CAPweb :
a Web based platform for CGH-array management and analysis

This project is a collaboration co-ordinated by Philippe La Rosa.
CAPweb is developed by Stéphane Liva and involves the following partners from the Institut Curie Bioinformatics Unit:

  • Stéphane Liva, Philippe Hupé(*), Pierre Neuvial, Isabel Brito, Emmanuel Barillot and Philippe La Rosa.
  • We address a special thanks to Gaelle Pierron, Elodie Manié, Ahmed Idbaih (Unité 509 INSERM/IC) .
  • (*) P.Hupé's appartenance is both Bioinformatics Group and UMR 144 CNRS.

    CAPweb is available upon request at

    CAPweb (CGH-Array Analysis Platform) is a suite of tools for the management, visualization and analysis of Comparative Genomic Hybridization arrays (CGH-arrays). CAPweb has been developed in the Bioinformatics Unit of Institut Curie as a close collaboration with biologists and clinicians. It is currently used for processing the data from about 30 different projects and 3,000 arrays. CAPweb is a web interface which allows users to carry out the following bionformatics steps of their CGH-array projects :

  • Upload in a secure mode the results of CGH-array image analysis (under Genepix, Spot , MAIA, more formats soon avalaible) and the annotation of its clones/probes (name, genome, position). First level analysis of each array, which includes :

  • Automatic normalization of the data, for correcting experimental biaises. In our case, the main source of variability is spatial biases. This is solved with the MANOR package (Neuvial et al, subm), which implements an algorithm based on a spatial trend computation by two-dimensional LOESS (Cleveland, 1992) and unsupervised classification with spatial constraint (Ambroise, 1996).

  • Breakpoint detection and status assignment (gain, loss, normal, amplicon or double deletion) using the new version of the GLAD package ( Hupé et al, 2004). GL AD is based on an iterative, data-adaptative smoothing technique : the Adaptative Weights Smoothing (AWS) procedure (Polzehl et al, 2000).

  • Synoptic reporting of these results which is proposed to the user for validation, further analysis or discarding of the analysis.

  • Integration into VAMP, a graphical interface for Visualisation and Analysis of Molecular Profiles.

  • VAMP allows the visual comparison of the array-CGH profiles of a cohort of patients, or the confrontation of array-CGH, expression and loss of heterozygosity profiles. VAMP offers many functionalities such as computing recurrent alterations, clustering profiles, crossing with clinical or biological annotations, performing syntenic projection onto the genome of another species.

    We have also set up an integrative public database for the integration of cancer CGH arrays, which comprises data from Snijders et al (2001), Pollack et al (2002), Veltman et al (2003), Nakao et al 2004, Douglas et al (2004) and de Leeuw et al (2004).

    Have a look at the CAPweb tutorial

    Access to CAPweb :