Guide

Use Cases

Five step-by-step examples showing how to answer real scientific questions with DKDM. Each example links directly to the relevant tools so you can follow along.

1

Find dysregulated pathways in podocytes

Question: Which signaling pathways are significantly enriched in podocytes, and which genes drive that enrichment?

Podocytes are specialized epithelial cells of the glomerular filtration barrier and a primary site of injury in DKD. Identifying enriched pathways helps pinpoint the signaling programs most active in this cell type.

Steps

  1. Go to the Pathway Explorer page.
  2. Ensure Browse by Cell Type mode is selected.
  3. Select Podocyte Cell from the dropdown.
  4. Set the FDR filter to FDR ≤ 0.05 (or stricter if desired).
  5. Review the ranked pathway list. The top results include inflammatory pathways such as Interleukin-6 signaling, Interleukin-27 signaling, and Signaling by Leptin, along with AKT phosphorylates targets in the cytosol.
  6. Click Show next to any pathway to reveal the overlapping genes. Each gene links to the Gene Search page for deeper investigation.
  7. Click the pathway name link to open the full pathway page in Reactome or KEGG for complete context.
Open Pathway Explorer →
2

Identify hub genes in proximal tubule cells

Question: Which genes are the most central hubs in the proximal tubule cell signaling network, and what are their roles?

Hub genes — those with high network centrality — often represent critical regulatory nodes and potential therapeutic targets. The proximal tubule is a major site of DKD-related injury and metabolic dysregulation.

Steps

  1. Go to the Gene Search page.
  2. Search for ALB (rank #1 in proximal tubule centrality). The centrality table shows its rank, degree, betweenness, and PageRank scores across all cell types where it appears.
  3. Next, search for TP53 (rank #2), TGFB1 (rank #3), HIF1A (rank #4), and BCL2 (rank #5) to explore the top hub genes in proximal tubule cells.
  4. For each gene, check the Cell types section to see which other cells contain it, and click a cell type link to open its Dynamic DKDM network.
  5. Use the External links (NCBI Gene, UniProt, Open Targets) to investigate druggability and disease associations.
  6. Check the Associated pathways section to see which enriched pathways each hub gene participates in.
Search ALB (PT hub #1) → Search TP53 (#2)
3

Find cell communication via a specific ligand

Question: Which kidney cell types produce VEGFA as a signaling ligand, and which cells receive the signal?

VEGFA is a key angiogenic factor implicated in DKD-associated vascular changes. Understanding which cells send VEGFA signals and which cells bear the receptors reveals the intercellular communication architecture.

Steps

  1. Go to the Gene Search page and search for VEGFA.
  2. In the result, look at the Cell–cell communication role section. VEGFA acts as a ligand in 12 cell populations including podocytes, mesangial cells, endothelial cells, and proximal tubule cells.
  3. Check the Present in section to see all 13 cell types containing VEGFA, with links to open each in Dynamic DKDM.
  4. Click the UniProt external link to access the full protein annotation, including known receptors.
  5. To explore the full ligand–receptor network visually, open the Cell–Cell Interaction Map and download the CSV to filter for VEGFA-specific interactions.
Search VEGFA → Open CCI Map
4

Discover miRNA regulation of a gene

Question: Which miRNAs regulate HIF1A in DKD, and what experimental evidence supports these interactions?

HIF1A is a central hypoxia-responsive transcription factor and a top hub gene in multiple kidney cell types. Identifying its miRNA regulators reveals the post-transcriptional layer controlling its expression.

Steps

  1. Go to the Gene Search page and search for HIF1A.
  2. Scroll to the miRNA regulation section. You will see 4 experimentally validated miRNA interactions plus 1 predicted-only interaction.
  3. The validated table shows: hsa-miR-142-5p (luciferase assay, PMID 28069592), hsa-miR-199a-5p (luciferase assay, PMID 21847633), hsa-miR-199b-5p (luciferase assay, PMID 21557766), and hsa-miR-429 (qRT-PCR, PMID 25550463).
  4. Click any PMID link to open the original publication in PubMed.
  5. Check the Network centrality section to see that HIF1A is rank #4 in proximal tubule cells — a major hub under miRNA control.
  6. For the full miRNA–target network, open the miRNA–Target Regulatory Network map.
Search HIF1A → Open miRNA Map
5

Explore the ODE model of a cell type

Question: What does the dynamic signaling network of mesangial cells look like, and how can I find a specific gene within it?

Mesangial cells provide structural support to the glomerulus and are key players in DKD fibrosis. The Dynamic DKDM app lets you interactively explore their ODE model.

Steps

  1. Go to the Cell Types page and click Mesangial Cells, or go directly to the Mesangial Cell network in Dynamic DKDM.
  2. The interactive network graph loads, showing all molecular species (genes, proteins, RNA) as nodes and regulatory interactions as edges.
  3. Use the search bar at the top to type a gene symbol (e.g., TGFB1). Matching nodes are highlighted with an orange border and centered in the view; non-matching nodes are dimmed.
  4. Click any node to open the detail panel, showing the clean gene symbol, species type, and external database links (NCBI Gene, UniProt, HGNC, Open Targets).
  5. Use the filter controls to show only genes, only proteins, or only RNA species.
  6. Click Download SBML to export the model for simulation in COPASI, tellurium, or other SBML-compatible tools.
Open Mesangial Cell network → Browse all cell types