Aniseed release notes
- ANISEED V1.0 - Introduction (02/2004)
- ANISEED V2.0 - System enhancements (05/2005)
- ANISEED V3.0 - System enhancements (04/2007)
Download or view Aniseed V3.0 release notes
Gene expression data:
Thanks to a collaborative agreement with Yutaka Satou, the
system now includes the annotated ISH data from Transcription factor/signalling
molecules carried out in Yutaka Satou and Nori Satoh's lab. Pictures
are not yet available, but will be in the coming months. For now if
you want to see the pictures from this screen, click on the link in
the result page that will bring you to the home page of the Ghost database
where you will find the original images. When refering to any gene from
this screen, please refer to the original publication in Development,
NOT to Aniseed. The same applies when refering to the Halocynthia data
found on Aniseed: refer to the initial paper, not to Aniseed. We have
also started in Collaboration with Yutaka to reannotate more precisely
the expression profiles, making use of the more detailed Aniseed anatomical
dictionaries. This reannotation will be put online progressively.
Most gene annotation, and in particular Gene Ontology terms
and names was derived from orthology relationships, which only exist
for about 50% of gene models. We have added GO terms (localisation and
molecular function) and names (highly similar to... similar to...) on
the basis of the best blast hit.
During the past months, we have corrected some earlier problems
in the Ciona anatomical dictionaries, and horizontally linked them,
by introducing lineage information. You can now trace the lineage of
a structure and use this to query for genes expressed in a precise lineage
across developmental stages. We also defined 17 keywords defining the
final fates of given blastomeres or structures from Ciona intestinalis.
Thanks to the 3D data we obtained and quantified using the 3D embryo
Handler software and 3D embryo reconstructions, we provide some informations
relative to neighborhood relationships, shape of blastomeres, etc....
This is currently only available for two stages of Ciona embryos: 16-
and 32-cell, but we are now building up a collection of reconstructed
embryos and their biometrical analysis will gradually be put online.
Some embryological information (inductions, competence of cells) is
available for the late 32-cell stage. This is only very preliminary
and subject to changes wihout notice. Use it with precautions. It is
just there to give a flavour of what we would like to develop in the
Upon selection of a dictionary, it is possible to ask to display
the structures that will eventually adopt one or several fates of interest.
They will be marked by a green dot on the results page. At the top of
the results page, all buttons are now active. Upon selection of a structure:
The "In situ data" button will give access to all genes expressed in
this structure, The "lineage" button will show you all progenitors and
progeny (the interface will improve soon), The "biometry" button only
works with cells, and gives access to the volume, surface, shape, and
neighbours of the selected cell with a quantitation of the surface of
contacts (only for 16- and 32-cell stages so far). The "fates" button
gives the fates of the selected structure (works only for cells). The
"induction" button indicates whether the cell is subject to an induction
process at this stage. This is still work in progress, very few data
are entered but please give us feed back on what you like or dislike
Select one or several stages, one or several fates, which
boolean syntax you want to use, and the results page will indicate all
relevant cells and structures. The format of the results page is OK
but not yet great but it will improve with time (and with the help of
Select your favorite cells within the anatomical dictionary
(beware this only works with cells, not higher order structures), a
maximal( or minimal) distance for cells of interest, a minimal or maximal
surface of contact and the system will retrieve a list of relevant cells.
Clicking on a cell opens a new page showing its position in the anatomical
Select a species and a stage (works only on 16 cell and late
32 cell in Ciona intestinalis), and some properties of interest for
your cell (entropy (meaning compactness), sphericity, elongation, flatness,
large or small volume, etc...). The results page lists all cells satisfying
the criteria, and with all their shape descriptor values. Click on a
cell and you will see its position in the anatomical tree.
select species, a stage and a structure, tick the boxes according
to whether you want to see the progenitors, progeny or both of the selected
cells. The system will return a list of cells with an indication of
the stage they are present. A tree-based representation will soon replace
the current interface.
DDD: (alias Digital Differential Display):
This interface allows to find genes that have differential
EST representation between sequenced cDNA libraries. It uses the idea
(put forward in Ciona by Yutaka Satou and N. Satoh) that as the libraries
were not normalised , the number of ESTs in a library reflects the abundance
of the transcript in the starting population. The DDD interface allows
you to find genes expressed at statistically higher levels between sets
of libraries. This is a very powerful tool, with ONE MAJOR LIMITATION:
each request mobilises a large proportion of the resources of our current
server. So please, for the sake of others, do not play with it, only
place the requests that make sense for your research. If the use of
this interface significantly reduces the speed of the system, we will
remove the interface until we have migrated to a new more powerful server
the last tool is the tiny "refine" button that appears at
the bottom of most results page (except the ISH results pages). By selecting
another interface and pressing refine, you tell the system you want
to use the results on your page as the search space of the next query.
In short, it allows you to place sequential queries such as find the
zinc finger genes (Interpro search) that are annotated transcription
factors (Refine with Gene Ontology search), etc... Play with it and
you will see how powerful this small addition makes the system.
From Oracle to PostgreSQL:
Aniseed version 1.0 was using a commercial SQL database system,
Oracle, as is the released version 2.0. However, in the next few weeks,
version 2.0 will migrate to a different, non-commercial SQL engine:
PostgreSQL. Advantage of this is that it will be possible to install
mirror sites of Aniseed away from Marseille, making the system less
sensitive to server troubles. It will also make the system truely generic
and easier to use for other model systems.
Migration to a new server:
While postgreSQL opens the way to mirror sites, we will be
migrating within a month to a more powerful independent server within
an IBM cluster. This should allow faster processing of more complex
queries. No change of URL address is anticipated.
At present we estimate that the development of new interfaces,
besides the ones mentioned above, will slow down and that the focus
will be placed on:
Getting as many data into the system as possible.
This includes more ISH (currently a bit over 10000 for Ciona and Halocynthia
combined) and promoter expression data (currently less than 10.....),
more anatomical data (for Halocynthia for instance), more embryological
data (inductions, competence, etc...) and more 3D data and reconstructed
embryos. We would like the whole community to contribute to this aim
and will therefore release the loader software for remote submission
of ISH and Cis-regulatory element data, probably during the Santa Barbara
meeting. We will make all efforts that submitted data are be tracable,
and properly attributed to their contributing author. We are currently
reconstructing in 3D a more important set of embryos, and expect to
release the 3D Embryo Handler software at the beginning of autumn, with
the associated reconstructed embryos. Again, this should allow the community
to contribute additional models to the other labs.
Making all data downlodable as flat or XML files.
We have started to put some flat files in the download section, but
this is still incomplete. We plan to release the rest of the data by
summer, so that people can donwload them and use them for large or small
scale bioinformatics analysis.
Community decisions over the future of the system.
The system is now getting rather large and it may be time for it to
become steered by the community rather than by my lab. May be it would
be a good idea to include a discussion of its future during the Monday
July 11 evening round table in Santa Barbara? For instance, should we
decide to nominate a steering committee to oversee future developments?
The Aniseed (Ascidian Network of In Situ Expression and Embryological
Data) system is a community resource for ascidian developmental studies.
It allows one to mine and download available embryological, anatomical,
genomic and gene expression data.
It is an Oracle database organised in six main parts:
For each of the 22 stages we defined, the anatomical field describes,
using a controlled hierarchical dictionary, the different biological
structures and blastomeres present in each ascidian species. This ontology
is represented as a directed graph, which allows one to organise terms
as the nodes of a tree and to link them according to the characteristics
they share. We thus described each organ and structure in a hierarchical
way where terms at the top of the hierarchy represent a global structure
(eg. Mesoderm) while child terms correspond to more precise parts (eg.
Secondary notochord lineage). This description has a single-cell resolution
level up to the beginning of gastrulation, a stage up to which the lineage
was completely worked out. Following this stage, the ontology follows
the germ layers and was designed to be as compatible as possible with
The system hosts all available ESTs, cDNAs, and gene models for the
two species Ciona intestinalis (mainly the very big Kyoto set and the
small Marseille set) and Halocynthia roretzi (the set contributed by
the Halocynthia consortium via Kaz Makabe and Takeshi Kawashima). 400.000
Ciona EST and cDNA clones are clustered according to the predicted gene
model they correspond to. The remaining 80.000 clones could not be matched
either because of the draft quality of the assembly (5% of genes are
estimated to be missing) or of the gene predictions (these predictions
do not at present take into account the EST data and frequently miss
the 5' and 3' ends of genes). The proportion of clones correctly clustered
will increase with the accuracy of the assembled annotated genome.
Functional annotation of proteins:
Functional annotation of the predicted proteins was achieved by three
methods. We first run a programme, Inparanoid (Remm et al., 2001), which
identifies orthologues by comparing in a pairwise fashion proteomes
from completely sequenced organisms. Clear fly, human or mouse orthologues
for approximately 50% of predicted Ciona genes (8119/15592) are detected
this way. The relatively small % of detected orthologues is again probably
due to the incompleteness of the JGI gene models. The orthologues are
then used to name, but also to attribute a Gene Ontology classification
to the Ciona gene. In parallel, we run Interproscan (Zdobnov et al.,
2001) for each Ciona protein and deduced the presence of functional
motifs. These were in turn used to attribute GO terms to proteins without
clear orthologues. Finally, a BlastP search against trembl and swissprot
with a cut off of 1e-06, will soon be used to complement the GO information
for proteins without clear orthologues or motifs, but with similarity
to proteins previously assigned a function. The identification
of orthologues also opens the way to a comparison of expression profiles
Additional tables were included in the design of the database to more
precisely characterise the function of proteins. These tables include
for example protein interaction data, and DNA binding specificity of
transcription factors. At present, however, they remain empty.
Two types of expression data are currently supported.
The ESTs generated in the Ciona genome projects originate from a collection
of non-normalised cDNA libraries from different stages and adult tissues.
Clustering of the ESTs on the basis of their correspondance to a given
gene model allows one to calculate the abundance of the clones corresponding
to this gene in the different sequenced libraries. This EST count proves
to be a reliable measure of the level of expression of a gene at a given
time or in a given tissue (Satou et al., 2003).
In addition, Aniseed currently hosts In situ hybridisation data for
around 200 Ciona intestinalis genes with a restricted expression pattern,
mainly coming from the in situ screen carried out in the Lemaire lab
(Marseille, France). In situ hybridisation patterns are illustrated
by standardised pictures (orientation, format) and described using the
controlled vocabulary anatomical dictionary for the relevant stage.
In addition to In situ data, Aniseed supports the description of promoter
analyses and immunohistochemistry.
A unique feature of Aniseed is that it supports both wild type expression
patterns, as well as expression patterns in manipulated embryos. Manipulations
supported include both embryological (blastomere explantation, or ablation)
and genetic (over-expression, Morpholino knock-down, treatment with
pharmacological inhibitors or recombinant signalling proteins) treatment.
This type of information is of crucial importance for the reconstruction of genetic cascades.
How to query Aniseed:
This part describes the source of the data either published or unpublished.
The web interface allows one to search Aniseed by
. In situ data
. Gene ontology
. InterPro domains
In situ data:
Following the selection of a species and a developmental stage, this
page allows one to search for genes that are expressed in individual
or multiple structures from the anatomical dictionary. Conversely, the
expression data for a given gene model can be obtained. In addition
to wild type embryos, it is possible to search for expression patterns
in deregulated contexts. It is also possible to search for pictures
showing co-expression of two genes.
The result page displays the species and stage, thumbnails of the relevant
in situ pictures, a brief description of the staining and the identity
of the stained molecule according to the controlled dictionary, corresponding
gene model(s) and the labelled territories. All these fields can be
clicked for further information. Upon clicking on "more" a
second page appears showing a larger picture, a recap of all expression
domains at this stage, the name of the annotator with direct e-mail
link, the experimental conditions, and references. Included as well
is the possibility to search for other genes expressed in the same territories,
to perform expression clustering analysis and to search for expression
data for the same gene, but in deregulated contexts (i.e. overexpression,
morpholino injections, mutant background or ablation of embryo parts,
explants, etc. ).
This page displays the anatomical dictionary at a given stage in a given
species. The displayed anatomical dictionary can be used as an alternative
interface to look for genes expressed in selected structures. The "get
lineage", "get position" and "get fates" buttons
are currently being implemented.
This page allows one to search for molecules by species, clone name,
clone sequence name (Genbank accession number), and also gene name (biological
name). The results window gives access to all genes matching the query.
Selection of one gene leads to a detailed description of its features:
link to the JGI genome project page, display of Interpro domains, link
to EST counts and in situ data, prediction of orthologues in other complete
genomes (Inparanoid predictions) or of paralogues in Ciona, and best
BlastP hits in the Swissprot database. These pieces of information form
the basis for the Gene Ontology classifications of the genes.
This function allows one to search for Ciona molecules showing similarity
to a sequences of interest.
Gene Ontology/InterPro search pages:
Allows one to search for genes according to their associated Gene Ontology
or InterPro terms (search for proteins involved in a given process,
molecular function, subcellular localisation or with given protein motifs.)
How can you contribute to Aniseed?
The aim of Aniseed is to form a community tool that will help us all
in our research, but may also in the future, allow one to start some
modelling work on Ciona embryogenesis. The more labs that participate
inthe project, the more satisfying the tool will be for all. Key in
our mind is that the future of the tool will be determined by the participating
labs. You can participate at many levels.
Entering your expression data:
This is the most simple way to participate and a very important one.
You can already request from us the loader as a beta tester. You will
see that entering data is rather simple and we welcome your views on
how to make the process even more simple. There are several types of
data you can enter:
1) published expression data on your favourite gene(s). These are usually
very high quality data and most sought after.
2) expression data on genes you are not very interested in and do not
want to take time to publish. These data are usually of lesser quality
but are still very valuable to the community as they can guide other
people's steps. You will see that entering the data in Aniseed is much
simpler than publishing them, and your name (and e-mail) will remain
attached to the data.
3) large scale in situ screens. These data are usually of lesser quality,
but they are invaluable again as a guide for others.
Communicating embryo models:
Making embryo models is a rate limiting step. If you are interested
in participating to this task, let us know. We will then let you have
all the information about formats, etc..; so that your work is compatible
with the system.
Expressing your wishes:
Once you have tried Aniseed you will probably have comments and suggestions
for new pages allowing new searches, for types of data that are not
yet supported, etc.... You are most welcome to communicate them to us
and we will try and see what we can do, especially for reiterated requests.
If you are interested in developing new tools, we are most happy to
help you do so...... Just let us know so that we can organise this.
We hope you will have fun with Aniseed, and look forward to your participation,
All the best,
Olivier Tassy and Patrick Lemaire