Recently, accumulating evidence has supported that circular RNA (circRNA) plays important roles in tumorigenesis by regulating gene expression at transcriptional and post-transcriptional levels. Expression of circRNAs can be epigenetically silenced by DNA methylation; however, the underlying regulatory mechanisms of circRNAs ...
Read More »TCGA2BED – extracting, extending, integrating, and querying The Cancer Genome Atlas
Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of ...
Read More »RNA-Seq no longer required – a new machine learning-based model predicts gene expression as a consequence of epigenetic modification
from Lung Cancer News Today by Patricia Silva Researchers at Johns Hopkins University and the University of Hawaii created a model based on epigenomics data capable of predicting differential gene expression in lung cancer. The study was recently published in ...
Read More »PD_NGSAtlas – a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders
Psychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BP) are projected to lead the global disease burden within the next decade. Several lines of evidence suggest that epigenetic- or genetic-mediated dysfunction is frequently present in these disorders. To date, ...
Read More »A protocol for RNA methylation differential analysis with MeRIP-Seq data
Despite the prevalent studies of DNA/Chromatin related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m6A) ...
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