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 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...-
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04-22-2024, 07:01 AM -
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by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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04-04-2024, 04:25 PM -
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