Gene lists.

<div><p>Superoxide Dismutase 3 (SOD3) scavenges extracellular superoxide giving a hydrogen peroxide metabolite. Both Reactive Oxygen Species diffuse through aquaporins causing oxidative stress and biomolecular damage. <i>SOD3</i> is differentially expressed in cancer and this research utilises Gene Expression Omnibus data series GSE2109 with 2,158 cancer samples. Genome-wide expression correlation analysis was conducted with <i>SOD3</i> as the seed gene. Categorical <i>SOD3</i> Pearson Correlation gene lists incrementing in correlation strength by 0.01 from ρ≥|0.34| to ρ≥|0.41| were extracted from the data. Positively and negatively <i>SOD3</i> correlated genes were separated for each list and checked for significance against disease overlapping genes in the ClinVar and Orphanet databases via Enrichr. Disease causal genes were added to the relevant gene list and checked against Gene Ontology, Phenotype Ontology, and Elsevier Pathways via Enrichr before the significant ontologies containing causal and non-overlapping genes were reviewed with a literature search for possible disease and oxidative stress associations. 12 significant individually discriminated disorders were identified: Autosomal Dominant Cutis Laxa (p = 6.05x10<sup>-7</sup>), Renal Tubular Dysgenesis of Genetic Origin (p = 6.05x10<sup>-7</sup>), Lethal Arteriopathy Syndrome due to Fibulin-4 Deficiency (p = 6.54x10<sup>-9</sup>), EMILIN-1-related Connective Tissue Disease (p = 6.54x10<sup>-9</sup>), Holt-Oram Syndrome (p = 7.72x10<sup>-10</sup>), Multisystemic Smooth Muscle Dysfunction Syndrome (p = 9.95x10<sup>-15</sup>), Distal Hereditary Motor Neuropathy type 2 (p = 4.48x10<sup>-7</sup>), Congenital Glaucoma (p = 5.24x210<sup>-9</sup>), Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome (p = 3.77x10<sup>-16</sup>), Classical-like Ehlers-Danlos Syndrome type 1 (p = 3.77x10<sup>-16</sup>), Retinoblastoma (p = 1.9x10<sup>-8</sup>), and Lynch Syndrome (p = 5.04x10<sup>-9</sup>). 35 novel (21 unique) genes across 12 disorders were identified: <i>ADNP</i>, <i>AOC3</i>, <i>CDC42EP2</i>, <i>CHTOP</i>, <i>CNN1</i>, <i>DES</i>, <i>FOXF1</i>, <i>FXR1</i>, <i>HLTF</i>, <i>KCNMB1</i>, <i>MTF2</i>, <i>MYH11</i>, <i>PLN</i>, <i>PNPLA2</i>, <i>REST</i>, <i>SGCA</i>, <i>SORBS1</i>, <i>SYNPO2</i>, <i>TAGLN</i>, <i>WAPL</i>, <i>and ZMYM4</i>. These genes are proffered as potential biomarkers or therapeutic targets for the corresponding rare diseases discussed.</p></div>

Publication Details

Journal
Figshare
Published
2024-10-31
DOI
https://doi.org/10.1371/journal.pone.0313139.s002
Primary Topic
Mycorrhizal Fungi and Plant Interactions
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article
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article

Gene lists.

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Mycorrhizal Fungi and Plant Interactions
article

Gene lists.

article en

Abstract

<div><p>Superoxide Dismutase 3 (SOD3) scavenges extracellular superoxide giving a hydrogen peroxide metabolite. Both Reactive Oxygen Species diffuse through aquaporins causing oxidative stress and biomolecular damage. <i>SOD3</i> is differentially expressed in cancer and this research utilises Gene Expression Omnibus data series GSE2109 with 2,158 cancer samples. Genome-wide expression correlation analysis was conducted with <i>SOD3</i> as the seed gene. Categorical <i>SOD3</i> Pearson Correlation gene lists incrementing in correlation strength by 0.01 from ρ≥|0.34| to ρ≥|0.41| were extracted from the data. Positively and negatively <i>SOD3</i> correlated genes were separated for each list and checked for significance against disease overlapping genes in the ClinVar and Orphanet databases via Enrichr. Disease causal genes were added to the relevant gene list and checked against Gene Ontology, Phenotype Ontology, and Elsevier Pathways via Enrichr before the significant ontologies containing causal and non-overlapping genes were reviewed with a literature search for possible disease and oxidative stress associations. 12 significant individually discriminated disorders were identified: Autosomal Dominant Cutis Laxa (p = 6.05x10<sup>-7</sup>), Renal Tubular Dysgenesis of Genetic Origin (p = 6.05x10<sup>-7</sup>), Lethal Arteriopathy Syndrome due to Fibulin-4 Deficiency (p = 6.54x10<sup>-9</sup>), EMILIN-1-related Connective Tissue Disease (p = 6.54x10<sup>-9</sup>), Holt-Oram Syndrome (p = 7.72x10<sup>-10</sup>), Multisystemic Smooth Muscle Dysfunction Syndrome (p = 9.95x10<sup>-15</sup>), Distal Hereditary Motor Neuropathy type 2 (p = 4.48x10<sup>-7</sup>), Congenital Glaucoma (p = 5.24x210<sup>-9</sup>), Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome (p = 3.77x10<sup>-16</sup>), Classical-like Ehlers-Danlos Syndrome type 1 (p = 3.77x10<sup>-16</sup>), Retinoblastoma (p = 1.9x10<sup>-8</sup>), and Lynch Syndrome (p = 5.04x10<sup>-9</sup>). 35 novel (21 unique) genes across 12 disorders were identified: <i>ADNP</i>, <i>AOC3</i>, <i>CDC42EP2</i>, <i>CHTOP</i>, <i>CNN1</i>, <i>DES</i>, <i>FOXF1</i>, <i>FXR1</i>, <i>HLTF</i>, <i>KCNMB1</i>, <i>MTF2</i>, <i>MYH11</i>, <i>PLN</i>, <i>PNPLA2</i>, <i>REST</i>, <i>SGCA</i>, <i>SORBS1</i>, <i>SYNPO2</i>, <i>TAGLN</i>, <i>WAPL</i>, <i>and ZMYM4</i>. These genes are proffered as potential biomarkers or therapeutic targets for the corresponding rare diseases discussed.</p></div>

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Mycorrhizal Fungi and Plant Interactions
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