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Gene: SMC2 |
Gene summary for SMC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMC2 | Gene ID | 10592 |
| Gene name | structural maintenance of chromosomes 2 | |
| Gene Alias | CAP-E | |
| Cytomap | 9q31.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024R158 |
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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 |
| 10592 | SMC2 | LZE2T | Human | Esophagus | ESCC | 5.52e-10 | 1.08e+00 | 0.082 |
| 10592 | SMC2 | LZE4T | Human | Esophagus | ESCC | 1.33e-04 | 3.30e-01 | 0.0811 |
| 10592 | SMC2 | LZE24T | Human | Esophagus | ESCC | 4.91e-10 | 3.09e-01 | 0.0596 |
| 10592 | SMC2 | LZE6T | Human | Esophagus | ESCC | 6.29e-05 | 3.68e-01 | 0.0845 |
| 10592 | SMC2 | P1T-E | Human | Esophagus | ESCC | 3.33e-05 | 4.00e-01 | 0.0875 |
| 10592 | SMC2 | P2T-E | Human | Esophagus | ESCC | 2.87e-41 | 1.03e+00 | 0.1177 |
| 10592 | SMC2 | P4T-E | Human | Esophagus | ESCC | 3.39e-25 | 6.58e-01 | 0.1323 |
| 10592 | SMC2 | P5T-E | Human | Esophagus | ESCC | 8.18e-28 | 7.01e-01 | 0.1327 |
| 10592 | SMC2 | P8T-E | Human | Esophagus | ESCC | 6.56e-15 | 3.50e-01 | 0.0889 |
| 10592 | SMC2 | P9T-E | Human | Esophagus | ESCC | 5.52e-08 | 3.29e-01 | 0.1131 |
| 10592 | SMC2 | P10T-E | Human | Esophagus | ESCC | 1.04e-39 | 9.10e-01 | 0.116 |
| 10592 | SMC2 | P11T-E | Human | Esophagus | ESCC | 8.02e-03 | 2.08e-01 | 0.1426 |
| 10592 | SMC2 | P12T-E | Human | Esophagus | ESCC | 2.03e-09 | 2.29e-01 | 0.1122 |
| 10592 | SMC2 | P15T-E | Human | Esophagus | ESCC | 3.18e-10 | 3.71e-01 | 0.1149 |
| 10592 | SMC2 | P16T-E | Human | Esophagus | ESCC | 1.25e-19 | 4.17e-01 | 0.1153 |
| 10592 | SMC2 | P17T-E | Human | Esophagus | ESCC | 2.19e-11 | 4.94e-01 | 0.1278 |
| 10592 | SMC2 | P19T-E | Human | Esophagus | ESCC | 8.01e-03 | 4.20e-01 | 0.1662 |
| 10592 | SMC2 | P20T-E | Human | Esophagus | ESCC | 2.23e-12 | 2.29e-01 | 0.1124 |
| 10592 | SMC2 | P21T-E | Human | Esophagus | ESCC | 3.38e-37 | 8.47e-01 | 0.1617 |
| 10592 | SMC2 | P22T-E | Human | Esophagus | ESCC | 2.22e-08 | 2.30e-01 | 0.1236 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0045732110 | Oral cavity | LP | positive regulation of protein catabolic process | 103/4623 | 231/18723 | 2.68e-11 | 1.81e-09 | 103 |
| GO:0031331110 | Oral cavity | LP | positive regulation of cellular catabolic process | 163/4623 | 427/18723 | 3.03e-10 | 1.59e-08 | 163 |
| GO:1903364110 | Oral cavity | LP | positive regulation of cellular protein catabolic process | 72/4623 | 155/18723 | 2.93e-09 | 1.28e-07 | 72 |
| GO:190180019 | Oral cavity | LP | positive regulation of proteasomal protein catabolic process | 57/4623 | 114/18723 | 4.56e-09 | 1.91e-07 | 57 |
| GO:190305218 | Oral cavity | LP | positive regulation of proteolysis involved in cellular protein catabolic process | 61/4623 | 133/18723 | 8.17e-08 | 2.72e-06 | 61 |
| GO:000150315 | Oral cavity | LP | ossification | 123/4623 | 408/18723 | 6.55e-03 | 3.84e-02 | 123 |
| GO:000164916 | Oral cavity | LP | osteoblast differentiation | 73/4623 | 229/18723 | 8.09e-03 | 4.40e-02 | 73 |
| GO:001049828 | Skin | cSCC | proteasomal protein catabolic process | 243/4864 | 490/18723 | 7.85e-30 | 4.10e-27 | 243 |
| GO:004217629 | Skin | cSCC | regulation of protein catabolic process | 198/4864 | 391/18723 | 6.03e-26 | 1.89e-23 | 198 |
| GO:004316128 | Skin | cSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 205/4864 | 412/18723 | 1.46e-25 | 4.16e-23 | 205 |
| GO:190336229 | Skin | cSCC | regulation of cellular protein catabolic process | 139/4864 | 255/18723 | 2.06e-22 | 4.17e-20 | 139 |
| GO:014001415 | Skin | cSCC | mitotic nuclear division | 149/4864 | 287/18723 | 3.59e-21 | 6.43e-19 | 149 |
| GO:190305029 | Skin | cSCC | regulation of proteolysis involved in cellular protein catabolic process | 121/4864 | 221/18723 | 6.75e-20 | 1.01e-17 | 121 |
| GO:006113629 | Skin | cSCC | regulation of proteasomal protein catabolic process | 106/4864 | 187/18723 | 4.31e-19 | 5.87e-17 | 106 |
| GO:000081912 | Skin | cSCC | sister chromatid segregation | 110/4864 | 202/18723 | 5.56e-18 | 6.58e-16 | 110 |
| GO:000007012 | Skin | cSCC | mitotic sister chromatid segregation | 96/4864 | 168/18723 | 9.55e-18 | 1.05e-15 | 96 |
| GO:000705912 | Skin | cSCC | chromosome segregation | 161/4864 | 346/18723 | 8.34e-17 | 8.57e-15 | 161 |
| GO:004586229 | Skin | cSCC | positive regulation of proteolysis | 169/4864 | 372/18723 | 2.43e-16 | 2.21e-14 | 169 |
| GO:000989628 | Skin | cSCC | positive regulation of catabolic process | 206/4864 | 492/18723 | 6.06e-15 | 4.64e-13 | 206 |
| GO:190336429 | Skin | cSCC | positive regulation of cellular protein catabolic process | 85/4864 | 155/18723 | 1.87e-14 | 1.31e-12 | 85 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 |
| SMC2 | SNV | Missense_Mutation | novel | c.1472N>C | p.Arg491Thr | p.R491T | O95347 | protein_coding | tolerated(0.56) | benign(0.01) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| SMC2 | SNV | Missense_Mutation | rs776131090 | c.2308N>A | p.Glu770Lys | p.E770K | O95347 | protein_coding | tolerated(0.36) | benign(0.101) | TCGA-A8-A075-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | epirubicin | CR |
| SMC2 | SNV | Missense_Mutation | c.2269N>C | p.Glu757Gln | p.E757Q | O95347 | protein_coding | tolerated(0.29) | benign(0.088) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SMC2 | SNV | Missense_Mutation | novel | c.2271N>T | p.Glu757Asp | p.E757D | O95347 | protein_coding | tolerated(0.07) | benign(0.049) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMC2 | SNV | Missense_Mutation | novel | c.3260G>A | p.Gly1087Asp | p.G1087D | O95347 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMC2 | SNV | Missense_Mutation | novel | c.2713N>A | p.Asp905Asn | p.D905N | O95347 | protein_coding | deleterious(0.02) | benign(0.012) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SMC2 | SNV | Missense_Mutation | novel | c.2899N>G | p.Gln967Glu | p.Q967E | O95347 | protein_coding | tolerated(0.08) | benign(0.007) | TCGA-PE-A5DD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | |
| SMC2 | SNV | Missense_Mutation | c.1367N>A | p.Arg456Lys | p.R456K | O95347 | protein_coding | tolerated(1) | benign(0) | TCGA-C5-A1MK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD | |
| SMC2 | SNV | Missense_Mutation | c.1831N>A | p.Glu611Lys | p.E611K | O95347 | protein_coding | tolerated(0.43) | benign(0.061) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR | |
| SMC2 | SNV | Missense_Mutation | c.2521G>A | p.Glu841Lys | p.E841K | O95347 | protein_coding | tolerated(0.84) | benign(0.005) | TCGA-MA-AA3Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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 |
| Page: 1 |
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