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Glioblastoma (GBM) is a malignant brain tumor associated with high mortality. Long non‑coding RNAs (lncRNAs) are increasingly being recognized as its modulators. However, it remains mostly unexplored how lncRNAs are mediated by DNA methylation in GBM. The present study integrated multi‑omics data to analyze the epigenetic dysregulation of lncRNAs in GBM. Widely aberrant methylation in the lncRNA promoters was observed, and the lncRNA promoters exhibited a more hypomethylated pattern in GBM. By combining transcriptional datasets, it was possible identify the lncRNAs whose transcriptional changes might be associated with the aberrant promoter methylation. Then, a methylation‑mediated lncRNA regulatory network and functional enrichment analysis of aberrantly methylated lncRNAs showed that lncRNAs with different methylation patterns were involved in diverse GBM progression‑related biological functions and pathways. Specifically, four lncRNAs whose increased expression may be regulated by the corresponding promoter hypomethylation were evaluated to have an excellent diagnostic effect and clinical prognostic value. Finally, through the construction of drug‑target association networks, the present study identified potential therapeutic targets and small‑molecule drugs for GBM treatment. The present study provides novel insights for understanding the regulation of lncRNAs by DNA methylation and developing cancer biomarkers in GBM.
Pubmed ID: 32319552
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Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.
View all literature mentionsBioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
View all literature mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
View all literature mentionsDatabase that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.
View all literature mentionsSoftware package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsA unified data repository of the National Cancer Institute (NCI)'s Genomic Data Commons (GDC) that enables data sharing across cancer genomic studies in support of precision medicine. The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Cancer Genome Characterization Initiative (CGCI). The GDC Data Portal provides a platform for efficiently querying and downloading high quality and complete data. The GDC also provides a GDC Data Transfer Tool and a GDC API for programmatic access.
View all literature mentionsHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
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