Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

12.7K
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.7K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

13.8K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
13.8K

You might also read

Related Articles

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

Sort by
Same author

Microglia up‑regulate thromboxane A2 synthesis genes in response to C6 glioma‑conditioned medium.

Acta neurobiologiae experimentalis·2026
Same author

Defining functional states and roles of microglia in neuropsychiatric disorders.

Frontiers in cellular neuroscience·2026
Same author

In Vitro Reduction of Extractable Zearalenone and Screening of Tentative Transformation Products by <i>Metschnikowia pulcherrima</i> KKP 1368 Under Selected Buffered pH Conditions Relevant to the Porcine Gastrointestinal Tract.

Toxins·2026
Same author

Comparison of zero-contrast left atrial appendage occlusion to contrast-guided left atrial appendage occlusion.

Kardiologia polska·2026
Same author

Consensus statement on microglial and macrophage functions in gliomas.

Acta neuropathologica·2026
Same author

Chitinase-3-like protein 1 depletion in glioma cells alters tumor microenvironment and normalizes neovasculature in human glioma xenografts.

Cell communication and signaling : CCS·2026

Related Experiment Video

Updated: Apr 13, 2026

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

17.4K

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data.

Michal Dabrowski1, Norbert Dojer2, Izabella Krystkowiak3

  • 1Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Pasteura 3, Warszawa, 02-093, Poland. m.dabrowski@nencki.gov.pl.

BMC Bioinformatics
|May 1, 2015
PubMed
Summary
This summary is machine-generated.

This study compares methods for identifying transcription factor binding sites. Public databases and community-developed tools offer superior performance over commercial options, with a common false-positive rate providing the most accurate predictions.

More Related Videos

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.8K
Chromatin Immunoprecipitation of Murine Brown Adipose Tissue
07:50

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

8.7K

Related Experiment Videos

Last Updated: Apr 13, 2026

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip DAP-chip Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

17.4K
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

9.8K
Chromatin Immunoprecipitation of Murine Brown Adipose Tissue
07:50

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

8.7K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Transcription factor (TF) binding preferences are traditionally modeled using motifs (e.g., position weight matrices).
  • Numerous motif models exist, but optimal methods for identifying TF binding sites in genomes remain unclear.
  • Experimental TF-ChIP-seq data provides a basis for comprehensive analysis.

Purpose of the Study:

  • To comprehensively analyze and compare methods for identifying transcription factor binding sites.
  • To evaluate the quality and coverage of TF motif models across different databases.
  • To benchmark the performance of various motif scanning tools and thresholding strategies.

Main Methods:

  • Comparative analysis of TF motif models from public and commercial databases.
  • Benchmarking of different motif scanning tools using experimental TF-ChIP-seq datasets.
  • Calculation and comparison of motif detection thresholds to optimize prediction accuracy.
  • Evaluation of thresholding strategies based on false-positive rates.

Main Results:

  • Public databases offer comparable TF coverage and superior motif performance to commercial databases.
  • Scientific community-developed motif scanners outperform commercial tools.
  • Optimizing prediction accuracy involves calculating motif-specific detection thresholds.
  • A common false-positive rate yields the most uniformly accurate and least biased predictions across motifs.

Conclusions:

  • This study provides a guide for researchers using TF motifs, based on comprehensive analysis.
  • Recommendations are offered for selecting optimal motif models, scanners, and thresholding strategies.
  • Benchmark datasets and detailed results are available to aid researchers.