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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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Integration by Parts: Indefinite Integrals01:26

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Integration by parts is a fundamental technique in calculus for evaluating integrals involving the product of two functions. It is particularly useful when direct integration is not feasible. The method is based on the product rule for differentiation, which states that the derivative of a product equals the derivative of the first function times the second, plus the first function times the derivative of the second. By integrating this identity and rearranging terms, the integration by parts...
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Integration by Parts: Definite Integrals01:23

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Definite integrals involving the product of two functions over a fixed interval can be evaluated using integration by parts. This method rewrites the integral as the difference of a product evaluated at the endpoints and a remaining definite integral that is often simpler to compute.A representative example is the definite integral of the inverse tangent function. Since there is no direct integration formula for arctan ⁡x, the integrand is rewritten as a product of arctan⁡ x and the...
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Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
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How Data are Classified: Categorical Data01:11

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A variable, usually notated by capital letters such as X and Y, is a characteristic or measurement that can be determined for each member of a population. Data are the actual values of variables. They may be numbers, or they may be words. Datum is a single value.
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How Data are Classified: Numerical Data00:59

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Data that are countable or measurable in specific units are called numerical or quantitative data. Quantitative data are always numbers. Quantitative data are the result of counting or measuring the attributes of a population. Amount of money, pulse rate, weight, number of people living in a town, and number of students who opt for statistics are examples of quantitative data.
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The jPOST environment: an integrated proteomics data repository and database.

Yuki Moriya1, Shin Kawano1, Shujiro Okuda2

  • 1Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan.

Nucleic Acids Research
|October 9, 2018
PubMed
Summary
This summary is machine-generated.

The jPOST database integrates mass spectrometry proteomics data. It provides standardized analysis and tools for comparing datasets, facilitating research across institutions.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Data Science

Background:

  • Mass spectrometry (MS)-based proteomics is rapidly advancing, generating large, high-quality datasets.
  • Integrating diverse proteomics datasets from various projects and institutions presents a significant challenge.
  • Standardized data repositories and analysis platforms are crucial for advancing the field.

Purpose of the Study:

  • To establish a standardized repository and database for mass spectrometry proteomics data.
  • To facilitate the integration and reanalysis of proteomics datasets from multiple sources.
  • To provide tools for comparative analysis and visualization of post-translational modifications and proteoforms.

Main Methods:

  • Development of jPOST (Japan ProteOme STandard Repository/Database).
  • Establishment of jPOSTrepo for data submission and storage (over 10 TB accepted).
  • Implementation of standardized reanalysis protocols for datasets within jPOSTdb.
  • Development of viewers for post-translational modifications, phosphorylation site co-occurrence, and peptide sharing.
  • Integration of basic statistical analysis tools for dataset comparison.

Main Results:

  • jPOSTrepo has successfully collected over 10 TB of MS-based proteomics data.
  • jPOSTdb provides reanalyzed datasets with standardized protocols, enhancing data comparability.
  • Novel viewers enable visualization of complex proteomic features like post-translational modifications and proteoform sharing.
  • Statistical tools allow for effective comparison of different proteomics datasets.

Conclusions:

  • The jPOST project provides a vital resource for integrating and analyzing large-scale proteomics data.
  • Standardized data handling and analysis in jPOSTdb improve the accessibility and utility of published proteomics datasets.
  • The developed tools support deeper insights into post-translational modifications and proteoform dynamics, advancing proteomics research.