Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Signal Sequences and Sorting Receptors

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...

Ribosome Profiling

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...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in <i>Talaromyces marneffei</i>-infected THP-1 macrophage.

PeerJ·2021

Same author

Single-cell RNA-seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs.

Reproduction in domestic animals = Zuchthygiene·2021

Same author

Effects of the histone acetylase inhibitor C646 on growth and differentiation of adipose-derived stem cells.

Cell cycle (Georgetown, Tex.)·2021

Same author

A Method for Estimating 24-Hour Urinary Sodium Excretion by Casual Urine Specimen in Chinese Hypertensive Patients.

American journal of hypertension·2021

Same author

<i>Scutellaria baicalensis</i> extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease <i>in vitro</i>.

Journal of enzyme inhibition and medicinal chemistry·2021

Same author

Frequent reassortment and potential recombination shape the genetic diversity of influenza D viruses.

The Journal of infection·2021

Search research articles

Related Experiment Video

Updated: Dec 13, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Significance-Based Essential Protein Discovery.

Yan Liu, Hao Liang, Quan Zou

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|August 6, 2020

Summary

This summary is machine-generated.

Identifying essential proteins is crucial. A new method, SigEP, uses statistical significance testing to accurately identify essential proteins in biological networks, overcoming limitations of existing approaches.

More Related Videos

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Related Experiment Videos

Last Updated: Dec 13, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

Bioinformatics
Computational Biology
Network Science

Background:

Identifying essential proteins is vital for understanding cellular functions.
Existing centrality measures have limitations in interpretability and threshold setting.
Current methods lack statistically sound quality control for essential protein identification.

Purpose of the Study:

To develop a statistically rigorous method for essential protein discovery.
To address limitations of existing centrality-based approaches.
To introduce a significance testing framework for identifying essential proteins.

Main Methods:

Formulated essential protein discovery as a multiple hypothesis testing problem.
Developed a p-value calculation using degree and local clustering coefficient.
Employed the Erdös-Rényi model as a random graph model.
Utilized the false discovery rate for multiple testing correction.

Main Results:

Introduced SigEP, a significance-based essential protein discovery method.
Demonstrated superior performance compared to competing algorithms on simulated and real PPI networks.
Provided a statistically sound approach for essential protein identification.

Conclusions:

SigEP offers a robust and interpretable method for essential protein discovery.
The significance testing perspective overcomes key limitations of traditional centrality measures.
SigEP enhances the reliability of essential protein identification in bioinformatics.