Related Experiment Video
Updated: Jul 11, 2025
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
9.6K
Omic horizon expression: a database of gene expression based on RNA sequencing data
Yuzhe Hu1,2, Dong Xie3, Xixi Li1,2
1Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), School of Basic Medical Sciences, Peking University Health Science Center, No. 38 Xueyuan Road, Beijing, 100191, China.
BMC Genomics
|November 8, 2023
Summary
A new database, Omic Horizon Expression Database, offers comprehensive rat gene expression profiles from RNA sequencing data. This resource aids in understanding rat gene function and identifying novel genes for biomedical research.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Gene expression profiles are crucial for understanding gene function, yet rat data is less explored than human or mouse.
- Rat models are vital in biomedical research, necessitating better genomic resources.
Purpose of the Study:
- To create a comprehensive database of rat gene expression profiles.
- To facilitate the study of rat gene expression and function.
Main Methods:
- Analyzed over 2,700 RNA sequencing (RNA-Seq) samples across 48 tissues, 40 primary cell types, and 25 cell lines.
- Mapped data to the mRatBN7.2 rat genome reference.
- Developed the Omic Horizon Expression Database for querying gene expression.
Main Results:
- The Omic Horizon Expression Database provides expression profiles for over 25,000 rat genes.
- Supports queries using gene symbols, Ensemble IDs, and Entrez IDs.
- Enables expression profiling, comparison, and identification of novel rat genes.
Conclusions:
- The Omic Horizon Expression Database serves as a valuable omic resource for rat gene expression.
- Facilitates identification of rat genes and provides functional insights for research.
More Related Videos
Related Concept Videos
02:24Ribosome Profiling
3.5K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.5K
03:21RNA-seq
10.0K
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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
02:34DNA Microarrays
17.5K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
17.5K
02:15Experimental RNAi
6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K
01:42What is Gene Expression?
167.8K
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
167.8K
01:22MicroRNAs
3.0K
MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
3.0K