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  • 1
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    MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-06
    Description: Motivation: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC x GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC x GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis. Results: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC x GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery. Availability: The source code of MetPP is available at http://metaopen.sourceforge.net Contact: xiang.zhang@louisville.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Dicer interacts with SIRT7 and regulates H3K18 deacetylation in response to DNA damaging agents (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Dicer participates in heterochromatin formation in fission yeast and plants. However, whether it has a similar role in mammals remains controversial. Here we showed that the human Dicer protein interacts with SIRT7, an NAD + -dependent H3K18Ac (acetylated lysine 18 of histone H3) deacetylase, and holds a proportion of SIRT7 in the cytoplasm. Dicer knockdown led to an increase of chromatin-associated SIRT7 and simultaneously a decrease of cytoplasmic SIRT7, while its overexpression induced SIRT7 reduction in the chromatin-associated fraction and increment in the cytoplasm. Furthermore, DNA damaging agents promoted Dicer expression, leading to decreased level of chromatin-associated SIRT7 and increased level of H3K18Ac, which can be alleviated by Dicer knockdown. Taken together with that H3K18Ac was exclusively associated with the chromatin, our findings suggest that Dicer induction by DNA damaging treatments prevents H3K18Ac deacetylation, probably by trapping more SIRT7 in the cytoplasm.
    Keywords: Protein-protein interaction, Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps (2016)
    Oxford University Press
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    Publication Date: 2016-06-16
    Description: Motivation: The three-dimensional structure of genomes makes it possible for genomic regions not adjacent in the primary sequence to be spatially proximal. These DNA contacts have been found to be related to various molecular activities. Previous methods for analyzing DNA contact maps obtained from Hi-C experiments have largely focused on studying individual interactions, forming spatial clusters composed of contiguous blocks of genomic locations, or classifying these clusters into general categories based on some global properties of the contact maps. Results: Here, we describe a novel computational method that can flexibly identify small clusters of spatially proximal genomic regions based on their local contact patterns. Using simulated data that highly resemble Hi-C data obtained from real genome structures, we demonstrate that our method identifies spatial clusters that are more compact than methods previously used for clustering genomic regions based on DNA contact maps. The clusters identified by our method enable us to confirm functionally related genomic regions previously reported to be spatially proximal in different species. We further show that each genomic region can be assigned a numeric affinity value that indicates its degree of participation in each local cluster, and these affinity values correlate quantitatively with DNase I hypersensitivity, gene expression, super enhancer activities and replication timing in a cell type specific manner. We also show that these cluster affinity values can precisely define boundaries of reported topologically associating domains, and further define local sub-domains within each domain. Availability and implementation: The source code of BNMF and tutorials on how to use the software to extract local clusters from contact maps are available at http://yiplab.cse.cuhk.edu.hk/bnmf/ . Contact: kevinyip@cse.cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Advances in GPR data acquisition and analysis for archaeology (2015)
    Oxford University Press
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    Publication Date: 2015-04-24
    Description: The primary objective of this study is to evaluate the applicability and the effectiveness of ground-penetrating radar (GPR) to identify a thin burnt soil layer, buried more than 2 m below the topographic surface at the Liangzhu Site, in Southeastern China. The site was chosen for its relatively challenging conditions of GPR techniques due to electrical conductivity and to the presence of peach tree roots that produced scattering. We completed the data acquisition by using 100 and 200 MHz antennas in TE and TM broadside and cross-polarized configurations. In the data processing and interpretation phase, we used GPR attribute analysis, including instantaneous phase and geometrical attributes. Validation analysis ground-truthing performed after the geophysical surveys, validated the GPR imaging, confirmed the electrical conductivity and relative dielectric permittivity (RDP) measurements performed at different depths, and allowed a reliable quantitative correlation between GPR results and subsurface physical properties. The research demonstrates that multiple antenna configurations in GPR data acquisition combined with attribute analysis can enhance the ability to characterize prehistoric archaeological remains even in complex subsurface conditions.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 5
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    Doubly misspecified models (2012)
    Oxford University Press
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    Publication Date: 2012-05-22
    Description: Estimation bias arising from local model uncertainty and incomplete data has been studied by Copas & Eguchi (2005) under the assumption of a correctly specified marginal model. We extend the approach to allow additional local uncertainty in the assumed marginal model, arguing that this is almost unavoidable for nonlinear problems. We present a general bias analysis and sensitivity procedure for such doubly misspecified models and illustrate the breadth of application through three examples: logistic regression with a missing confounder, measurement error for binary responses and survival analysis with frailty. We show that a double-the-variance rule is not conservative under double misspecification. The ideas are brought together in a meta-analysis of studies of rehabilitation rates for juvenile offenders.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
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  • 6
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    Crustal and uppermost mantle S-wave velocity structure beneath the Japanese islands from seismic ambient noise tomography (2013)
    Oxford University Press
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    Publication Date: 2013-03-12
    Description: In this study, the crustal and uppermost mantle shear wave velocities beneath the Japanese islands have been determined by inversion from seismic ambient noise tomography using data recorded at 75 Full Range Seismograph Network of Japan broad-band seismic stations, which are uniformly distributed across the Japanese islands. By cross-correlating 2 yr of vertical component seismic ambient noise recordings, we are able to extract Rayleigh wave empirical Green's functions, which are subsequently used to measure phase velocity dispersion in the period band of 6–50 s. The dispersion data are then inverted to yield 2-D tomographic phase velocity maps and 3-D shear wave velocity models. Our results show that the velocity variations at short periods (~10 s), or in the uppermost crust, correlate well with the major known surface geological and tectonic features. In particular, the distribution of low-velocity anomalies shows good spatial correlation with active faults, volcanoes and terrains of sediment exposure, whereas the high-velocity anomalies are mainly associated with the mountain ranges. We also observe that large upper crustal earthquakes (5.0 ≤ M ≤ 8.0, depth ≤ 25 km) mainly occurred in low-velocity anomalies or along the boundary between low- and high-velocity anomalies, suggesting that large upper crustal earthquakes do not strike randomly or uniformly; rather they are inclined to nucleate within or adjacent to low-velocity areas.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 7
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    Mining unusual and rare stellar spectra from large spectroscopic survey data sets using the outlier-detection method (2013)
    Oxford University Press
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    Publication Date: 2013-04-13
    Description: The large number of spectra obtained from sky surveys such as the Sloan Digital Sky Survey (SDSS) and the survey executed by the Large sky Area Multi-Object fibre Spectroscopic Telescope (LAMOST, also called GuoShouJing Telescope) provide us with opportunities to search for peculiar or even unknown types of spectra. In response to the limitations of existing methods, a novel outlier-mining method, the Monte Carlo Local Outlier Factor (MCLOF), is proposed in this paper, which can be used to highlight unusual and rare spectra from large spectroscopic survey data sets. The MCLOF method exposes outliers automatically and efficiently by marking each spectrum with a number, i.e. using outlier index as a flag for an unusual and rare spectrum. The Local Outlier Factor (LOF) represents how unusual and rare a spectrum is compared with other spectra and the Monte Carlo method is used to compute the global LOF for each spectrum by randomly selecting samples in each independent iteration. Our MCLOF method is applied to over half a million stellar spectra (classified as STAR by the SDSS Pipeline) from the SDSS data release 8 (DR8) and a total of 37 033 spectra are selected as outliers with signal-to-noise ratio (S/N) ≥ 3 and outlier index  ≥0.85. Some of these outliers are shown to be binary stars, emission-line stars, carbon stars and stars with unusual continuum. The results show that our proposed method can efficiently highlight these unusual spectra from the survey data sets. In addition, some relatively rare and interesting spectra are selected, indicating that the proposed method can also be used to mine rare, even unknown, spectra. The proposed method can be applicable not only to spectral survey data sets but also to other types of survey data sets. The spectra of all peculiar objects selected by our MCLOF method are available from a user-friendly website: http://sciwiki.lamost.org/Miningdr8/ .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Functional Effects of a Retained Ancestral Polymorphism in Prestin (2017)
    Oxford University Press
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    Publication Date: 2017-01-05
    Description: Molecular basis for mammalian echolocation has been receiving much concerns. Recent findings on the parallel evolution of prestin sequences among echolocating bats and toothed whales suggest that adaptations for high-frequency hearing have occurred during the evolution of echolocation. Here, we report that although the species tree for echolocating bats emitting echolocation calls with frequency modulated (FM) sweeps is paraphyletic, prestin exhibits similar functional changes between FM bats. Site-directed mutagenesis shows that the amino acid 308S in FM bats is responsible for the similar functional changes of prestin . We strongly support that the occurrence of serine at position 308 is a case of hemiplasy, caused by incomplete lineage sorting of an ancestral polymorphism. Our study not only reveals sophisticated molecular basis of echolocation in bats, but also calls for caution in the inference of molecular convergence in species experiencing rapid radiation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity (2015)
    Oxford University Press
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    Publication Date: 2015-01-10
    Description: Motivation: Protein phosphorylation is the most common post-translational modification (PTM) regulating major cellular processes through highly dynamic and complex signaling pathways. Large-scale comparative phosphoproteomic studies have frequently been done on whole cells or organs by conventional bottom-up mass spectrometry approaches, i.e at the phosphopeptide level. Using this approach, there is no way to know from where the phosphopeptide signal originated. Also, as a consequence of the scale of these studies, important information on the localization of phosphorylation sites in subcellular compartments (SCs) is not surveyed. Results: Here, we present a first account of the emerging field of subcellular phosphoproteomics where a support vector machine (SVM) approach was combined with a novel algorithm of discrete wavelet transform (DWT) to facilitate the identification of compartment-specific phosphorylation sites and to unravel the intricate regulation of protein phosphorylation. Our data reveal that the subcellular phosphorylation distribution is compartment type dependent and that the phosphorylation displays site-specific sequence motifs that diverge between SCs. Availability and implementation: The method and database both are available as a web server at: http://bioinfo.ncu.edu.cn/SubPhos.aspx . Contact: jdqiu@ncu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Measures for the degree of overlap of gene signatures and applications to TCGA (2015)
    Oxford University Press
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    Publication Date: 2015-09-16
    Description: For cancer and many other complex diseases, a large number of gene signatures have been generated. In this study, we use cancer as an example and note that other diseases can be analyzed in a similar manner. For signatures generated in multiple independent studies on the same cancer type and outcome, and for signatures on different cancer types, it is of interest to evaluate their degree of overlap. Many of the existing studies simply count the number (or percentage) of overlapped genes shared by two signatures. Such an approach has serious limitations. In this study, as a demonstrating example, we consider cancer prognosis data under the Cox model. Lasso, which is representative of a large number of regularization methods, is adopted for generating gene signatures. We examine two families of measures for quantifying the degree of overlap. The first family is based on the Cox-Lasso estimates at the optimal tunings, and the second family is based on estimates across the whole solution paths. Within each family, multiple measures, which describe the overlap from different perspectives, are introduced. The analysis of TCGA (The Cancer Genome Atlas) data on five cancer types shows that the degree of overlap varies across measures, cancer types and types of (epi)genetic measurements. More investigations are needed to better describe and understand the overlaps among gene signatures.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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