Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization

<p>Abstract</p> <p>Background</p> <p>The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express under certain conditions only <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. Thus, biclustering which clusters genes and conditions simultaneously is preferred over the traditional clustering technique in discovering these coherent genes. Various biclustering algorithms have been developed using different bicluster formulations. Unfortunately, many useful formulations result in NP-complete problems. In this article, we investigate an efficient method for identifying a popular type of biclusters called additive model. Furthermore, parallel coordinate (PC) plots are used for bicluster visualization and analysis.</p> <p>Results</p> <p>We develop a novel and efficient biclustering algorithm which can be regarded as a greedy version of an existing algorithm known as pCluster algorithm. By relaxing the constraint in homogeneity, the proposed algorithm has polynomial-time complexity in the worst case instead of exponential-time complexity as in the pCluster algorithm. Experiments on artificial datasets verify that our algorithm can identify both additive-related and multiplicative-related biclusters in the presence of overlap and noise. Biologically significant biclusters have been validated on the yeast cell-cycle expression dataset using Gene Ontology annotations. Comparative study shows that the proposed approach outperforms several existing biclustering algorithms. We also provide an interactive exploratory tool based on PC plot visualization for determining the parameters of our biclustering algorithm.</p> <p>Conclusion</p> <p>We have proposed a novel biclustering algorithm which works with PC plots for an interactive exploratory analysis of gene expression data. Experiments show that the biclustering algorithm is efficient and is capable of detecting co-regulated genes. The interactive analysis enables an optimum parameter determination in the biclustering algorithm so as to achieve the best result. In future, we will modify the proposed algorithm for other bicluster models such as the coherent evolution model.</p

The different molecular forms of urine neutrophil gelatinase-associated lipocalin present in dogs with urinary diseases

Neutrophil gelatinase-associated lipocalin (NGAL) is a useful biomarker for the early prediction of renal diseases. NGAL may exist as monomer, dimer and/or NGAL/MMP-9 complex forms in humans. In this study, the existence of various forms of NGAL in urine (uNGAL) was determined and whether these forms are related to the different urinary diseases found in dogs is further discussed

YamSat: the First Picosatellite being Developed in Taiwan

This paper describes the current planning and design of the YamSat, the first picosatellite being developed in Taiwan. The design, analysis, manufacture, integration, test and operation of the YamSat will be performed by the National Space Program Office (NSPO), Taiwan, R.O.C, in cooperation with other domestic organizations and companies. It is a member of the CubeSat [1], 10cm x 10cm x 10cm size and within 1kg mass. The major objective of the YamSat is to qualify in space the components and technology developed in Taiwan, including a micro-spectrometer payload using Micro Electro Mechanical Systems (MEMS) technology. The YamSat will be ready for flight in the middle of 2002

Regulatory T Cells: Potential Target in Anticancer Immunotherapy

SummaryThe concept of regulatory T cells was first described in the early 1970s, and regulatory T cells were called suppressive T cells at that time. Studies that followed have demonstrated that these suppressive T cells negatively regulated tumor immunity and contributed to tumor growth in mice. Despite the importance of these studies, there was extensive skepticism about the existence of these cells, and the concept of suppressive T cells left the center stage of immunologic research for decades. Interleukin-2 receptor α-chain, CD25, was first demonstrated in 1995 to serve as a phenotypic marker for CD4+ regulatory cells. Henceforth, research of regulatory T cells boomed. Regulatory T cells are involved in the pathogenesis of cancer, autoimmune disease, transplantation immunology, and immune tolerance in pregnancy. Recent evidence has demonstrated that regulatory T cellmediated immunosuppression is one of the crucial tumor immune evasion mechanisms and the main obstacle of successful cancer immunotherapy. The mechanism and the potential clinical application of regulatory T cells in cancer immunotherapy are discussed

Tellurium substitution effect on superconductivity of the alpha-phase Iron Selenide

We have carried out a systematic study of the PbO-type compound FeSe_{1-x}Te_x (x = 0~1), where Te substitution effect on superconductivity is investigated. It is found that superconducting transition temperature reaches a maximum of Tc=15.2K at about 50% Te substitution. The pressure-enhanced Tc of FeSe0.5Te0.5 is more than 10 times larger than that of FeSe. Interestingly, FeTe is no longer superconducting. A low temperature structural distortion changes FeTe from triclinic symmetry to orthorhombic symmetry. We believe that this structural change breaks the magnetic symmetry and suppresses superconductivity in FeTe.Comment: Some typing errors are corrected; we take out one figures, now the paper has 14 pages, 5 figure