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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Related Experiment Video

Updated: Apr 17, 2026

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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CLIPdb: a CLIP-seq database for protein-RNA interactions.

Yu-Cheng T Yang1, Chao Di2, Boqin Hu3

  • 1MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. yang.thomas.yucheng@gmail.com.

BMC Genomics
|February 6, 2015
PubMed
Summary
This summary is machine-generated.

CLIPdb is a new database that consolidates RNA-binding protein (RBP) and RNA interaction data from numerous CLIP-seq studies. This resource enables unified analysis of RBP binding sites across different experiments to advance understanding of gene regulation.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA-binding proteins (RBPs) regulate gene expression by interacting with various RNA molecules.
  • Crosslinking immunoprecipitation (CLIP)-seq technologies generate high-resolution data on RBP binding sites across the transcriptome.

Purpose of the Study:

  • To create a comprehensive database, CLIPdb, for RBP-RNA interactions.
  • To provide a unified platform for analyzing and comparing CLIP-seq data.

Main Methods:

  • Compiled and annotated 395 CLIP-seq datasets for 111 RBPs across human, mouse, worm, and yeast.
  • Developed a unified computational method for identifying and comparing RBP binding sites.
  • Implemented a user-friendly interface with whole-genome visualization and data download capabilities.

Main Results:

  • Established CLIPdb, a centralized resource for RBP-RNA interaction data.
  • Enabled consistent identification and comparison of RBP binding sites across diverse studies.
  • Facilitated visualization and retrieval of RBP binding site information for protein-coding and non-coding genes.

Conclusions:

  • CLIPdb provides curated metadata and uniformly identified binding sites, forming a foundation for integrative analyses.
  • The database will be a valuable resource for understanding post-transcriptional regulatory networks.
  • Ongoing updates and functional improvements will enhance its utility for researchers.