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

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...

What is Gene Expression?

What is Gene Expression?

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...

DNA Microarrays

DNA Microarrays

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...

Reporter Genes

Reporter Genes

Reporter genes are a type of protein-coding gene that are often tagged to a gene of interest. Once inside a target cell, reporter genes usually produce visually identifiable characteristics like fluorescence and luminescence when expressed along with the gene of interest. Thus, reporter genes “report” the presence or absence of genes of interest in an organism, determine the gene expression pattern, or track the physical location of a DNA segment or protein in the cell.

Cell Specific Gene Expression

Cell Specific Gene Expression

You might also read

Related Articles

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

Sort by

Same author

Connectivity Regression.

Biostatistics (Oxford, England)·2025

Same author

Robust Bayesian graphical regression models for assessing tumor heterogeneity in proteomic networks.

Biometrics·2025

Same author

Evaluating Immune Checkpoint Blockade in Metastatic Castration-Resistant Prostate Cancers with Deleterious CDK12 Alterations in the Phase 2 IMPACT Trial.

Clinical cancer research : an official journal of the American Association for Cancer Research·2024

Same author

Optimizing Precision Medicine for Breast Cancer Brain Metastases with Functional Drug Response Assessment.

Cancer research communications·2023

Same author

Bayesian hierarchical quantile regression with application to characterizing the immune architecture of lung cancer.

Biometrics·2022

Same author

Integrative Bayesian models using Post-selective inference: A case study in radiogenomics.

Biometrics·2022

Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026

Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026

Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026

Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026

Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026

Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 27, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

SpaceX: gene co-expression network estimation for spatial transcriptomics.

Satwik Acharyya¹, Xiang Zhou¹, Veerabhadran Baladandayuthapani¹

¹Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.

Bioinformatics (Oxford, England)

|September 30, 2022

Summary

This summary is machine-generated.

We developed SpaceX, a Bayesian method to find gene co-expression patterns in spatial transcriptomics data. This tool enhances biological discovery by revealing spatially dependent gene networks in tissues.

More Related Videos

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Published on: January 13, 2019

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Related Experiment Videos

Last Updated: Aug 27, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Published on: January 13, 2019

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Spatially resolved transcriptome analysis reveals cellular interactions and transcriptional regulation.
Gene-gene co-expression patterns within distinct tissue locations are crucial for understanding spatial co-regulatory networks.
Existing methods often focus on single gene analysis, limiting the discovery of complex spatial interactions.

Purpose of the Study:

To develop a statistical framework for detecting gene co-expression patterns in spatially structured tissues.
To enhance the capabilities of spatial transcriptomics technologies for biological discovery.
To identify shared and cluster-specific co-expression networks across different cell types or tissue domains.

Main Methods:

Development of SpaceX (spatially dependent gene co-expression network), a Bayesian methodology.
Utilizing an over-dispersed spatial Poisson model combined with a high-dimensional factor model for efficiency.
Incorporating dimension reduction techniques for computational performance.

Main Results:

SpaceX accurately estimates co-expression networks and structures by accounting for spatial correlation and noise.
Analysis of mouse hypothalamus data identified hub genes related to cognitive abilities.
Analysis of human breast cancer data revealed cancer-associated genes, including the collagen family, in tumor regions.

Conclusions:

SpaceX provides a robust statistical framework for analyzing spatial transcriptomics data.
The method effectively identifies biologically relevant gene co-expression patterns in complex tissues.
SpaceX advances the potential of spatial transcriptomics for uncovering novel biological insights.