you are interested in linking to Genevestigator meta-profiles. Additionally, we have improved the chaching mechanism which temporarily stores information retrieved from the server on the client. This increases the speed of analyses in many cases.

  

5 July 2010. Tooltip improvements and better server reliabilty.

Several improvements have been made to the tooltips which provide additional information about various elements. In particular, the description of comparisons in the stimulus and mutation meta-profile tools was extended. Additionally, we have installed a new failover system for our webserver for further increasing the reliability of the Genevestigator website and tool.

  

3 June 2010. New neoplasm tool and a large set of cancer data.

We have added a new discovery module for cancer research, including a large set of tumor data (7,914 microarrays). These samples cover a broad variety of tumor types and subtypes. A tumor classification ontology was developed that groups neoplasms by tissue of origin and subtype. This allows to analyze neoplasms alongside healthy tissues, which is particularly useful in biomarker identification and validation. We also released a new tool called "Neoplasm" that is similar to the existing "Anatomy" tool, but represents expression across hundreds of tumor types. In parallel, we expanded the Anatomy tool in the Biomarker Search module to include neoplasm categories. This allows you to look for genes that are specifically expressed in a chosen set of neoplasms.

  

16 February 2010. New Genevestigator Curation and Input Pipeline

We have finished our new input pipeline which is used for all steps of our curation process. This system supports our curation team much better and will lead to a significant increase in both rate of curation of new experiments and quality. For ENTERPRISE customers the input pipeline is now available to insert proprietary data into the local installation of the Genevestigator system.

  

9 December 2009. Annotation ontologies reworked.

In a large effort, we have overhauled the ontology system used for annotating experiments in categories such as anatomical part, external stimulus etc.. On the software side, a new ontology subsystem was introduced and stimulus and mutation ontologies are structured as trees. On the content side all ontologies were revised, updated and restructured where appropriate.

  

25 June 2009. Genevestigator Export API available for ENTERPRISE customers

The Genevestigator Export API provides a possibility to integrate Genevestigator more tightly into a customers bioinformatics infrastructure. This Java API allows access to all expression data, annotation and experiment information in Genevestigator in an efficient and easy way.

  

3 June 2009. Release of Genevestigator ENTERPRISE

Genevestigator ENTERPRISE consists of an in-house installation of the Genevestigator Engine, including the complete data content of high quality curated microarray data.

  

27 May 2009. Improvements to the Pathway Projector

The pathway tool which contains pathway information for Arabidopsis and mouse has been improved in several respects. Reactions are now labeled with EC numbers and tooltips on proteins link to the corresponding entry in the Expasy protemics server. We have also optimized navigation through the pathways.

  

18 May 2009. Release of yeast and E. coli as new organisms, and updates of the mouse and barley databases. User interface and documentation improved.

Genevestigator has been expanded to microorganisms, with 1,794 yeast arrays and 627 E. coli arrays. The mouse database has been complemented with 1,126 full-genome arrays, and also 329 barley arrays have been added. The user interface has been improved to facilitate the selection of genes and probe sets. For users of ADVANCED, the export of numeric data from figures is now available.

  

15 January 2009. Updates of Arabidopsis and Human databases. Release of soybean as a new organism.

Good news for Arabidopsis researchers: more than 1000 new ATH1 arrays have been added, covering many new stimuli and a large number of new mutant lines. Also good news for the biomedical field: 1770 new human arrays were added, including many new diseases and treatments.

  

11 December 2008. RefGenes is a new tool to find suitable reference genes for qRT-PCR experiments

A new tool has been added to the Biomarker Search toolset. Rather than finding genes that have a particular pattern of expression, RefGenes looks for genes that have minimal variance across a chosen set of conditions.

  

10 September 2008. Rice is made available as a new organism. Updates to the human dataset are released.

Genevestigator now includes rice as a new plant model organism. The human dataset was also extended with exciting new experiments.

  

5 February 2008. February 5. The software has been updated with several improvements in usability and functionality.

  

3 November 2007. Genevestigator releases human expression data

Genevestigator releases a first set of more than 2400 human full-genome Affymetrix arrays.

  

23 August 2007. Genevestigator releases major data updates

Genevestigator releases barley as a new organism and several major data updates.

 

15 May 2007. Genevestigator V3 is released with major data updates

A stable version of Genevestigator V3 is released to the public. Major data updates from rat and mouse were performed. An update for Arabidopsis data will be released in the coming 2-3 months.

 

24 April 2007. Custom legend formatting, port changed to 443, and other updates

Several updates have been performed to improve the use of Genevestigator. First, a new feature allows users to work with other gene annotations than only with probesets. Second, the access port was changed to 443. And several further updates have been implemented.

 

13 March 2007. New custom coloring feature. Port 8443 to be changed to 443.

A new coloring tool in the gene selection panel allows to choose which colors one wants to give to each probe set. A color palette is now placed above the selection lists. (...)

We have decided to change our system to an access via 443, which requires several larger technical changes. This will be done within the next couple of weeks.

 

20 February 2007. Genevestigator V3 beta is released to the public.

As of 20 February 2007, a new Genevestigator version (V3 beta) is released to the public. V3 beta exhibits several novelties such as a new website, the use of Java technology, novel tools, and also more client-side analysis capability.

 

8 February 2007. Pre-release information

Dear Genevestigator user, This is a message sent to all Genevestigator users to inform you that a new version of Genevestigator (V3 beta) will be released in approximately two weeks.