ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) has been developed to explore the regulatory networks between transcription factors and genes (proteins, lncRNAs, miRNAs, snoRNAs, tRNAs... ). ChIPBase v2.0 integrated ~10,200 curated ChIP-seq datasets. We identified thousands of Binding Motif Matrices and their binding sites from ChIP-seq data of DNA-binding proteins and predicted millions of transcriptional regulatory relationships between transcription factors and genes. We constructed “Regulator” module to predict hundreds of transcription factors that were involved in or affected transcription of ncRNAs and protein-coding genes. Moreover, we built a web-based tool, Co-Expression, to explore the co-expression patterns between DNA-binding proteins and various types of genes by integrating the gene expression profiles of ~10,000 tumor samples and ~9,100 normal tissues or cell lines. ChIPBase also provides a ChIP-Function tool and a genome browser to predict functions of diverse genes and visualize various ChIP-seq data. This study will greatly expand our understanding of the transcriptional regulations of ncRNAs and protein-coding genes.
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by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
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05-06-2024, 07:48 AM -
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by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
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