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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 |
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Transcriptomic changes along malignancy continuum. |
∗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:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
GO:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
GO:19033629 | Breast | Precancer | regulation of cellular protein catabolic process | 36/1080 | 255/18723 | 6.03e-07 | 2.55e-05 | 36 |
GO:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
GO:19030509 | Breast | Precancer | regulation of proteolysis involved in cellular protein catabolic process | 31/1080 | 221/18723 | 4.10e-06 | 1.27e-04 | 31 |
GO:00611369 | Breast | Precancer | regulation of proteasomal protein catabolic process | 24/1080 | 187/18723 | 1.99e-04 | 3.14e-03 | 24 |
GO:00431619 | Breast | Precancer | proteasome-mediated ubiquitin-dependent protein catabolic process | 42/1080 | 412/18723 | 2.49e-04 | 3.72e-03 | 42 |
GO:00098969 | Breast | Precancer | positive regulation of catabolic process | 48/1080 | 492/18723 | 2.62e-04 | 3.84e-03 | 48 |
GO:00313319 | Breast | Precancer | positive regulation of cellular catabolic process | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
GO:00016496 | Breast | Precancer | osteoblast differentiation | 27/1080 | 229/18723 | 3.35e-04 | 4.73e-03 | 27 |
GO:19033649 | Breast | Precancer | positive regulation of cellular protein catabolic process | 20/1080 | 155/18723 | 6.10e-04 | 7.67e-03 | 20 |
GO:19030527 | Breast | Precancer | positive regulation of proteolysis involved in cellular protein catabolic process | 17/1080 | 133/18723 | 1.68e-03 | 1.70e-02 | 17 |
GO:00457329 | Breast | Precancer | positive regulation of protein catabolic process | 25/1080 | 231/18723 | 1.87e-03 | 1.82e-02 | 25 |
GO:19018007 | Breast | Precancer | positive regulation of proteasomal protein catabolic process | 15/1080 | 114/18723 | 2.31e-03 | 2.15e-02 | 15 |
GO:00015036 | Breast | Precancer | ossification | 36/1080 | 408/18723 | 7.53e-03 | 4.98e-02 | 36 |
GO:004586214 | Breast | IDC | positive regulation of proteolysis | 66/1434 | 372/18723 | 9.76e-11 | 1.29e-08 | 66 |
GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
GO:004217614 | Breast | IDC | regulation of protein catabolic process | 63/1434 | 391/18723 | 1.32e-08 | 9.61e-07 | 63 |
GO:190336214 | Breast | IDC | regulation of cellular protein catabolic process | 46/1434 | 255/18723 | 4.00e-08 | 2.68e-06 | 46 |
GO:190305014 | Breast | IDC | regulation of proteolysis involved in cellular protein catabolic process | 41/1434 | 221/18723 | 9.77e-08 | 5.84e-06 | 41 |
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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 |
SMC2 | SNV | Missense_Mutation | c.1460N>A | p.Arg487His | p.R487H | O95347 | protein_coding | tolerated(0.28) | benign(0.005) | TCGA-BR-4292-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMC2 | SNV | Missense_Mutation | c.3294N>G | p.Ile1098Met | p.I1098M | O95347 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMC2 | SNV | Missense_Mutation | c.1277C>T | p.Ala426Val | p.A426V | O95347 | protein_coding | tolerated(0.21) | benign(0.179) | TCGA-BR-8361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
SMC2 | SNV | Missense_Mutation | c.2717N>T | p.Ser906Phe | p.S906F | O95347 | protein_coding | tolerated(0.59) | benign(0.024) | TCGA-BR-A4PD-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMC2 | SNV | Missense_Mutation | c.865N>C | p.Asp289His | p.D289H | O95347 | protein_coding | deleterious(0) | possibly_damaging(0.897) | TCGA-D7-6822-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SMC2 | SNV | Missense_Mutation | novel | c.2771N>A | p.Ala924Asp | p.A924D | O95347 | protein_coding | deleterious(0.02) | benign(0.053) | TCGA-D7-A6EY-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
SMC2 | SNV | Missense_Mutation | c.1443N>C | p.Lys481Asn | p.K481N | O95347 | protein_coding | tolerated(0.05) | benign(0.005) | TCGA-SW-A7EB-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | fluorouracil | SD | |
SMC2 | SNV | Missense_Mutation | novel | c.2173N>A | p.Glu725Lys | p.E725K | O95347 | protein_coding | deleterious(0.02) | possibly_damaging(0.823) | TCGA-VQ-A8PE-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
SMC2 | insertion | Frame_Shift_Ins | novel | c.528_529insA | p.Ile179AsnfsTer13 | p.I179Nfs*13 | O95347 | protein_coding | TCGA-BR-4201-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | SD | ||
SMC2 | deletion | Frame_Shift_Del | c.2251delA | p.Thr751ProfsTer9 | p.T751Pfs*9 | O95347 | protein_coding | TCGA-BR-4280-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | 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 |
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