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Gene: SGCD |
Gene summary for SGCD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SGCD | Gene ID | 6444 |
| Gene name | sarcoglycan delta | |
| Gene Alias | 35DAG | |
| Cytomap | 5q33.2-q33.3 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q92629 |
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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 |
| 6444 | SGCD | AEH-subject1 | Human | Endometrium | AEH | 1.61e-66 | 1.31e+00 | -0.3059 |
| 6444 | SGCD | AEH-subject2 | Human | Endometrium | AEH | 3.21e-28 | 8.90e-01 | -0.2525 |
| 6444 | SGCD | AEH-subject3 | Human | Endometrium | AEH | 4.54e-35 | 8.74e-01 | -0.2576 |
| 6444 | SGCD | AEH-subject4 | Human | Endometrium | AEH | 2.11e-17 | 7.22e-01 | -0.2657 |
| 6444 | SGCD | AEH-subject5 | Human | Endometrium | AEH | 5.86e-68 | 1.44e+00 | -0.2953 |
| 6444 | SGCD | EEC-subject1 | Human | Endometrium | EEC | 3.73e-61 | 1.24e+00 | -0.2682 |
| 6444 | SGCD | EEC-subject2 | Human | Endometrium | EEC | 5.32e-106 | 1.65e+00 | -0.2607 |
| 6444 | SGCD | EEC-subject4 | Human | Endometrium | EEC | 1.73e-22 | 8.47e-01 | -0.2571 |
| 6444 | SGCD | EEC-subject5 | Human | Endometrium | EEC | 9.46e-13 | 5.27e-01 | -0.249 |
| 6444 | SGCD | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 7.25e-03 | 1.81e-01 | -0.1869 |
| 6444 | SGCD | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.33e-05 | 2.84e-01 | -0.1875 |
| 6444 | SGCD | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 6.29e-05 | 2.52e-01 | -0.1883 |
| 6444 | SGCD | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 3.04e-05 | 2.49e-01 | -0.1917 |
| 6444 | SGCD | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 3.16e-05 | 2.41e-01 | -0.1916 |
| 6444 | SGCD | PTC07 | Human | Thyroid | PTC | 2.03e-04 | -8.56e-03 | 0.2044 |
| 6444 | SGCD | ATC13 | Human | Thyroid | ATC | 1.62e-68 | 1.22e+00 | 0.34 |
| 6444 | SGCD | ATC5 | Human | Thyroid | ATC | 1.77e-68 | 1.30e+00 | 0.34 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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:00605376 | Endometrium | AEH | muscle tissue development | 83/2100 | 403/18723 | 2.57e-08 | 1.50e-06 | 83 |
| GO:00147065 | Endometrium | AEH | striated muscle tissue development | 75/2100 | 384/18723 | 1.06e-06 | 3.62e-05 | 75 |
| GO:00075174 | Endometrium | AEH | muscle organ development | 60/2100 | 327/18723 | 8.19e-05 | 1.22e-03 | 60 |
| GO:0048738 | Endometrium | AEH | cardiac muscle tissue development | 43/2100 | 236/18723 | 9.06e-04 | 8.30e-03 | 43 |
| GO:006053713 | Endometrium | EEC | muscle tissue development | 82/2168 | 403/18723 | 2.14e-07 | 9.38e-06 | 82 |
| GO:001470612 | Endometrium | EEC | striated muscle tissue development | 74/2168 | 384/18723 | 6.64e-06 | 1.57e-04 | 74 |
| GO:000751712 | Endometrium | EEC | muscle organ development | 59/2168 | 327/18723 | 3.49e-04 | 3.85e-03 | 59 |
| GO:00487381 | Endometrium | EEC | cardiac muscle tissue development | 42/2168 | 236/18723 | 3.00e-03 | 2.10e-02 | 42 |
| GO:006053719 | Thyroid | PTC | muscle tissue development | 156/5968 | 403/18723 | 1.98e-03 | 1.06e-02 | 156 |
| GO:001470617 | Thyroid | PTC | striated muscle tissue development | 144/5968 | 384/18723 | 1.05e-02 | 4.22e-02 | 144 |
| GO:006053724 | Thyroid | ATC | muscle tissue development | 181/6293 | 403/18723 | 1.27e-06 | 1.62e-05 | 181 |
| GO:001470622 | Thyroid | ATC | striated muscle tissue development | 168/6293 | 384/18723 | 1.91e-05 | 1.73e-04 | 168 |
| GO:000751716 | Thyroid | ATC | muscle organ development | 139/6293 | 327/18723 | 4.45e-04 | 2.64e-03 | 139 |
| GO:004873811 | Thyroid | ATC | cardiac muscle tissue development | 103/6293 | 236/18723 | 7.93e-04 | 4.37e-03 | 103 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0541625 | Endometrium | AEH | Viral myocarditis | 27/1197 | 60/8465 | 6.98e-09 | 1.13e-07 | 8.30e-08 | 27 |
| hsa05416111 | Endometrium | AEH | Viral myocarditis | 27/1197 | 60/8465 | 6.98e-09 | 1.13e-07 | 8.30e-08 | 27 |
| hsa0541626 | Endometrium | EEC | Viral myocarditis | 28/1237 | 60/8465 | 2.81e-09 | 5.77e-08 | 4.30e-08 | 28 |
| hsa0541635 | Endometrium | EEC | Viral myocarditis | 28/1237 | 60/8465 | 2.81e-09 | 5.77e-08 | 4.30e-08 | 28 |
| 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 |
| SGCD | SNV | Missense_Mutation | c.277N>C | p.Glu93Gln | p.E93Q | Q92629 | protein_coding | tolerated(0.06) | probably_damaging(0.969) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SGCD | SNV | Missense_Mutation | rs876658001 | c.506C>T | p.Ala169Val | p.A169V | Q92629 | protein_coding | tolerated(0.07) | possibly_damaging(0.615) | TCGA-BH-A0B9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| SGCD | SNV | Missense_Mutation | novel | c.220N>A | p.Glu74Lys | p.E74K | Q92629 | protein_coding | tolerated(1) | benign(0.003) | TCGA-BH-A42V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SGCD | SNV | Missense_Mutation | c.479N>T | p.Gly160Val | p.G160V | Q92629 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EW-A1P8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | fluorouracil | PD | |
| SGCD | SNV | Missense_Mutation | c.349N>A | p.Asp117Asn | p.D117N | Q92629 | protein_coding | tolerated(0.39) | benign(0) | TCGA-JW-A5VJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD | |
| SGCD | SNV | Missense_Mutation | novel | c.197N>A | p.Gly66Glu | p.G66E | Q92629 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-VS-A9U5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SGCD | SNV | Missense_Mutation | c.65N>C | p.Val22Ala | p.V22A | Q92629 | protein_coding | tolerated(0.08) | benign(0.075) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SGCD | SNV | Missense_Mutation | c.609N>T | p.Glu203Asp | p.E203D | Q92629 | protein_coding | tolerated(0.8) | probably_damaging(0.98) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SGCD | SNV | Missense_Mutation | c.845N>T | p.Cys282Phe | p.C282F | Q92629 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AA-A01T-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| SGCD | SNV | Missense_Mutation | c.180G>T | p.Met60Ile | p.M60I | Q92629 | protein_coding | deleterious(0) | benign(0.085) | TCGA-AY-5543-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | oxaliplatin | SD |
| Page: 1 2 3 4 5 6 |
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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 |
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