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Association rule mining is an important machine learning tool for unveiling critical biological relations between genes from omics data. Previous approaches typically are designed for one single genomic dataset, and most of them use a single minimum support threshold globally. To overcome the above two general limitations, in this work, we present a novel Transcriptomic and Proteomic Rule Mining (TrapRM)...
The recent success of genome-wide association (GWA) studies has greatly expanded our understanding of many complex diseases by delivering previously unknown loci and genes. A large number of GWAS datasets have already been made available, with more being generated. To explore the underlying moderate and weak signals, we recently developed a network-based dense module search (DMS) method for identification...
Glioblastoma is the most aggressive form of brain cancer. Transcriptional aberrations may play an important role in etiology of glioblastoma, which might be caused through genomic alterations: nucleotide mutation, copy number variation, DNA mythelation. Here, we explored another possible mechanism involving cooperative deregulation of microRNAs (miRNAs) and transcription factors (TFs). Several miRNA-TF...
Schizophrenia is a major brain-related mental disorder. Many genes are likely associated with schizophrenia; their gene-gene interactions as well as gene-environment interactions may contribute as a major risk to the disorder. Rather than the traditional studies of single gene or marker, in this study we hypothesized that positional candidate genes under linkage peaks may play a major role in causing...
It has been commonly accepted that protein-protein interaction network contains valuable information for elucidation of biological processes. Such information, which is difficult to be identified from traditional genetic studies, is important for uncovering the mechanisms of complex diseases such as cancers. In this study, we performed a systematic analysis of global network characteristics for the...
Schizophrenia is a heritable complex disease that involves multiple genes interacting themselves or with environment. Its genetic mechanisms have not been well understood. Currently, studies have revealed hundreds of genes associated with schizophrenia. This provides us an opportunity to explore the molecular characteristics of schizophrenia genes (SCZGenes) using genomics and systems biology approaches...
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