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Related Concept Videos

General Transcription Factors01:30

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Predictive Immune Modeling of Solid Tumors
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Predicting tissue-specific expressions based on sequence characteristics.

Hyojung Paik1, Taewoo Ryu, Hyoung-Sam Heo

  • 1Plant Systems Engineering Center, KRIBB, Daejeon, Korea.

BMB Reports
|April 29, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to predict tissue-specific gene expression in humans using sequence features. The approach accurately classifies tissue-specific genes, improving upon previous methods.

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Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue
17:38

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue

Published on: April 27, 2012

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding tissue-specific gene expression is crucial for interpreting protein function and tissue differentiation in multicellular organisms.
  • Housekeeping (HK) and tissue-specific (TS) genes exhibit distinct expression patterns that are key to cellular function.

Purpose of the Study:

  • To develop and validate a novel prediction approach for classifying tissue-specific gene expression in humans.
  • To leverage sequence-derived features, including overrepresented patterns in HK and TS genes, for improved classification accuracy.

Main Methods:

  • Generated sequence features from overrepresented patterns in housekeeping and tissue-specific genes.
  • Utilized tissue-specific domains and transcriptional factor binding sites (TFBSs) as predictive features.
  • Employed a Random Forest algorithm, scoring exclusive patterns based on biological insights into gene regulation and function.

Main Results:

  • The developed prediction approach demonstrated superior performance compared to existing methods.
  • Sequence characteristics, including TFBSs and TS domains, effectively served as indices for expressed tissues.
  • The model's efficacy was confirmed through both computational simulations and experimental validation.

Conclusions:

  • The novel sequence-feature-based approach provides a robust method for predicting tissue-specific gene expression in humans.
  • This advancement aids in understanding protein function and tissue differentiation by accurately identifying tissue-specific genes.
  • The validated method offers a valuable tool for genomic and molecular biology research.