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Gene: SCN9A |
Gene summary for SCN9A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SCN9A | Gene ID | 6335 |
| Gene name | sodium voltage-gated channel alpha subunit 9 | |
| Gene Alias | ETHA | |
| Cytomap | 2q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0001508 | UniProtAcc | Q15858 |
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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 |
| 6335 | SCN9A | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.45e-31 | -8.06e-01 | 0.0155 |
| 6335 | SCN9A | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.99e-19 | -8.06e-01 | -0.1808 |
| 6335 | SCN9A | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.38e-03 | -7.56e-01 | 0.0216 |
| 6335 | SCN9A | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.64e-17 | -8.42e-01 | -0.0811 |
| 6335 | SCN9A | HTA11_78_2000001011 | Human | Colorectum | AD | 9.20e-21 | -7.89e-01 | -0.1088 |
| 6335 | SCN9A | HTA11_347_2000001011 | Human | Colorectum | AD | 1.48e-05 | -4.21e-01 | -0.1954 |
| 6335 | SCN9A | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.10e-04 | -7.46e-01 | -0.2196 |
| 6335 | SCN9A | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.57e-12 | -7.57e-01 | -0.1207 |
| 6335 | SCN9A | HTA11_83_2000001011 | Human | Colorectum | SER | 1.62e-09 | -7.50e-01 | -0.1526 |
| 6335 | SCN9A | HTA11_696_2000001011 | Human | Colorectum | AD | 6.85e-32 | -7.45e-01 | -0.1464 |
| 6335 | SCN9A | HTA11_866_2000001011 | Human | Colorectum | AD | 1.27e-23 | -6.95e-01 | -0.1001 |
| 6335 | SCN9A | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.00e-25 | -7.99e-01 | -0.059 |
| 6335 | SCN9A | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.10e-05 | -7.99e-01 | -0.1706 |
| 6335 | SCN9A | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.41e-06 | -8.05e-01 | -0.2061 |
| 6335 | SCN9A | HTA11_546_2000001011 | Human | Colorectum | AD | 4.80e-08 | -7.20e-01 | -0.0842 |
| 6335 | SCN9A | HTA11_9341_2000001011 | Human | Colorectum | SER | 3.02e-02 | -8.10e-01 | -0.00410000000000005 |
| 6335 | SCN9A | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.91e-05 | -6.57e-01 | -0.0179 |
| 6335 | SCN9A | HTA11_866_3004761011 | Human | Colorectum | AD | 8.63e-32 | -8.36e-01 | 0.096 |
| 6335 | SCN9A | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.28e-03 | -7.56e-01 | 0.0446 |
| 6335 | SCN9A | HTA11_9408_2000001011 | Human | Colorectum | AD | 6.59e-05 | -8.55e-01 | 0.0451 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:0009636 | Colorectum | AD | response to toxic substance | 88/3918 | 262/18723 | 1.12e-06 | 3.72e-05 | 88 |
| GO:0009791 | Colorectum | AD | post-embryonic development | 29/3918 | 80/18723 | 1.13e-03 | 1.03e-02 | 29 |
| GO:00096361 | Colorectum | SER | response to toxic substance | 71/2897 | 262/18723 | 8.63e-07 | 4.07e-05 | 71 |
| GO:00097911 | Colorectum | SER | post-embryonic development | 22/2897 | 80/18723 | 4.12e-03 | 3.36e-02 | 22 |
| GO:00096362 | Colorectum | MSS | response to toxic substance | 73/3467 | 262/18723 | 1.26e-04 | 1.94e-03 | 73 |
| GO:00097912 | Colorectum | MSS | post-embryonic development | 26/3467 | 80/18723 | 1.91e-03 | 1.66e-02 | 26 |
| GO:0035725 | Colorectum | FAP | sodium ion transmembrane transport | 44/2622 | 178/18723 | 9.31e-05 | 1.60e-03 | 44 |
| GO:0001508 | Colorectum | FAP | action potential | 34/2622 | 134/18723 | 3.30e-04 | 4.22e-03 | 34 |
| GO:0006814 | Colorectum | FAP | sodium ion transport | 54/2622 | 245/18723 | 3.98e-04 | 4.85e-03 | 54 |
| GO:00097913 | Colorectum | FAP | post-embryonic development | 23/2622 | 80/18723 | 4.51e-04 | 5.32e-03 | 23 |
| GO:00096363 | Colorectum | FAP | response to toxic substance | 53/2622 | 262/18723 | 3.35e-03 | 2.46e-02 | 53 |
| GO:00015081 | Colorectum | CRC | action potential | 32/2078 | 134/18723 | 2.02e-05 | 5.90e-04 | 32 |
| GO:00357251 | Colorectum | CRC | sodium ion transmembrane transport | 39/2078 | 178/18723 | 2.30e-05 | 6.60e-04 | 39 |
| GO:00068141 | Colorectum | CRC | sodium ion transport | 49/2078 | 245/18723 | 3.01e-05 | 7.86e-04 | 49 |
| GO:00097914 | Colorectum | CRC | post-embryonic development | 20/2078 | 80/18723 | 3.62e-04 | 5.45e-03 | 20 |
| GO:0035637 | Colorectum | CRC | multicellular organismal signaling | 31/2078 | 160/18723 | 1.39e-03 | 1.52e-02 | 31 |
| GO:0042391 | Colorectum | CRC | regulation of membrane potential | 67/2078 | 434/18723 | 3.27e-03 | 2.81e-02 | 67 |
| GO:00097919 | Esophagus | ESCC | post-embryonic development | 56/8552 | 80/18723 | 9.08e-06 | 8.71e-05 | 56 |
| GO:000963620 | Esophagus | ESCC | response to toxic substance | 150/8552 | 262/18723 | 1.00e-04 | 7.12e-04 | 150 |
| GO:000979114 | Thyroid | PTC | post-embryonic development | 48/5968 | 80/18723 | 1.99e-07 | 3.56e-06 | 48 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| SCN9A | SNV | Missense_Mutation | c.2632G>T | p.Gly878Cys | p.G878C | Q15858 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A2-A04W-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| SCN9A | SNV | Missense_Mutation | rs766441372 | c.1954C>G | p.Gln652Glu | p.Q652E | Q15858 | protein_coding | tolerated(1) | benign(0.001) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| SCN9A | SNV | Missense_Mutation | novel | c.2260N>T | p.His754Tyr | p.H754Y | Q15858 | protein_coding | tolerated(0.05) | possibly_damaging(0.888) | TCGA-A8-A09Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD |
| SCN9A | SNV | Missense_Mutation | novel | c.4168N>G | p.Gln1390Glu | p.Q1390E | Q15858 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| SCN9A | SNV | Missense_Mutation | c.3542N>C | p.Ser1181Thr | p.S1181T | Q15858 | protein_coding | deleterious(0.03) | benign(0.05) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SCN9A | SNV | Missense_Mutation | c.3436N>A | p.Asp1146Asn | p.D1146N | Q15858 | protein_coding | deleterious(0) | possibly_damaging(0.728) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SCN9A | SNV | Missense_Mutation | c.2668N>A | p.Asp890Asn | p.D890N | Q15858 | protein_coding | tolerated(0.42) | benign(0.006) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SCN9A | SNV | Missense_Mutation | novel | c.4009T>C | p.Tyr1337His | p.Y1337H | Q15858 | protein_coding | tolerated(0.34) | benign(0.274) | TCGA-AC-A3TM-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | CR |
| SCN9A | SNV | Missense_Mutation | novel | c.5503N>G | p.Thr1835Ala | p.T1835A | Q15858 | protein_coding | deleterious(0.03) | possibly_damaging(0.66) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SCN9A | SNV | Missense_Mutation | rs202083986 | c.553N>T | p.Arg185Cys | p.R185C | Q15858 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 |
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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 |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | DWJ-208 | |||
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL16 | PHENYTOIN | |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | blocker | 135652722 | TETRODOTOXIN | |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | Benzene sulfonamide derivative 11 | |||
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL1200773 | TOCAINIDE HYDROCHLORIDE | |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | Benzene sulfonamide derivative 15 | |||
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL1200597 | ETIDOCAINE HYDROCHLORIDE | |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL2107771 | RALFINAMIDE | |
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | Aryl carboxamide derivative 4 | |||
| 6335 | SCN9A | DRUGGABLE GENOME, ION CHANNEL | RANOLAZINE | RANOLAZINE |
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