GeneHarmony: A Knowledge-Based Tool for Biomarker Discovery in Disease: Sjögren’s Disease vs. Rheumatoid Arthritis and Systemic Lupus Erythematosus
Abstract
1. Introduction
2. Results
Data Usage and Application Results
3. Discussion
4. Methods
4.1. Database Architecture and Data Collection
4.2. Download and Usage
4.3. Application: Utilizing GeneHarmony for Cross-Disease Gene Association Analysis
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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KEGG Pathway a | Pathway ID b | Total # Genes c | # Genes Included in Network d | Genes Included from Analysis in Network e | FDR f |
---|---|---|---|---|---|
Antifolate resistance | hsa01523 | 31 | 2 | IL6; TNF | 0.0017 |
Graft-versus-host disease | hsa05332 | 36 | 2 | IL6; TNF | 0.0021 |
African trypanosomiasis | hsa05143 | 36 | 2 | IL6; TNF | 0.0021 |
Primary immunodeficiency | hsa05340 | 37 | 2 | CD4; CD8A | 0.0021 |
Inflammatory bowel disease | hsa05321 | 59 | 3 | IL6; IL17A; TNF | 6.91 × 10−5 |
Rheumatoid arthritis | hsa05323 | 83 | 4 | IL6; IL17A; TNF; TNFSF13B | 4.13 × 10−6 |
Antigen processing and presentation | hsa04612 | 64 | 3 | CD4; CD8A; TNF | 7.29 × 10−5 |
Intestinal immune network for IgA production | hsa04672 | 43 | 2 | IL6; TNFSF13B | 0.0024 |
Hematopoietic cell lineage | hsa04640 | 90 | 4 | CD4; CD8A; IL6; TNF | 4.13 × 10−6 |
Malaria | hsa05144 | 46 | 2 | IL6; TNF | 0.0025 |
Legionellosis | hsa05134 | 55 | 2 | IL6; TNF | 0.0034 |
IL-17 signaling pathway | hsa04657 | 91 | 3 | IL6; IL17A; TNF | 0.00017 |
Yersinia infection | hsa05135 | 124 | 4 | CD4; CD8A; IL6; TNF | 4.92 × 10−6 |
T cell receptor signaling pathway | hsa04660 | 100 | 3 | CD4; CD8A; TNF | 0.00019 |
Th17 cell differentiation | hsa04659 | 99 | 3 | CD4; IL6; IL17A | 0.00019 |
Pertussis | hsa05133 | 73 | 2 | IL6; TNF | 0.0055 |
Hypertrophic cardiomyopathy | hsa05410 | 88 | 2 | IL6; TNF | 0.0075 |
Systemic lupus erythematosus | hsa05322 | 94 | 2 | TNF; TRIM21 | 0.0082 |
AGE-RAGE signaling pathway in diabetic complications | hsa04933 | 96 | 2 | IL6; TNF | 0.0082 |
Viral protein interaction with cytokine and cytokine receptor | hsa04061 | 96 | 2 | IL6; TNF | 0.0082 |
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Beckman, M.F.; Alexander, A.; Mougeot, J.-L.C.; Bahrani Mougeot, F. GeneHarmony: A Knowledge-Based Tool for Biomarker Discovery in Disease: Sjögren’s Disease vs. Rheumatoid Arthritis and Systemic Lupus Erythematosus. Int. J. Mol. Sci. 2025, 26, 6379. https://doi.org/10.3390/ijms26136379
Beckman MF, Alexander A, Mougeot J-LC, Bahrani Mougeot F. GeneHarmony: A Knowledge-Based Tool for Biomarker Discovery in Disease: Sjögren’s Disease vs. Rheumatoid Arthritis and Systemic Lupus Erythematosus. International Journal of Molecular Sciences. 2025; 26(13):6379. https://doi.org/10.3390/ijms26136379
Chicago/Turabian StyleBeckman, Micaela F., Adam Alexander, Jean-Luc C. Mougeot, and Farah Bahrani Mougeot. 2025. "GeneHarmony: A Knowledge-Based Tool for Biomarker Discovery in Disease: Sjögren’s Disease vs. Rheumatoid Arthritis and Systemic Lupus Erythematosus" International Journal of Molecular Sciences 26, no. 13: 6379. https://doi.org/10.3390/ijms26136379
APA StyleBeckman, M. F., Alexander, A., Mougeot, J.-L. C., & Bahrani Mougeot, F. (2025). GeneHarmony: A Knowledge-Based Tool for Biomarker Discovery in Disease: Sjögren’s Disease vs. Rheumatoid Arthritis and Systemic Lupus Erythematosus. International Journal of Molecular Sciences, 26(13), 6379. https://doi.org/10.3390/ijms26136379