ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. ITTACA is developed by the Institut Curie Bioinformatics group and the Molecular Oncology group of UMR144 CNRS/Institut Curie.
A web interface allows users to carry out different class comparison analyses, including comparison of expression distribution profiles, tests for differential expression, patient survival analyses, and users can define their own patient groups according to clinical data or gene expression levels.
The different functionalities implemented in ITTACA are:
- To test if one or more gene, of your choice, is differentially expressed between two groups of samples exhibiting distinct phenotypes (Student and Wilcoxon tests).
- The detection of genes differentially expressed (Significance Analysis of Microarrays) between two groups of samples.
- The creation of histograms which represent the expression level according to a clinical parameter for each sample.
- The computation of Kaplan Meier survival curves for each group.
ITTACA has been developed to be a useful tool for comparing personal results to the existing results in the field of transcriptome studies with microarrays.
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Transcriptome microarrays have become one of the tools of choice for investigating the genes involved in tumorigenesis and tumor progression, as well as finding new biomarkers and gene expression signatures for the diagnosis and prognosis of cancer. Here, we describe a new database for Integrated Tumor Transcriptome Array and Clinical data Analysis (ITTACA). ITTACA centralizes public datasets containing both gene expression and clinical data. ITTACA currently focuses on the types of cancer that are of particular interest to research teams at Institut Curie: breast carcinoma, bladder carcinoma and uveal melanoma. A web interface allows users to carry out different class comparison analyses, including the comparison of expression distribution profiles, tests for differential expression and patient survival analyses. ITTACA is complementary to other databases, such as GEO and SMD, because it offers a better integration of clinical data and different functionalities. It also offers more options for class comparison analyses when compared with similar projects such as Oncomine. For example, users can define their own patient groups according to clinical data or gene expression levels. This added flexibility and the user-friendly web interface makes ITTACA especially useful for comparing personal results with the results in the existing literature. ITTACA is accessible online at http://bioinfo.curie.fr/ittaca.
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