353 research outputs found
On Spectral Graph Embedding: A Non-Backtracking Perspective and Graph Approximation
Graph embedding has been proven to be efficient and effective in facilitating
graph analysis. In this paper, we present a novel spectral framework called
NOn-Backtracking Embedding (NOBE), which offers a new perspective that
organizes graph data at a deep level by tracking the flow traversing on the
edges with backtracking prohibited. Further, by analyzing the non-backtracking
process, a technique called graph approximation is devised, which provides a
channel to transform the spectral decomposition on an edge-to-edge matrix to
that on a node-to-node matrix. Theoretical guarantees are provided by bounding
the difference between the corresponding eigenvalues of the original graph and
its graph approximation. Extensive experiments conducted on various real-world
networks demonstrate the efficacy of our methods on both macroscopic and
microscopic levels, including clustering and structural hole spanner detection.Comment: SDM 2018 (Full version including all proofs
High-dimensional quantile mediation analysis with application to a birth cohort study of mother-newborn pairs
MOTIVATION: There has been substantial recent interest in developing methodology for high-dimensional mediation analysis. Yet, the majority of mediation statistical methods lean heavily on mean regression, which limits their ability to fully capture the complex mediating effects across the outcome distribution. To bridge this gap, we propose a novel approach for selecting and testing mediators throughout the full range of the outcome distribution spectrum.
RESULTS: The proposed high-dimensional quantile mediation model provides a comprehensive insight into how potential mediators impact outcomes via their mediation pathways. This method\u27s efficacy is demonstrated through extensive simulations. The study presents a real-world data application examining the mediating effects of DNA methylation on the relationship between maternal smoking and offspring birthweight.
AVAILABILITY AND IMPLEMENTATION: Our method offers a publicly available and user-friendly function qHIMA(), which can be accessed through the R package HIMA at https://CRAN.R-project.org/package=HIMA
Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations
Array-based comparative genomic hybridization (aCGH) allows measuring DNA copy number at the whole genome scale. In cancer studies, one may be interested in identifying DNA copy number aberrations (CNAs) associated with certain clinicopathological characteristics such as cancer metastasis. We proposed to define test regions based on copy number pattern profiles across multiple samples, using either smoothed log2-ratio or discrete data of copy number gain/loss calls. Association test performed on the refined test regions instead of the probes has improved power due to reduced number of tests. We also compared three types of measurement of copy number levels, normalized log2-ratio, smoothed log2-ratio, and copy number gain or loss calls in statistical hypothesis testing. The relative strengths and weaknesses of the proposed method were demonstrated using both simulation studies and real data analysis of a liver cancer study
HIMA2: High-dimensional mediation analysis and its application in epigenome-wide DNA methylation data
Mediation analysis plays a major role in identifying significant mediators in the pathway between environmental exposures and health outcomes. With advanced data collection technology for large-scale studies, there has been growing research interest in developing methodology for high-dimensional mediation analysis. In this paper we present HIMA2, an extension of the HIMA method (Zhang in Bioinformatics 32:3150-3154, 2016). First, the proposed HIMA2 reduces the dimension of mediators to a manageable level based on the sure independence screening (SIS) method (Fan in J R Stat Soc Ser B 70:849-911, 2008). Second, a de-biased Lasso procedure is implemented for estimating regression parameters. Third, we use a multiple-testing procedure to accurately control the false discovery rate (FDR) when testing high-dimensional mediation hypotheses. We demonstrate its practical performance using Monte Carlo simulation studies and apply our method to identify DNA methylation markers which mediate the pathway from smoking to reduced lung function in the Coronary Artery Risk Development in Young Adults (CARDIA) Study
OR-009 The expression and roles of lncRNAs in the regeneration of skeletal muscle contusion
Objective In recent years, Accumulating evidence from myoblast differentiation in vitro, cardiotoxin (CTX)-mediated injury or mdx mice suggested that some lncRNAs such as Malat1, H19, linc-MD1, linc-YY1, Sirt1 AS and lnc-mg may modulate myogenesis and muscle regeneration. However, the change of lncRNAs in skeletal muscle contusion and their possible roles are still unclear. We hypothesize that the lncRNAs may be involved in the repair of skeletal muscle contusion.
Methods Forty C57BL/6 male mice were randomly divided into two groups, uninjured control group (group C) and muscle contusion group (group S). The mice of group S suffered from contusion injury. All the mice were killed to harvest gastrocnemius at 3, 6, 12 and 24 days post-injury. The gene expression were detected by PCR technique. Gastrocnemius were stained with H & E to evaluate the general morphology. Data were analyzed by One-way analysis of variance, with statistical significance being set at p ≤ 0.05.
Results The expression levels of linc-MD1 and Sirt1 AS were significantly higher than that of the uninjured control group at 3, 6 and 12 days post-injury (p<0.01). And Malat1 was highly expressed in the skeletal muscle of the muscle contusion group at 3 days post-injury and continuously up-regulated at 6 days (p<0.01). Moreover, linc-YY1 and H19 were all elevated significantly at 6 days (all p<0.01), but their gene expression levels did not change significantly at 3, 12 and 24 days post-injury, as compared to the uninjured control group. Furthermore, lnc-mg mRNA level did not change significantly in the whole process of regeneration after muscle contusion except the time point of 12 days post-injury which decreased significantly (p<0.01). The expression of myogenic regulatory factors (MyoD, myogenin, myf5, myf6) were studied, they were all elevated significantly at 3 and 6 days (all p<0.01; except myogenin ), and returned to normal at 24 days post-injury, as compared to the uninjured control group. Meanwhile, Pearson correlations showed that there was an correlation between lincRNAs and myogenic regulatory factors mentioned above.
Conclusions The expression of myogenic regulatory factors increased significantly after muscle contusion. Meanwhile, varieties of lncRNAs (Malat1, H19, lnc-mg, linc-MD1, linc-YY1, Sirt1 AS) were also up-regulated. Moreover, there was correlation between lncRNAs and myogenic regulatory factors for skeletal muscle regeneration. These results suggest that lncRNAs may play important roles in the regeneration of skeletal muscle contusion
Identification and characterization of novel B-cell epitopes within EBV latent membrane protein 2 (LMP2)
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