Skip to content. | Skip to navigation

Personal tools

You are here: Home / Publications / 2008


SQUAT: A web tool to mine human, murine and avian SAGE data.

Author(s) : Leyritz J, Schicklin S, Blachon S, Keime C, Robardet C, Boulicaut J, Besson J, Pensa R, Gandrillon O,
Journal : BMC Bioinformatics
BACKGROUND: There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns. DESCRIPTION: We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situationsis my favorite gene expressed?" as well as much more complex queries like: <<what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?>>. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated. CONCLUSION: SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.

Stem cell antigen 2: a new gene involved in the self-renewal of erythroid progenitors.

Author(s) : Bresson-Mazet C, Gandrillon O, Gonin-Giraud S,
Journal : Cell Prolif
OBJECTIVES: Stem cell antigen 2 (SCA2), also known as TSA1 and LY6E, is a glycosylphosphatidylinositol-anchored molecule that belongs to the Ly-6 family and whose function remains largely unknown. We have previously shown that SCA2 is overexpressed in self-renewing avian erythroid progenitors (T2ECs) as opposed todifferentiating T2ECs. The aim of this study was to define the role of SCA2 in the switch between self-renewal and differentiation of erythroid progenitors. MATERIALS AND METHODS: We have investigated the cellular processes controlled bySCA2 in T2ECs by RNA interference and overexpression approaches. Moreover, we have used a SAGE Querying and analysis tools developed in our laboratory, to investigate the expression level of SCA2 gene in different human cell types. RESULTS: We demonstrate the regulation of SCA2 expression by TGF-beta, a growth factor essential for self-renewal of T2ECs. We establish that SCA2 knockdown by RNA interference reduced the proliferation and promoted the differentiation of T2ECs. In contrast, SCA2 overexpression inhibited differentiation of T2ECs only.Furthermore, by using a bioinformatic approach, we found that SCA2 is highly expressed in a variety of human cancer cells. We confirmed this result by quantitative PCR on human colon and kidney tissues. CONCLUSIONS: Altogether, these findings imply that SCA2 may function in a dose-dependent manner to support the self-renewal state and that its deregulation might contribute to the development of some human cancers.