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See detailGene expression data analysis using spatiotemporal blind source separation
Sainlez, Matthieu ULg; Absil, Pierre-Antoine; Teschendorff, Andrew E.

in Verleysen, Michel (Ed.) ESANN'2009 proceedings, European Symposium on Artificial Neural Networks - Advances in Computational Intelligence and Learning. (2009, April)

We propose a “time-biased” and a “space-biased” method for spatiotemporal independent component analysis (ICA). The methods rely on computing an orthogonal approximate joint diagonalizer of a collection ... [more ▼]

We propose a “time-biased” and a “space-biased” method for spatiotemporal independent component analysis (ICA). The methods rely on computing an orthogonal approximate joint diagonalizer of a collection of covariance-like matrices. In the time-biased version, the time signatures of the ICA modes are imposed to be white, whereas the space-biased version imposes the same condition on the space signatures. We apply the two methods to the analysis of gene expression data, where the genes play the role of the space and the cell samples stand for the time. This study is a step towards addressing a question first raised by Liebermeister, on whether ICA methods for gene expression analysis should impose independence across genes or across cell samples. Our preliminary experiment indicates that both approaches have value, and that exploring the continuum between these two extremes can provide useful information about the interactions between genes and their impact on the phenotype. [less ▲]

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See detailGene expression following hypoxia/ischemia injury
Plumier, Jean-Christophe ULg; Armstrong, John N.; Currie, R. William

Poster (1994)

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See detailGene expression of antimicrobial peptides in colonic mucosa of patients with inflammatory bowel disease before and after first infliximab treatment.
Arijs, I.; Lemaire, K.; Quintens, R. et al

in Gut (2008), 57(Suppl II), 102-103

Detailed reference viewed: 10 (3 ULg)
See detailGene expression of the lipoxygenase pathway in a tomato species tolerant to salt stress
Ghars, Mohamed Ali ULg; Muhovski, Y.; Ghanem, M. et al

Poster (2010)

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See detailGene expression pattern of synovial cells from inflammatory and normal areas of osteoarthritis synovial membrane.
Lambert, Cécile ULg; Dubuc, Jean-Emile; Montell, Eulalia et al

in Arthritis and Rheumatism (2014), sous presse

Objective: The aim of this study was to compare the gene expression pattern of synovial cells from inflammatory (I) or normal/reactive (N/R) areas of a synovial membrane harvested from the same ... [more ▼]

Objective: The aim of this study was to compare the gene expression pattern of synovial cells from inflammatory (I) or normal/reactive (N/R) areas of a synovial membrane harvested from the same osteoarthritis (OA) patient. Methods: Synovial tissues were obtained from 12 knee OA patients at the time of total knee replacement. The inflammatory status of the synovial membrane was characterized according to macroscopic criteria and sorted as N/R and I. Biopsies were cultured separately for 7 days. Microarray gene expression profiling between N/R and I areas was performed. Western blot and immunohistochemistry confirmed the identified genes that were differentially expressed. Results: 896 differentially expressed genes between N/R and I zones were identified. The key pathways were related to inflammation, cartilage metabolism, Wnt signaling and angiogenesis. In the inflammatory network, TREM1 and S100A9 were strongly up-regulated. MMP-3 and -9, cathepsin H and S were significantly up-regulated in the cartilage catabolism pathway, whereas the most up-regulated anabolism enzyme was HAS1. Wnt-5A and LRP5 were up-regulated whereas FZD2 and DKK3 were down-regulated in the Wnt signaling. Finally, STC1, a protein involved in angiogenesis was identified as the most up-regulated gene in I zones compared to N/R zones. Conclusion: This study is the first to identify different expression pattern between two areas of the synovial membrane in the same patient. These differences concern several key pathways involved in OA pathogenesis. This analysis also provides information regarding new genes and proteins as potential targets for the future therapeutic. (c) 2013 American College of Rheumatology. [less ▲]

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See detailGene expression profile of human lymphocytes exposed to (211)At alpha particles
Turtoi, Andrei ULg; Brown, Ian; Schläger, Martin et al

in Radiation Research (2010), 174

In this study, the Whole Human Genome 44K DNA microarray assay was used for the first time to obtain gene expression profiles in human peripheral blood lymphocytes 2 h after exposure (in suspension) to 6 ... [more ▼]

In this study, the Whole Human Genome 44K DNA microarray assay was used for the first time to obtain gene expression profiles in human peripheral blood lymphocytes 2 h after exposure (in suspension) to 6.78 MeV mean energy alpha particles from extracellular (211)At. Lymphocytes were exposed to fluences of 0.3-9.6 x 10(6) alpha particles/cm(2) [corresponding to mean absorbed alpha-particle doses (D(alpha)) of 0.05-1.60 Gy] over 30 min. Significantly modulated expression was identified in 338 early-response genes. Up-regulated expression was evident in 183 early-response genes, while the remaining 155 were down-regulated. Over half of the up-regulated genes and 40% of the down-regulated genes had a known biological process related primarily to cell growth and maintenance and cell communication. Genes associated with cell death were found only in the up-regulated genes and those with development only in the down-regulated genes. Eight selected early-response genes that displayed a sustained up- or down-regulation (CD36, HSPA2, MS4A6A, NFIL3, IL1F9, IRX5, RASL11B and SULT1B1) were further validated in alpha-particle-irradiated lymphocytes of two human individuals using the TaqMan(R) RT-qPCR technique. The results confirmed the observed microarray gene expression patterns. The expression modulation profiles of IL1F9, IRX5, RASL11B and SULT1B1 genes demonstrated similar trends in the two individuals studied. However, no significant linear correlation between increasing relative gene expression and the alpha-particle dose was evident. The results suggest the possibility that a panel of genes that react to alpha-particle radiation does exist and that they merit further study in a greater number of individuals to determine their possible value regarding alpha-particle biodosimetry. [less ▲]

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See detailThe gene expression profile of nodal peripheral T-cell lymphoma demonstrates a molecular link between angioimmunoblastic T-cell lymphoma (AITL) and follicular helper T (T-FH) cells
de Leval, Laurence ULg; Rickman, David; Thielen, Caroline ULg et al

in Blood (2007), 109(11), 4952-4963

The molecular alterations underlying the pathogenesis of angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma, unspecified (PTCL-u) are largely unknown. In order to characterize the ... [more ▼]

The molecular alterations underlying the pathogenesis of angioimmunoblastic T-cell lymphoma (AITL) and peripheral T-cell lymphoma, unspecified (PTCL-u) are largely unknown. In order to characterize the ontogeny and molecular differences between both entities, a series of AITLs (n = 18) and PTCLs-u (n = 16) was analyzed using gene expression profiling. Unsupervised clustering correlated with the pathological classification and with CD30 expression in PTCL-u. The molecular profile of AITLs was characterized by a strong microenvironment imprint (overexpression of B-cell- and follicular dendritic cell-related genes, chemokines, and genes related to extracellular matrix and vascular biology), and overexpression of several genes characteristic of normal follicular helper T (T-FH) cells (CXCL13, BCL6, PDCD1, CD40L, NFATC1). By gene set enrichment analysis, the AITL molecular signature was significantly enriched in published T-FH-specific genes. The enrichment was higher for sorted AITL cells than for tissue samples. Overexpression of several T-FH genes was validated by immunohistochemistry in AITLs. A few cases with molecular T-FH-like features were identified among CD30(-) PTCLs-u. Our findings strongly support that TFH cells represent the normal counterpart of AITL, and suggest that the AITL spectrum may be wider than suspected, as a subset of CD30(-) PTCLs-u may derive from or be related to AITL. [less ▲]

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See detailGene expression profiles in canine idiopathic pulmonary fibrosis
Krafft, Emilie ULg; Heikkilä, H.P.; Peters, I. et al

in Proceedings of 17th International consortium on lung and airways fibrosis (2012, October 01)

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See detailGene expression profiles in canine idiopathic pulmonary fibrosis
Krafft, Emilie ULg; Heikkilä, HP; Vanherberghen, Morgane ULg et al

in Proceedings of the 29th ACVIM Forum (2011, June)

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See detailGene expression profiling from leukocytes of horses affected by osteochondrosis.
Serteyn, Didier ULg; Piquemal, D.; Vander Heyden, Laurent ULg et al

in Journal of Orthopaedic Research (2010)

Osteochondrosis (OC) is a developmental disease that affects growing horses and that severely affects their ability to perform. The genetic basis of its pathogenesis is poorly understood. The aim of the ... [more ▼]

Osteochondrosis (OC) is a developmental disease that affects growing horses and that severely affects their ability to perform. The genetic basis of its pathogenesis is poorly understood. The aim of the study was to analyze the transcript profile of leukocytes from horses affected with OC. Two transcriptome libraries were constructed from leukocytes of OC-affected and non-OC-affected horses using digital gene expression analysis (DGE) and real-time PCR. Statistical analysis allowed selection of 1,008 tags upregulated in the non-OC-affected group and 1,545 tags upregulated in the OC-affected group. Among these genes, 16 regulated genes and 5 housekeeping genes were selected. Metabolic pathways analysis showed an obvious dysregulation of several signaling pathways related to cartilage formation or cartilage repair, including Wnt, Indian hedgehog, and TGF-beta signaling. Other genes, including ISG, ApoB, MGAT4, and TBC1D9, showed a significantly different expression between groups. These genes may play a role in high carbohydrate diet, abnormal insulin metabolism, or inflammation, mechanisms suspected to be involved in OC. This DGE analysis of the transcript profile of leukocytes from OC-affected horses demonstrated significant differences in comparison to the control library. These results open new perspectives for the understanding of equine OC. (c) 2010 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res. [less ▲]

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See detailGene expression profiling of hypothalamic hamartomas: a search for genes associated with central precocious puberty
Parent, Anne-Simone ULg; Matagne, Valérie; Westphal, Manfred et al

in Hormone Research (2008), 69

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See detailGene expression profiling to predict the response of infliximab in patients with UC
Arijs, Ingrid; Van lommel, Leertje; Van Steen, Kristel ULg et al

in Gastroenterology (2007), 132(4), 174-174

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See detailGene expression profiling to predict the response of infliximab in patients with UC
Arijs, I.; Van Lommel, L.; Van Steen, Kristel ULg et al

in Journal of Crohn’s and Colitis [=JCC] (2007), 1(1), 34

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See detailGene flow among wild Phaseolus lunatus L. populations in the Central Valley of Costa Rica
Ouedraogo, M.; Maquet, A.; Baudoin, Jean-Pierre ULg

in Annual Report Bean Improvement Cooperative (2003), 46

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See detailThe gene INPPL1, encoding the lipid phosphatase SHIP2, is a candidate for type 2 diabetes in rat and man
Marion, Evelyne; Kaisaki, Pamela Jane; Pouillon, Valérie et al

in Diabetes (2002), 51

Genetic susceptibility to type 2 diabetes involves many genes, most of which are still unknown. The lipid phosphatase SHIP2 is a potent negative regulator of insulin signaling and sensitivity in vivo and ... [more ▼]

Genetic susceptibility to type 2 diabetes involves many genes, most of which are still unknown. The lipid phosphatase SHIP2 is a potent negative regulator of insulin signaling and sensitivity in vivo and is thus a good candidate gene. Here we report the presence of SHIP2 gene mutations associated with type 2 diabetes in rats and humans. The R1142C mutation specifically identified in Goto-Kakizaki (GK) and spontaneously hypertensive rat strains disrupts a potential class II ligand for Src homology (SH)-3 domain and slightly impairs insulin signaling in cell culture. In humans, a deletion identified in the SHIP2 3' untranslated region (UTR) of type 2 diabetic subjects includes a motif implicated in the control of protein synthesis. In cell culture, the deletion results in reporter messenger RNA and protein overexpression. Finally, genotyping of a cohort of type 2 diabetic and control subjects showed a significant association between the deletion and type 2 diabetes. Altogether, our results show that mutations in the SHIP2 gene contribute to the genetic susceptibility to type 2 diabetes in rats and humans [less ▲]

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See detailGene knock down via antisense oligonucleotides to the steroid receptor coactivator SRC-1 modulates testosterone-dependent male sexual behavior and neural gene expression
Charlier, Thierry ULg; Ball, Gregory F; Balthazart, Jacques ULg

in Hormones & Behavior (2004), 46

Studies of eukaryotic genome expression demonstrate the importance of steroid receptor coactivators in mediating efficient gene transcription. Little is know about the physiological role of these ... [more ▼]

Studies of eukaryotic genome expression demonstrate the importance of steroid receptor coactivators in mediating efficient gene transcription. Little is know about the physiological role of these coactivators in vivo. We recently showed that the Steroid Receptor Coactivator SRC-1 is densely expressed in steroid-sensitive brain areas in birds and its expression is steroid-dependent and sexually differentiated. We tested the role of SRC-1 in the activation by testosterone of male sexual behavior in quail. Daily injections of LNA antisense oligonucleotides in the third ventricle (AS group) significantly reduced the expression of male copulatory behavior in response to exogenous testosterone compared to control animals (Ctrl group) receiving the vehicle alone or scrambled LNA. Sexual behavior was restored and even enhanced within 48 hours after interruption of LNA injection (ASSC group). Western blot analysis confirmed the decrease of SRC-1 expression in AS animals and suggested an over-expression of the coactivator in ASSC animals. The effect of SRC-1 knock down on behavior was correlated with a reduced volume of the medial preoptic nucleus (POM) defined by Nissl-staining and aromatase immunohistochemistry. In addition, the amount of aromatase-immunoreactive material in POM, defined as the relative optical density of the aromatase immunoreactivity multiplied by the percentage of surface covered within the nucleus and by the total POM volume of the POM, was decreased in the AS compared to the Ctrl group, suggesting a blockade of aromatase transcription. Together, these data indicate that SRC-1 functions as a critical regulatory molecule in the brain that modulates steroid-dependent gene transcription and behavior. [less ▲]

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See detailGene regulation in Arabidopsis halleri, a model system to understand zinc homeostasis in plants.
Hanikenne, Marc ULg; Talke, Ina N.; Lanz, Christa et al

Conference (2006, December 18)

Detailed reference viewed: 17 (1 ULg)