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Gene: FXN |
Gene summary for FXN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FXN | Gene ID | 2395 |
| Gene name | frataxin | |
| Gene Alias | CyaY | |
| Cytomap | 9q21.11 | |
| Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | A0A0S2Z3G4 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 2395 | FXN | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.41e-07 | 1.84e-01 | 0.0155 |
| 2395 | FXN | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.14e-02 | 1.53e-01 | -0.1808 |
| 2395 | FXN | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.85e-11 | 3.30e-01 | -0.0811 |
| 2395 | FXN | HTA11_347_2000001011 | Human | Colorectum | AD | 1.88e-15 | 3.36e-01 | -0.1954 |
| 2395 | FXN | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.46e-03 | 1.57e-01 | -0.1207 |
| 2395 | FXN | HTA11_83_2000001011 | Human | Colorectum | SER | 1.12e-08 | 3.34e-01 | -0.1526 |
| 2395 | FXN | HTA11_696_2000001011 | Human | Colorectum | AD | 2.00e-05 | 1.78e-01 | -0.1464 |
| 2395 | FXN | HTA11_866_2000001011 | Human | Colorectum | AD | 4.28e-10 | 2.13e-01 | -0.1001 |
| 2395 | FXN | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.01e-20 | 4.88e-01 | -0.059 |
| 2395 | FXN | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.28e-02 | 1.93e-01 | -0.2061 |
| 2395 | FXN | HTA11_866_3004761011 | Human | Colorectum | AD | 7.84e-09 | 2.17e-01 | 0.096 |
| 2395 | FXN | HTA11_4255_2000001011 | Human | Colorectum | SER | 2.79e-07 | 3.63e-01 | 0.0446 |
| 2395 | FXN | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.45e-03 | 1.83e-01 | 0.0528 |
| 2395 | FXN | HTA11_7663_2000001011 | Human | Colorectum | SER | 7.76e-08 | 4.07e-01 | 0.0131 |
| 2395 | FXN | HTA11_10623_2000001011 | Human | Colorectum | AD | 6.46e-07 | 3.17e-01 | -0.0177 |
| 2395 | FXN | HTA11_10711_2000001011 | Human | Colorectum | AD | 6.02e-03 | 1.35e-01 | 0.0338 |
| 2395 | FXN | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.83e-12 | 2.89e-01 | 0.0674 |
| 2395 | FXN | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.38e-07 | 3.09e-01 | 0.0112 |
| 2395 | FXN | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.40e-07 | 2.77e-01 | 0.0588 |
| 2395 | FXN | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.96e-10 | 2.10e-01 | 0.294 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00453331 | Colorectum | SER | cellular respiration | 103/2897 | 230/18723 | 2.35e-26 | 3.61e-23 | 103 |
| GO:00060911 | Colorectum | SER | generation of precursor metabolites and energy | 168/2897 | 490/18723 | 1.39e-25 | 1.70e-22 | 168 |
| GO:00061191 | Colorectum | SER | oxidative phosphorylation | 75/2897 | 141/18723 | 2.35e-25 | 2.40e-22 | 75 |
| GO:00159801 | Colorectum | SER | energy derivation by oxidation of organic compounds | 119/2897 | 318/18723 | 5.28e-22 | 4.62e-19 | 119 |
| GO:20012331 | Colorectum | SER | regulation of apoptotic signaling pathway | 101/2897 | 356/18723 | 3.05e-10 | 4.07e-08 | 101 |
| GO:00069791 | Colorectum | SER | response to oxidative stress | 114/2897 | 446/18723 | 1.75e-08 | 1.28e-06 | 114 |
| GO:00108211 | Colorectum | SER | regulation of mitochondrion organization | 48/2897 | 144/18723 | 7.51e-08 | 4.70e-06 | 48 |
| GO:00003021 | Colorectum | SER | response to reactive oxygen species | 65/2897 | 222/18723 | 1.21e-07 | 7.29e-06 | 65 |
| GO:00106391 | Colorectum | SER | negative regulation of organelle organization | 90/2897 | 348/18723 | 3.14e-07 | 1.69e-05 | 90 |
| GO:20012341 | Colorectum | SER | negative regulation of apoptotic signaling pathway | 64/2897 | 224/18723 | 3.98e-07 | 2.06e-05 | 64 |
| GO:00621971 | Colorectum | SER | cellular response to chemical stress | 87/2897 | 337/18723 | 5.33e-07 | 2.59e-05 | 87 |
| GO:00086371 | Colorectum | SER | apoptotic mitochondrial changes | 35/2897 | 107/18723 | 6.75e-06 | 2.35e-04 | 35 |
| GO:00345991 | Colorectum | SER | cellular response to oxidative stress | 73/2897 | 288/18723 | 8.52e-06 | 2.86e-04 | 73 |
| GO:00550761 | Colorectum | SER | transition metal ion homeostasis | 41/2897 | 138/18723 | 1.66e-05 | 5.05e-04 | 41 |
| GO:00516041 | Colorectum | SER | protein maturation | 73/2897 | 294/18723 | 1.82e-05 | 5.38e-04 | 73 |
| GO:00425421 | Colorectum | SER | response to hydrogen peroxide | 42/2897 | 146/18723 | 3.10e-05 | 8.27e-04 | 42 |
| GO:00018361 | Colorectum | SER | release of cytochrome c from mitochondria | 21/2897 | 59/18723 | 1.17e-04 | 2.44e-03 | 21 |
| GO:00100381 | Colorectum | SER | response to metal ion | 84/2897 | 373/18723 | 1.87e-04 | 3.44e-03 | 84 |
| GO:00469161 | Colorectum | SER | cellular transition metal ion homeostasis | 33/2897 | 115/18723 | 2.20e-04 | 3.89e-03 | 33 |
| GO:00164851 | Colorectum | SER | protein processing | 55/2897 | 225/18723 | 2.84e-04 | 4.67e-03 | 55 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| FXN | SNV | Missense_Mutation | novel | c.485G>A | p.Gly162Glu | p.G162E | Q16595 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-C8-A26X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| FXN | SNV | Missense_Mutation | rs551991546 | c.446C>T | p.Thr149Met | p.T149M | Q16595 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| FXN | SNV | Missense_Mutation | c.320N>T | p.Ala107Val | p.A107V | Q16595 | protein_coding | deleterious(0.02) | possibly_damaging(0.571) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| FXN | SNV | Missense_Mutation | novel | c.392N>C | p.Val131Ala | p.V131A | Q16595 | protein_coding | deleterious(0.02) | probably_damaging(0.991) | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| FXN | SNV | Missense_Mutation | novel | c.470N>A | p.Ser157Tyr | p.S157Y | Q16595 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| FXN | SNV | Missense_Mutation | novel | c.560N>T | p.Ala187Val | p.A187V | Q16595 | protein_coding | deleterious(0.03) | benign(0.164) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| FXN | SNV | Missense_Mutation | novel | c.242N>A | p.Ser81Tyr | p.S81Y | Q16595 | protein_coding | deleterious(0) | benign(0.133) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| FXN | SNV | Missense_Mutation | novel | c.502N>C | p.Trp168Arg | p.W168R | Q16595 | protein_coding | deleterious(0.02) | benign(0.11) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
| FXN | SNV | Missense_Mutation | c.482G>T | p.Ser161Ile | p.S161I | Q16595 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-B5-A11Y-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| FXN | SNV | Missense_Mutation | c.327T>A | p.Phe109Leu | p.F109L | Q16595 | protein_coding | deleterious(0.04) | possibly_damaging(0.758) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 2395 | FXN | TRANSPORTER, ENZYME | CISPLATIN | CISPLATIN | 12928720 | |
| 2395 | FXN | TRANSPORTER, ENZYME | ERYTHROPOIETIN | EPOETIN BETA | 16269021 |
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