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Related Concept Videos

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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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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RNA-seq03:21

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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. 
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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Ribosome Profiling02:24

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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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Data collection refers to a systematic way of obtaining, observing, measuring, and analyzing accurate information. Observational studies are one of the most widely used methods of data collection. It involves collecting data by observing the behavior and physical characteristics of a sample without making any modifications to the sample.
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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ShinyOmics: collaborative exploration of omics-data.

Defne Surujon1, Tim van Opijnen2

  • 1Biology Department, Boston College, Chestnut Hill, MA, 02467, USA. surujon@bc.edu.

BMC Bioinformatics
|January 19, 2020
PubMed
Summary
This summary is machine-generated.

ShinyOmics is a new web application designed for collaborative exploration of large omics datasets. This tool simplifies data analysis, visualization, and sharing for researchers without extensive programming experience.

Keywords:
Data integrationFunctional genomicsSystems biologyTranscriptomicsVisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Omics-profiling generates large biological datasets, posing challenges for manual analysis and interpretation.
  • Lack of programming experience and increasing data volume create hurdles in data management, storage, and sharing.

Purpose of the Study:

  • To present ShinyOmics, a web-based application for rapid, collaborative exploration of omics data.
  • To provide a user-friendly platform for analyzing complex biological datasets.

Main Methods:

  • Utilized Tn-Seq, RNA-Seq, microarray, and proteomics datasets from two human pathogens.
  • Developed a web-based application (ShinyOmics) for data visualization and comparative analysis.

Main Results:

  • Identified upregulated protease and chaperone proteins under aminoglycoside stress.
  • Demonstrated that antibiotics with similar mechanisms induce comparable transcriptomic responses.
  • Highlighted differences across various omics profiles and overlaid transcriptional data onto a metabolic network.

Conclusions:

  • ShinyOmics facilitates hypothesis generation through diverse visualization and comparison tools.
  • The application supports data management, online sharing, and exploration.
  • ShinyOmics serves as an interactive supplement for research articles and presentations.