Gene Expression Data Explorer
Info Gene counts are sourced from ARCHS4, which provides uniform alignment of GEO samples. You can learn more about ARCHS4 and its pipeline here.
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GROUP CONDITION SAMPLES
Diabetic foot
GSM3946485 GSM3946486 GSM3946487 GSM3946488 GSM3946489 GSM3946490 GSM3946491 GSM3946492
GSM3946500 GSM3946501 GSM3946502 GSM3946503 GSM3946504 GSM3946505
GSM3946493 GSM3946494 GSM3946495 GSM3946496 GSM3946497 GSM3946498 GSM3946499
Description

Submission Date: Jul 17, 2019

Summary: We performed RNA-seq on tissue biopsies derived from patients with DFUs and compared it to human oral and skin wounds to identify the molecular mechanisms and transcriptional networks that are deregulated in DFUs. Our results identified a unique inflammatory transcriptional signature unique to oral and skin wounds involved in promoting cell proliferation and cell survival of immune cells that are deficient in DFUs. In addition, we identified a signature immune-cell profile in which activation and proliferation of macrophages and neutrophils were absent in DFUs. These results suggest that a deregulated immune response in which impaired activation, proliferation and survival of immune cells contribute to pathogenesis of DFUs and provides novel avenues for development of therapies aimed at reprogramming DFUs into healing-competent wounds.

GEO Accession ID: GSE134431

PMID: 32938916

Description

Submission Date: Jul 17, 2019

Summary: We performed RNA-seq on tissue biopsies derived from patients with DFUs and compared it to human oral and skin wounds to identify the molecular mechanisms and transcriptional networks that are deregulated in DFUs. Our results identified a unique inflammatory transcriptional signature unique to oral and skin wounds involved in promoting cell proliferation and cell survival of immune cells that are deficient in DFUs. In addition, we identified a signature immune-cell profile in which activation and proliferation of macrophages and neutrophils were absent in DFUs. These results suggest that a deregulated immune response in which impaired activation, proliferation and survival of immune cells contribute to pathogenesis of DFUs and provides novel avenues for development of therapies aimed at reprogramming DFUs into healing-competent wounds.

GEO Accession ID: GSE134431

PMID: 32938916

Visualize Samples

Info Visualizations are precomputed using the Python package scanpy on the top 5000 most variable genes.

Precomputed Differential Gene Expression

Info Differential expression signatures are automatically computed using the limma R package. More options for differential expression are available to compute below.

Signatures:

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Control Condition

Perturbation Condition

Only conditions with at least 1 replicate are available to select

Differential Gene Expression Analysis
Info Differential expression signatures can be computed using DESeq2 or characteristic direction.
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Bulk RNA-seq Appyter

This pipeline enables you to analyze and visualize your bulk RNA sequencing datasets with an array of downstream analysis and visualization tools. The pipeline includes: PCA analysis, Clustergrammer interactive heatmap, library size analysis, differential gene expression analysis, enrichment analysis, and L1000 small molecule search.