Table 2.
Top 20 enriched host DEGs in PEDIS 4 compared to PEDIS 2–3 diabetic foot infections. Values in log fold change (LogFC) column indicate fold change ranked from highest to lowest (FWER < 0.05).
| Gene | Description | Function/GO biological process | logFC | FWER |
|---|---|---|---|---|
| RGPD2 | RANBP2-like and grip domain-containing protein 2 | GTP-binding protein of the RAS superfamily that is associated with the nuclear membrane and is thought to control a variety of cellular functions through its interactions with other proteins | 7.0 | 0.00 |
| TG | Thyroglobulin | Primary functions include iodide storage and thyroid hormonogenesis. Other gene ontology processes include regulation of signaling receptor activity, and signal transduction | 5.9 | 0.01 |
| AC099343.3 | Novel transcript | Unknown | 4.1 | 0.01 |
| CST7 | Cystatin 7 | Role in immune regulation through inhibition of cysteine peptidases which effect varying immune cells (natural killer cells and Eosinophils) | 4.3 | 0.01 |
| FAM53C | Family with Sequence Similarity 53 Member C | Function unknown | 3.9 | 0.01 |
| GADD45B | Growth arrest and DNA damage-inducible protein GADD45 Beta | Levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The genes in this group respond to environmental stresses by mediating activation of the p38/JNK pathway via their proteins binding and activating MTK1/MEKK4 kinase, which is an upstream activator of both p38 and JNK MAPKs. The function of these genes or their protein products is involved in the regulation of growth and apoptosis | 6.5 | 0.01 |
| GADD45G | Growth arrest and DNA-damage-inducible protein GADD45 gamma | 6.5 | 0.01 | |
| AL031123.3 | Novel transcript | Function unknown | 5.4 | 0.02 |
| MSRB1 | Methionine sulfoxide reductase B1 | Plays a protective role against oxidative stress by restoring activity to proteins that have been inactivated by methionine oxidation | 3.4 | 0.02 |
| EIF4A3 | Eukaryotic translation initiation factor 4A3 | Protein coding gene belongs to the Asp-Glu-Ala-Asp (DEAD) box superfamily. Mostly unknown transcriptome wide functions but limited data to identify a role in cellular functions, such as cell cycle control | 4.9 | 0.02 |
| ROPN1L | Rhophilin associated tail protein 1 like | Involved in fibrous sheath integrity and sperm motility, plays a role in PKA-dependent signaling processes required for spermatozoa capacitation | 4.5 | 0.02 |
| ALAS1 | Delta-aminolevulinate synthase 1 | Involved in heme biosynthesis via negative feedback-mediated regulation | 4.6 | 0.03 |
| AC016876.2 | Novel transcript | Function unknown | 4.0 | 0.03 |
| TRIM25 | Tripartite motif containing 25 | Member of the tripartite motif (TRIM) family and TRIM25 has involvement in pathways for Interferon gamma signaling and cytokine signaling in immune system | 3.8 | 0.03 |
| FAM126B | Family with sequence similarity 126 member B | Function unknown | 3.8 | 0.03 |
| RAB11FIP1 | RAB11 family interacting protein 1 | A Rab11 effector protein involved in the endosomal recycling process. Also involved in controlling membrane trafficking along the phagocytic pathway and in phagocytosis | 4.4 | 0.03 |
| ARID3B | AT-rich interaction domain 3B | Function unknown | 5.0 | 0.04 |
| CDKN2D | Cyclin dependent kinase inhibitor 2D | Member of the INK4 family of cyclin-dependent kinase inhibitors. Prevents the activation of the CDK kinases, thus functions as a cell growth regulator that controls cell cycle | 4.8 | 0.04 |
| LRP5L | Low density lipoprotein receptor-related protein 5 like | Function unknown | 4.5 | 0.04 |
| IFRD1 | Interferon-related developmental regulator 1 | Gene coding protein expressed by mature neutrophils, modulating cell differentiation and increasing oxidative stress and pro-inflammatory cytokines | 4.3 | 0.04 |
| XPO6 | Exportin 6 | Mediates the nuclear export of actin and profilin-actin complexes in somatic cells | 3.3 | 0.04 |