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

You might also read

Related Articles

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

Sort by
Same author

HuBMAP Data Portal: A Resource for Multimodal Spatial and Single-Cell Data of Healthy Human Tissues.

ArXiv·2026
Same author

Safire: Similarity Framework for Visualization Retrieval.

IEEE Visualization Conference : VIS. IEEE Conference on Visualization·2026
Same author

SpatialQuery: scalable discovery and molecular characterization of multicellular motifs from spatial omics data.

bioRxiv : the preprint server for biology·2026
Same author

<i>scellop:</i> a scalable redesign of cell population plots for single-cell data.

Bioinformatics advances·2026
Same author

SenNet Portal: Build, Optimization and Usage.

bioRxiv : the preprint server for biology·2026
Same author

Lack of synergy between AR-targeted therapies and PARP inhibitors in homologous recombination-proficient prostate cancer.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 13, 2025

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.5K

Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.

Sehi L'Yi1, Mark S Keller1, Ariaki Dandawate2

  • 1Department of Biomedical Informatics, Harvard Medical School.

Bioinformatics (Oxford, England)
|January 23, 2023
PubMed
Summary
This summary is machine-generated.

Cistrome Explorer is a new tool for visualizing gene regulation. It helps researchers discover patterns in cis-regulatory elements (CREs) and transcription factor binding across many cell types.

More Related Videos

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells
10:10

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

2.5K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

409.5K

Related Experiment Videos

Last Updated: Aug 13, 2025

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
05:12

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

11.5K
Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells
10:10

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

2.5K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

409.5K

Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Gene regulation by cis-regulatory elements (CREs) is complex and varies across cell types.
  • Analyzing large datasets of chromatin profiles is crucial for understanding these variations.
  • Integrating visual and computational methods can yield significant biological insights.

Purpose of the Study:

  • To develop an interactive visual analytics tool for exploring chromatin profiles.
  • To facilitate the discovery of patterns in CREs and their associated transcription factor binding.
  • To provide a user-friendly platform for analyzing diverse cell type data.

Main Methods:

  • Development of Cistrome Explorer, a web-based visual analytics tool.
  • Integration with the Cistrome Data Browser, containing thousands of ChIP-seq, DNase-seq, and ATAC-seq samples.
  • Utilizing interactive visualization for exploring patterns across diverse cell types.

Main Results:

  • Cistrome Explorer enables exploration of thousands of chromatin profiles.
  • The tool facilitates the discovery of CRE patterns across different cell types.
  • Identification of transcription factor binding sites underlying observed CRE patterns is enabled.

Conclusions:

  • Cistrome Explorer is a valuable resource for researchers studying gene regulation.
  • The tool enhances the ability to uncover cell-type-specific regulatory mechanisms.
  • Visual analytics combined with large datasets offers powerful insights into genomic regulation.