Spatial Differential Expression Analysis Service

You have mapped your tissue. You know where the cells are. Now, the critical question is: How does their location change their behavior?

Our Spatial Differential Expression Analysis service moves beyond simple mapping to statistically quantify how gene expression varies across different tissue architectures. We help you define biological niches, compare distinct anatomical regions, and uncover the molecular drivers of health and disease.

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Why different
Workflow
Deliverables
Applications
FAQs

Why Spatial DE is Different

Standard differential expression (like in bulk or single-cell RNA-seq) treats cells as independent entities. Spatial DE is context-aware.

We do not just ask, "What makes these cells different?" We ask, "What makes these cells in this specific neighborhood different?"

Key Capabilities

Region-of-Interest (ROI) Comparison: Compare gene expression between manually defined histological regions (e.g., Tumor Core vs. Invasive Margin, or Cortical Layers vs. White Matter).
Condition-Based Spatial Analysis: Compare the same spatial region across different samples (e.g., Glomeruli in Healthy Kidney vs. Glomeruli in Diabetic Kidney).
Gradient & Trajectory Analysis: Identify genes that change expression progressively as they move away from a specific structure (e.g., distance from a blood vessel or necrotic core).

Workflow

workflow of spatial DE analysis

Deliverables

We provide publication-ready figures and comprehensive data files, including:

Spatially-Aware Volcano Plots: Highlighting significant up/down-regulated genes between regions.
Regional Heatmaps: Gene expression clustering grouped by anatomical annotation.
Feature Plots: Side-by-side visualization of H&E morphology and gene expression overlays.
Enrichment Tables: Ranked lists of pathways and biological processes active in each region.
Comprehensive Report: A detailed summary of methods, statistical parameters, and key findings.

Applications

Oncology: Dissect tumor heterogeneity and identify resistance markers in the tumor microenvironment (TME).
Neuroscience: Profile distinct cortical layers or identify stress responses surrounding plaques/lesions.
Immunology: Analyze "interaction zones" where immune cells directly contact disease tissue.
Development: Map gene expression gradients relative to signaling centers.

FAQs

Can I request customized analysis?

Yes, we offer highly customizable data analysis pipelines tailored to specific research needs, including in-depth gene set analysis, pathway mapping, and more.

Do I need to provide the histological annotations (regions of interest)?

Ideally, yes. The most biologically meaningful results come when a pathologist or researcher defines the regions (e.g., circling the necrotic core, the invasive margin, and healthy tissue) using the 10x Loupe Browser or similar software.

If you cannot provide annotations, we can perform unsupervised clustering based purely on gene expression to define "molecular regions" for you, which you can then verify against the H&E image.

What is the typical turnaround time?

Our Standard turnaround time is 3-4 weeks from sample receipt to final report delivery. Project timelines vary with sample number and complexity

Learn about other Q&A.

* For Research Use Only. Not for use in diagnostic procedures.

Our customer service representatives are available 24 hours a day, 7 days a week. Inquiry

From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.

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