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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:00513534 | Esophagus | ESCC | positive regulation of oxidoreductase activity | 37/8552 | 59/18723 | 6.23e-03 | 2.29e-02 | 37 |
| GO:00424401 | Esophagus | ESCC | pigment metabolic process | 50/8552 | 84/18723 | 7.34e-03 | 2.64e-02 | 50 |
| GO:004592717 | Esophagus | ESCC | positive regulation of growth | 137/8552 | 259/18723 | 1.13e-02 | 3.80e-02 | 137 |
| GO:00421681 | Esophagus | ESCC | heme metabolic process | 27/8552 | 42/18723 | 1.16e-02 | 3.90e-02 | 27 |
| GO:00068397 | Liver | Cirrhotic | mitochondrial transport | 112/4634 | 254/18723 | 1.03e-11 | 6.66e-10 | 112 |
| GO:19905425 | Liver | Cirrhotic | mitochondrial transmembrane transport | 41/4634 | 102/18723 | 4.08e-04 | 3.37e-03 | 41 |
| GO:00067303 | Liver | Cirrhotic | one-carbon metabolic process | 17/4634 | 40/18723 | 1.04e-02 | 4.61e-02 | 17 |
| GO:000609122 | Liver | HCC | generation of precursor metabolites and energy | 340/7958 | 490/18723 | 4.04e-34 | 2.85e-31 | 340 |
| GO:000906012 | Liver | HCC | aerobic respiration | 147/7958 | 189/18723 | 3.13e-23 | 6.61e-21 | 147 |
| GO:004533312 | Liver | HCC | cellular respiration | 171/7958 | 230/18723 | 6.35e-23 | 1.26e-20 | 171 |
| GO:004603422 | Liver | HCC | ATP metabolic process | 198/7958 | 277/18723 | 8.30e-23 | 1.55e-20 | 198 |
| GO:001598022 | Liver | HCC | energy derivation by oxidation of organic compounds | 221/7958 | 318/18723 | 1.02e-22 | 1.86e-20 | 221 |
| GO:000683912 | Liver | HCC | mitochondrial transport | 184/7958 | 254/18723 | 2.30e-22 | 3.83e-20 | 184 |
| GO:000697922 | Liver | HCC | response to oxidative stress | 281/7958 | 446/18723 | 9.75e-19 | 1.24e-16 | 281 |
| GO:000611912 | Liver | HCC | oxidative phosphorylation | 110/7958 | 141/18723 | 6.58e-18 | 7.45e-16 | 110 |
| GO:006219722 | Liver | HCC | cellular response to chemical stress | 216/7958 | 337/18723 | 6.86e-16 | 5.44e-14 | 216 |
| GO:200123322 | Liver | HCC | regulation of apoptotic signaling pathway | 226/7958 | 356/18723 | 7.26e-16 | 5.68e-14 | 226 |
| GO:000679021 | Liver | HCC | sulfur compound metabolic process | 212/7958 | 339/18723 | 5.60e-14 | 3.39e-12 | 212 |
| GO:003459922 | Liver | HCC | cellular response to oxidative stress | 183/7958 | 288/18723 | 3.65e-13 | 1.93e-11 | 183 |
| GO:199054212 | Liver | HCC | mitochondrial transmembrane transport | 78/7958 | 102/18723 | 2.73e-12 | 1.26e-10 | 78 |
| 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 |
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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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