M-CHiPS is a microarray data warehouse integrated with a software platform for microarray data analysis. It can be used as a LIMS for DNA chip experiments, also.
Unlike other microarray data repositories, it entirely dispenses with free-text format, instead holding all the information in a format ready for statistical analysis.

 

Wherefore ?


Characteristics


Publications and schema


Experiment annotation

Multi-Conditional Hybridization Intensity Processing System

Microarray Data Warehouse and Analysis Software

Microarray Bioinformatics Support

wherefore ?wherefore ?

Live since June 1999. Currently, 13039 hybridizations are stored in our databases.

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The Multi-Conditional Hybridization Intensity Processing System (M-CHiPS), a data warehousing concept, focuses on providing a structure suitable for statistical analysis of a microarray database's entire components including the experiment annotations. It accounts for a rapid growth of the amount of hybridisation data, more detailed experimental descriptions and new kinds of experiments expected for the future. We have developed a storage concept, a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape and standards are reduced to minimal conventions not usable for extensive description. An ontology-independent structure enables ontology-updates during normal database operation, avoiding structure-alterations.

 

 

Experiment annotation definition schemes

All defined values - no freetext !

 

 

Public data sets

Following datasets have been published:
  • Eurofan II, B2

    36 yeast experiments (253 hybridizations, complete array) dealing with filamentous growth, ceramide signalling, stresses, hypoxia, PKC pathway, C and N-limited growth in continous culture and other conditions;

    aquired by Alistair Brown/Helene Tournu (Aberdeen, GB), Rudi Planta/Arno Meijer (Amsterdam, NL), Esperanza Cerdan/Manuel Becerra/Luis Lombardía (La Coruna, ES), Joerg Hoheisel/Nicole Hauser (Heidelberg, DE), Steve Oliver/Andy Hayes (Manchester, GB);

    collected and uploaded by Nicole Hauser, annotated by the experimenters themselves via web annotator, processed in M-CHiPS and presented by the Munich Information Center for Protein Sequences (MIPS).

  • Drosophila - embryonic development

    Embryonic and pupal stages up to the adult fly recorded on two-channel glass slides (34 hybridizations, 22429 x 2 spots per array).

  • Pancreas cancer biopsies

    (87 hybridizations, 3559 x 2 spots per array).

  • Pancreas cancer: cystic tumors

    (x hybridizations, 3559 x 2 spots per array).

smaller sets:sets without raw data (which are still to come):

 

 

People involved

(formerly and present, in no particular order)

 

Bioinformatics: Kurt Fellenberg Christian Busold Tim Beißbarth Dieter Finkenzeller Benedikt Brors Martin Vingron
Liang Chunguang Meju Kaipparettu Radhika Upadhyayula Amit Agarwal Stefan Winter Amin Mohaddas Gholami
Mahesh Visvanathan Corinna Schmitt
 
Biological research: Nicole Hauser Judith Boer Marcel Scheideler Susanne Grahlmann Frank Diehl Verena Aign
Andrea Bauer Helene Tournu Arno Meijer Luis Lombardia Manuel Beccera Andy Hayes
Albert Neutzner Nikolaus Schlaich Tamara Korica Boris Beckmann Melanie Bey Claudia Hartmann
Diana Stjepandic Kerstin Hasenpusch-Theil Marcus Frohme Britta Koch Marc Hild Fabian Kruse
Marc Valls Julia Klopp Olaf Witt Kerstin Böhm Christian Weinel José Pérez-Ortín
Matthias Nees Arnaud Lagorce Melanie Bier Sonja Bastuck Gaelle Dubois Yana Syagailo
Jan Wiemer Wladislaw Kusnezow Patrick Kuery Daniel Wenzler Andrea Busch Sarah Marsal Barril
Rainer Schuler Benjamin Altenhein Angela Becker Li Zheng Stefanie Brems Rocio Alba
Bo Xu Duc van Luu Iana Siagailo Martina Brachold Klaudia Kuranda Enrico Ragni
Viola Denninger Martin Brenndoerfer Stephane Boeuf Karoliina Pelttari Eric Steck Michaela Burkhardt
Michaela Schanne Prachiti Narvekar Sandra Bloethner Anja Boos Sven Christian Yi-Ping Lin
Christoph Schröder Linda Ottoboni Frank Holtrup Mahmoud Youns Rafael Queiroz Rosa Hernandez-Barbado
Daniela Albrecht Neeme Tönisson Raphael Martinez Christopher Lößner Florian Haas Li Lu
Sheng-Jia Zhang Jörg Hoheisel Jorge Soza-Ried

 

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