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Related Concept Videos

Proteomics01:33

Proteomics

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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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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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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Ribosome Profiling02:24

Ribosome Profiling

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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.
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...
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What is Gene Expression?01:36

What is Gene Expression?

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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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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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DNA Microarrays02:34

DNA Microarrays

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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...
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Updated: Apr 20, 2026

Combined Nucleotide and Protein Extractions in Caenorhabditis elegans
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Combined Nucleotide and Protein Extractions in Caenorhabditis elegans

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Beyond protein expression, MOPED goes multi-omics.

Elizabeth Montague1, Imre Janko2, Larissa Stanberry1

  • 1Bioinformatics and High-Throughput Analysis Laboratory, Center for Developmental Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA 98101 High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, WA, USA 98101 CDO Analytics, Seattle Children's, Seattle, WA, USA 98101 Data-Enabled Life Sciences Alliance (DELSA Global), Seattle, WA, USA 98101.

Nucleic Acids Research
|November 19, 2014
PubMed
Summary
This summary is machine-generated.

The Multi-Omics Profiling Expression Database (MOPED) now integrates gene, protein, and pathway expression data for multiple organisms. This enhanced resource offers improved data quality, advanced searching, and visualizations for biological research.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Proteomics

Background:

  • The Multi-Omics Profiling Expression Database (MOPED) was initially a protein expression database.
  • There is a growing need for integrated multi-omics data resources in biological research.

Purpose of the Study:

  • To transition MOPED into a comprehensive multi-omics resource.
  • To enhance data quality, consistency, and usability for researchers.
  • To provide integrated gene, protein, and pathway expression data.

Main Methods:

  • Developed a web-based interface for accessing consistently processed multi-omics data.
  • Integrated metadata on experimental design and analysis methods.
  • Linked genes, proteins, pathways, and experiments for comprehensive data exploration.

Main Results:

  • MOPED now includes over 5 million records for approximately 75,000 genes and 50,000 proteins across four organisms (human, mouse, worm, yeast).
  • Introduced new features: pathway expression, Pathway Details pages, experimental metadata checklists, and advanced searching tools.
  • Implemented visualizations for comparing diverse data types.

Conclusions:

  • MOPED has successfully evolved into a robust multi-omics database.
  • The enhanced MOPED facilitates integrated analysis of gene, protein, and pathway expression data.
  • Future development will expand organism coverage and disease-related connections.