Laura Cammas1, Guillaume Berthommier2, Raymond Ripp2, Pascal Dollé1

1 Component B, Departement of Physiological Genetics2 Component T, Laboratoire de BioInformatique et Génomique Intégratives

IGBMC (CNRS UMR 7104, INSERM U 596), CERBM, 1 rue Laurent Fries, Illkirch 67404, Strasbourg France

ImAnno: a web-based tool to annotate tissue-specific gene expression patterns

General overview of ImAnno. An annotated database for ISH expression patterns in E14.5 developing mouse eye http://www-genoret.u-strasbg.fr/genoret/ImAnno

Abstract. High throughput analysis of gene expression generates large amounts of data that need to be analyzed and integrated. GenePaint.org is a digital atlas of gene expression patterns for thousands of genes in the E14.5 mouse embryo. The data, freely available on internet, are produced by large scale automated in situ hybridization (ISH) and are currently being annotated in another database (EURExpress.org). Our aim is to take advantage of this unique resource to identify novel genes specifically expressed in eye structures. We propose to systematically implement our analyses (‘annotations’) of gene expression patterns to the EVI-GENORET database. For this purpose, the ImAnno Genoret Image Annotation Tool was developed. It allows the rapid annotation of all types of images through a user friendly web interface that can be made available to all EVI-GENORET members. The annotations are stored in the Genoret Database and can be retrieved and queried by the Genoret search engines.

The goal of this work is to identify new candidate genes whose expression is specific of the eye and perform large scale bioinformatics analysis to define gene families and pathways that may function during eye development.

Results. The ImAnno tool can be adapted to all kind of projects

These annotations are processed using bioinformatic methods.

Currently we have included : - 14 eye tissues, - 5 non ocular head tissues , - 2 other body regions.

General information

such as the gene name, symbol and description, the accession number and useful links to the

GENORET database are automatically stored.

General expression pattern

Signal intensity

3 levels of expression are defined: negative, weak or strong

Some structures can be absent from the available images, and are therefore “not annotated”

Characterization of the expression (regionalized, etc)

Link to a reference image

Schematic of the expression domain and intensity

The level of expression is represented by a color code for rapid and intuitive evaluation.

After interpretation of the in situ hybridization images, the user completes the annotation form by defining the expression level in the selected tissues.2

3

1The form is organized as a hierarchical list of anatomical terms. The list of tissue types is defined by the user(s) and can be managed dynamically in order to add new tissue types in the course of the project.

The annotations will be released on the GENORET Database in the form of ‘ID cards’ (screens) for each gene allowing easy reading of the queried gene expression pattern.

Search tools will be developed to query ImAnno for genes expressed in particular organs or structures of interest, synexpression groups, etc.

4

staining

annotationeye

other tissues

all negative

eye negative

ubiquitous

eye specific

35%

20%

32%

13%To date 902 genes have been annotated using ImAnno. Of these, 119 show specific expression in one or several eye tissues. Some of them, like Pax6, are well known but interestingly this aproach allowed to identify genes not previously known to be expressed in the eye.

Gene searching

Clustering based on expression pattern

Automated bibliographical analysis

Eye Negative

All NegativeUbiquitous

Eye Specific

• From images to textual data • It offers a common organisation and is easily configurable• It is easy to use

through a web interface available through all web browsers by several people (history and ownership)

• Automatic storage & indexation in the Database relational database standardisation

• Quering tools web display accessible for programs from inside or outside

• GENORET user can annotate and store other sets of ISH or IHC data modified ImAnno forms have been derived forother projects in-team, in order to store informationon expression patterns in inner ear or tooth buds. the Eye fundus images ImAnno tool is already implemented and ready to use.