First steps towards a multi-dimensional iron regulatory network.

Iron homeostasis is central to many biological processes and thus imbalances in mammalian iron metabolism are associated with frequent iron overload and iron deficiency disorders. The iron regulatory network is a complex multi-dimensional network combining organ to organ communication (mediated by iron hormones), cellular interactions and biochemical pathways. This network can be addressed by several endogenous (e.g. cell cycle) and exogenous (e.g. infection) stimuli.

In order to define and ultimately visualize a complete iron regulatory network we produce and collect specific signature profiles derived from cell based and whole animal experiments and correlate them with biochemical, phenotype and physiological information. Gene expression profiles recorded on ‘IronChips’ form the basis for our ‘in silico’ iron regulatory network. ‘IronChips’ are cDNA based microarrays that sensitively and accurately measure expression changes of genes involved in iron uptake, storage and recycling, as well as from genes involved in a number of interlinked pathways (e.g. NO metabolism, redox pathways, stress responses as well as acute phase and immunity). Systematic ‘IronChip’ analysis of selected tissues derived from knock-out mice with defects in central players of iron metabolism inform us about the relationship of these genes within the network.

‘IronChip’ data evaluation and construction of such a multi-dimensional iron regulatory network requires the development of sophisticated algorithms. The recently developed IronChip Evaluation Package (ICEP) offers a solution for the automated data analysis associated with this specialized array platform.

IronChip Evaluation Package

ICEP consist of several utilities specialized for evaluation of raw data as well as for high level analysis of final results.

	Today ICEP consist of 3 utilities Analyse single array Analyse Colour Swap Align Results All utilities can be started independently or from the start panel.
	ICEP Single Array analysis tool assigns different quality flags to the data. Based on this flags, program later take a decision about statistical significance of the results.
	ICEP Colour Swap analysis tool make use of all quality flags, and based on the comparison between colour swapped arrays determine the final regulation for every single gene.

Microarrays require not only sophisticated algorisms for the data evaluation, but as well generates tremendous amount of the data. Therefore correct organisation of the data storage and careful documentation of every single step of microarray experiments is a requirement for success in this area.

IRON-LIMs

We are developing a database laboratory information and management system (IRON-LIMs) for recording of all information related to the IronChip experiment as long as for actual data storage. IRON-LIMs is the relational database based on ORACLE and build using principle of distribution of major components between different servers.

User can access the application server from the local network or from the Internet and perform all required operations with the database (search, update, manage). Access to the database will be restricted to authorized users only.	IRON-LIMs The database containing all information about microarray experiments and the information about all materials used stored in the Oracle database on the Database Sever. All raw data, images and resulting files stored on a file server. All communication between database and fileserver performed on the application server.
	Data relations inside the database can be illustrated by the scheme in the left panel.

If you want to know more about actual experiments with the IronChip, please visit the page of Mayka

If you want to find out more about iron metabolism and its regulation, please visit also the homepages of Dunja or Bruno.