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Gene: SCN1A |
Gene summary for SCN1A |
Gene summary. |
Gene information | Species | Human | Gene symbol | SCN1A | Gene ID | 6323 |
Gene name | sodium voltage-gated channel alpha subunit 1 | |
Gene Alias | DEE6 | |
Cytomap | 2q24.3 | |
Gene Type | protein-coding | GO ID | GO:0001508 | UniProtAcc | P35498 |
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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 |
6323 | SCN1A | RNA-P10T2-P10T2-1 | Human | Lung | AAH | 7.47e-04 | 1.04e+00 | -0.1271 |
6323 | SCN1A | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 4.14e-04 | 9.65e-01 | -0.1406 |
6323 | SCN1A | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 1.34e-03 | 9.21e-01 | -0.1408 |
6323 | SCN1A | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 8.78e-16 | 9.56e-01 | -0.2116 |
6323 | SCN1A | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 5.16e-14 | 1.12e+00 | -0.1941 |
6323 | SCN1A | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 3.17e-11 | 1.02e+00 | -0.2107 |
6323 | SCN1A | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.03e-20 | 1.07e+00 | -0.2119 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Lung | AAH: Atypical adenomatous hyperplasia | |
AIS: Adenocarcinoma in situ | ||
IAC: Invasive lung adenocarcinoma | ||
MIA: Minimally invasive adenocarcinoma |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003004812 | Lung | AIS | actin filament-based movement | 25/1849 | 127/18723 | 5.99e-04 | 9.14e-03 | 25 |
GO:008600111 | Lung | AIS | cardiac muscle cell action potential | 16/1849 | 76/18723 | 2.70e-03 | 2.72e-02 | 16 |
GO:000301211 | Lung | AIS | muscle system process | 63/1849 | 452/18723 | 3.18e-03 | 3.05e-02 | 63 |
GO:003004822 | Lung | AAH | actin filament-based movement | 12/613 | 127/18723 | 9.53e-04 | 2.94e-02 | 12 |
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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 |
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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. |
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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 |
SCN1A | SNV | Missense_Mutation | novel | c.1643N>C | p.Arg548Thr | p.R548T | P35498 | protein_coding | tolerated(0.13) | benign(0.079) | TCGA-CV-6933-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | novel | c.4418N>C | p.Phe1473Ser | p.F1473S | P35498 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CV-7089-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | novel | c.2619N>T | p.Trp873Cys | p.W873C | P35498 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-CV-7235-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | novel | c.3136G>C | p.Asp1046His | p.D1046H | P35498 | protein_coding | deleterious(0.03) | probably_damaging(0.95) | TCGA-CV-7245-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | novel | c.4316N>G | p.Tyr1439Cys | p.Y1439C | P35498 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CV-7411-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | rs143088184 | c.4570N>A | p.Pro1524Thr | p.P1524T | P35498 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CV-7432-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
SCN1A | SNV | Missense_Mutation | rs112244937 | c.5636N>A | p.Ser1879Asn | p.S1879N | P35498 | protein_coding | deleterious(0) | possibly_damaging(0.632) | TCGA-CV-A461-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SCN1A | SNV | Missense_Mutation | novel | c.847N>C | p.Thr283Pro | p.T283P | P35498 | protein_coding | tolerated(0.31) | benign(0.153) | TCGA-CV-A6K1-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
SCN1A | SNV | Missense_Mutation | c.3986N>A | p.Arg1329Gln | p.R1329Q | P35498 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-D6-6516-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SCN1A | SNV | Missense_Mutation | rs780809852 | c.5501C>T | p.Ala1834Val | p.A1834V | P35498 | protein_coding | deleterious(0) | benign(0.08) | TCGA-DQ-7591-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | taxol | 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 |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | levetiracetam | LEVETIRACETAM | 23859570,21747585,28753467,25155934 | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | ZONISAMIDE | ZONISAMIDE | ||
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL1201754 | RUFINAMIDE | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | 135652715 | SAXITOXIN | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL1200586 | PRILOCAINE HYDROCHLORIDE | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL861 | MEPHENYTOIN | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | inhibitor | 135651976 | ||
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | 135652722 | TETRODOTOXIN | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | phenytoin | PHENYTOIN | 17001291 | |
6323 | SCN1A | DRUGGABLE GENOME, ION CHANNEL | blocker | CHEMBL3545209 | NKTR-171 |
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