OLDER NEWS RELEASES
11 May 2013. Major database update & new tool features
- 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
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
- 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
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.
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!
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 RNA-Seq experiment (genes and the corresponding expression values)
and run the search.
19 October 2012. New function to filter samples by patient or clinical
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.
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
- Keyword search function: identify conditions or gene names in
- 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
5 October 2011. RefGenes becomes OPEN ACCESS. Release of RefGenes
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
11 May 2011. New normalization, data updates and new organisms.
This is one of the most significant releases during the past 12
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
13 March 2007. New custom coloring feature. Port 8443 to be changed
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