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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
RNA-seq03:21

RNA-seq

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. 
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Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Networks02:26

Protein Networks

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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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...

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RNA-Seq Analysis of Differential Gene Expression in Electroporated Chick Embryonic Spinal Cord
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Recounting the FANTOM CAGE-Associated Transcriptome.

Eddie Luidy Imada1,2, Diego Fernando Sanchez1, Leonardo Collado-Torres3

  • 1Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21827, USA.

Genome Research
|February 22, 2020
PubMed
Summary
This summary is machine-generated.

The FC-R2 atlas provides a comprehensive map of human gene expression, including long noncoding RNAs (lncRNAs). This resource aids in understanding gene roles in health and disease, particularly in cancer.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Molecular Biology

Background:

  • Long noncoding RNAs (lncRNAs) are crucial regulators of biological processes.
  • Understanding lncRNA expression is vital for elucidating their roles in human health and disease.
  • Existing resources often have limited gene annotation, hindering comprehensive analysis.

Purpose of the Study:

  • To present FC-R2, an extensive human transcriptome expression atlas.
  • To expand gene annotation beyond coding genes to include over 109,000 noncoding genes.
  • To demonstrate the utility of FC-R2 for biological and disease-related research.

Main Methods:

  • Developed FC-R2, a comprehensive expression atlas based on the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study.
  • Integrated over 109,000 coding and noncoding genes, significantly extending the recount2 resource.
  • Utilized the atlas to analyze gene expression profiles across normal and diseased human samples.

Main Results:

  • Identified tissue-specific transcription patterns for various coding and noncoding genes.
  • Performed differential expression analysis in thirteen cancer types, revealing novel noncoding genes in tumorigenesis.
  • Confirmed the prognostic significance of enhancer lncRNA expression in cancer patients.

Conclusions:

  • The FC-R2 atlas offers a powerful resource for systematic lncRNA characterization.
  • With over 70,000 samples, FC-R2 facilitates research into the functions of coding genes and novel lncRNAs.
  • This atlas is instrumental for advancing our understanding of gene function in human biology and disease.