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Gene: SGCA |
Gene summary for SGCA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SGCA | Gene ID | 6442 |
| Gene name | sarcoglycan alpha | |
| Gene Alias | 50DAG | |
| Cytomap | 17q21.33 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | A0A0S2Z4Q1 |
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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 |
| 6442 | SGCA | C43 | Human | Oral cavity | OSCC | 7.87e-03 | -1.35e-01 | 0.1704 |
| 6442 | SGCA | C06 | Human | Oral cavity | OSCC | 3.18e-02 | 7.63e-01 | 0.2699 |
| 6442 | SGCA | C07 | Human | Oral cavity | OSCC | 2.75e-03 | 1.54e+00 | 0.2491 |
| 6442 | SGCA | C08 | Human | Oral cavity | OSCC | 1.66e-02 | -1.35e-01 | 0.1919 |
| 6442 | SGCA | LP16 | Human | Oral cavity | LP | 9.58e-05 | 1.32e+00 | 0.1055 |
| 6442 | SGCA | SYSMH2 | Human | Oral cavity | OSCC | 6.69e-03 | -1.27e-01 | 0.2326 |
| 6442 | SGCA | SYSMH4 | Human | Oral cavity | OSCC | 1.66e-02 | -1.35e-01 | 0.1226 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:00310999 | Oral cavity | OSCC | regeneration | 114/7305 | 198/18723 | 8.54e-08 | 1.50e-06 | 114 |
| GO:00422464 | Oral cavity | OSCC | tissue regeneration | 42/7305 | 72/18723 | 6.89e-04 | 3.84e-03 | 42 |
| GO:00434034 | Oral cavity | OSCC | skeletal muscle tissue regeneration | 23/7305 | 37/18723 | 3.66e-03 | 1.51e-02 | 23 |
| GO:003109916 | Oral cavity | LP | regeneration | 76/4623 | 198/18723 | 1.25e-05 | 2.24e-04 | 76 |
| GO:00422461 | Oral cavity | LP | tissue regeneration | 30/4623 | 72/18723 | 1.13e-03 | 9.27e-03 | 30 |
| GO:004340311 | Oral cavity | LP | skeletal muscle tissue regeneration | 18/4623 | 37/18723 | 1.36e-03 | 1.08e-02 | 18 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05416210 | Oral cavity | LP | Viral myocarditis | 32/2418 | 60/8465 | 4.55e-05 | 2.91e-04 | 1.88e-04 | 32 |
| hsa0541637 | Oral cavity | LP | Viral myocarditis | 32/2418 | 60/8465 | 4.55e-05 | 2.91e-04 | 1.88e-04 | 32 |
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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 |
| SGCA | SNV | Missense_Mutation | novel | c.286G>A | p.Glu96Lys | p.E96K | Q16586 | protein_coding | tolerated(0.18) | possibly_damaging(0.503) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| SGCA | SNV | Missense_Mutation | c.968N>G | p.Asp323Gly | p.D323G | Q16586 | protein_coding | deleterious(0.02) | benign(0.197) | TCGA-A2-A1FV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| SGCA | SNV | Missense_Mutation | rs138254713 | c.662N>A | p.Arg221His | p.R221H | Q16586 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-A2-A3XZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| SGCA | SNV | Missense_Mutation | rs138254713 | c.662N>A | p.Arg221His | p.R221H | Q16586 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SGCA | SNV | Missense_Mutation | rs780200261 | c.974N>T | p.Ala325Val | p.A325V | Q16586 | protein_coding | tolerated(0.18) | benign(0.007) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SGCA | SNV | Missense_Mutation | rs780564461 | c.649G>A | p.Asp217Asn | p.D217N | Q16586 | protein_coding | deleterious(0.05) | benign(0.37) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SGCA | SNV | Missense_Mutation | rs763372958 | c.1054N>A | p.Glu352Lys | p.E352K | Q16586 | protein_coding | deleterious(0.04) | benign(0.202) | TCGA-VS-A9V1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| SGCA | SNV | Missense_Mutation | rs781380620 | c.982N>A | p.Asp328Asn | p.D328N | Q16586 | protein_coding | deleterious(0) | benign(0.027) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SGCA | SNV | Missense_Mutation | c.140G>A | p.Ser47Asn | p.S47N | Q16586 | protein_coding | tolerated(0.59) | benign(0.014) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SGCA | deletion | Frame_Shift_Del | novel | c.246delN | p.His84ThrfsTer127 | p.H84Tfs*127 | Q16586 | protein_coding | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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 |
| 6442 | SGCA | NA | rAAV1.tMCK.human-alpha-sarcoglycan |
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