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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
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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.
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Human Genetics01:28

Human Genetics

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Genes and Diseases: Insights from Transcriptomics Studies.

Dmitry S Kolobkov1, Darya A Sviridova1, Serikbai K Abilev1

  • 1The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.

Genes
|July 27, 2022
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Summary
This summary is machine-generated.

This study reveals that differentially expressed (DE) genes, particularly those linked to diseases, are often highly expressed in specific tissues. Understanding gene expression patterns aids in clarifying genotype-phenotype relationships and disease development.

Keywords:
differential expression (DE)disease genesgene expression omnibus (GEO)gene ontology (GO)human phenotype ontology (HPO)transcriptomics analysis of healthy tissues

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Area of Science:

  • Genomics
  • Transcriptomics
  • Human Disease Genetics

Background:

  • Differential gene expression (DE) studies are crucial for understanding genotype-phenotype relationships.
  • A significant number of genes are consistently identified as DE across various biological contexts, necessitating further investigation.
  • Existing research highlights the need for deeper analysis into the links between gene expression, differential expression, and human diseases.

Purpose of the Study:

  • To investigate the relationship between gene expression patterns in healthy tissues and disease association.
  • To analyze the transcriptomic profiles of disease-associated genes versus non-disease genes.
  • To explore the functional enrichment of differentially expressed genes and their connection to human phenotypes.

Main Methods:

  • Compiled a comprehensive dataset of 9972 disease genes from five major gene-phenotype databases and an immunological society report.
  • Utilized transcriptomic data from the Human Protein Atlas (HPA) for healthy tissues.
  • Employed Enrichr libraries to analyze the correlation between healthy tissue gene expression and occurrence in Gene Expression Omnibus (GEO) series, annotating with Gene Ontology (GO) and Human Phenotype Ontology (HPO) terms.

Main Results:

  • Validated findings that disease genes exhibit higher expression in pathologically relevant tissues.
  • Identified that preferentially DE genes are typically highly expressed in one or more tissues and are enriched for disease-associated genes.
  • GO enrichment analysis revealed that both up- and down-regulated DE genes are frequently involved in immune response, translation, and tissue-specific biological processes.
  • Established a correlation between DE-related pathologies and the diversity of HPO terms.

Conclusions:

  • Transcriptomic analysis of healthy tissues provides a valuable approach to understanding disease gene behavior.
  • Highly expressed genes in specific tissues are often linked to diseases, offering insights into their underlying mechanisms.
  • The study underscores the importance of integrating gene expression data with phenotypic information for a comprehensive understanding of human diseases and their progression.