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Gene: SMCHD1 |
Gene summary for SMCHD1 |
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Gene information | Species | Human | Gene symbol | SMCHD1 | Gene ID | 23347 |
Gene name | structural maintenance of chromosomes flexible hinge domain containing 1 | |
Gene Alias | BAMS | |
Cytomap | 18p11.32 | |
Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | A6NHR9 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
23347 | SMCHD1 | CA_HPV_1 | Human | Cervix | CC | 2.63e-05 | 1.83e-01 | 0.0264 |
23347 | SMCHD1 | CA_HPV_2 | Human | Cervix | CC | 3.72e-04 | 2.82e-01 | 0.0391 |
23347 | SMCHD1 | CCI_2 | Human | Cervix | CC | 1.07e-07 | 1.20e+00 | 0.5249 |
23347 | SMCHD1 | CCI_3 | Human | Cervix | CC | 5.71e-04 | 6.59e-01 | 0.516 |
23347 | SMCHD1 | L1 | Human | Cervix | CC | 3.46e-02 | -1.58e-01 | 0.0802 |
23347 | SMCHD1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.41e-17 | -7.13e-01 | 0.0155 |
23347 | SMCHD1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.81e-03 | -5.21e-01 | -0.0811 |
23347 | SMCHD1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.24e-03 | -5.33e-01 | -0.1088 |
23347 | SMCHD1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.75e-02 | -5.63e-01 | -0.1207 |
23347 | SMCHD1 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.67e-14 | -4.97e-01 | -0.1464 |
23347 | SMCHD1 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.67e-07 | -4.61e-01 | -0.1001 |
23347 | SMCHD1 | HTA11_7862_2000001011 | Human | Colorectum | AD | 8.57e-05 | -7.50e-01 | -0.0179 |
23347 | SMCHD1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.06e-11 | -6.67e-01 | 0.096 |
23347 | SMCHD1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 8.69e-04 | -8.38e-01 | 0.0446 |
23347 | SMCHD1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.50e-03 | -7.32e-01 | 0.0528 |
23347 | SMCHD1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 2.09e-02 | -6.66e-01 | -0.0177 |
23347 | SMCHD1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 7.06e-03 | -5.52e-01 | 0.0338 |
23347 | SMCHD1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.47e-27 | -6.99e-01 | 0.0674 |
23347 | SMCHD1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.13e-03 | -7.09e-01 | 0.0112 |
23347 | SMCHD1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.31e-04 | -6.30e-01 | 0.0588 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00063257 | Cervix | CC | chromatin organization | 78/2311 | 409/18723 | 5.40e-05 | 8.02e-04 | 78 |
GO:20010209 | Cervix | CC | regulation of response to DNA damage stimulus | 46/2311 | 219/18723 | 1.92e-04 | 2.23e-03 | 46 |
GO:00510528 | Cervix | CC | regulation of DNA metabolic process | 65/2311 | 359/18723 | 9.25e-04 | 7.84e-03 | 65 |
GO:00605413 | Cervix | CC | respiratory system development | 39/2311 | 203/18723 | 3.18e-03 | 2.07e-02 | 39 |
GO:0051052 | Colorectum | AD | regulation of DNA metabolic process | 116/3918 | 359/18723 | 2.47e-07 | 1.00e-05 | 116 |
GO:0051054 | Colorectum | AD | positive regulation of DNA metabolic process | 73/3918 | 201/18723 | 3.27e-07 | 1.29e-05 | 73 |
GO:2001020 | Colorectum | AD | regulation of response to DNA damage stimulus | 71/3918 | 219/18723 | 4.38e-05 | 7.65e-04 | 71 |
GO:0006325 | Colorectum | AD | chromatin organization | 119/3918 | 409/18723 | 4.85e-05 | 8.33e-04 | 119 |
GO:2001022 | Colorectum | AD | positive regulation of response to DNA damage stimulus | 36/3918 | 105/18723 | 1.02e-03 | 9.47e-03 | 36 |
GO:0006282 | Colorectum | AD | regulation of DNA repair | 42/3918 | 130/18723 | 1.57e-03 | 1.32e-02 | 42 |
GO:00510541 | Colorectum | SER | positive regulation of DNA metabolic process | 53/2897 | 201/18723 | 4.51e-05 | 1.13e-03 | 53 |
GO:00510521 | Colorectum | SER | regulation of DNA metabolic process | 83/2897 | 359/18723 | 8.03e-05 | 1.77e-03 | 83 |
GO:00063251 | Colorectum | SER | chromatin organization | 89/2897 | 409/18723 | 4.15e-04 | 6.17e-03 | 89 |
GO:20010201 | Colorectum | SER | regulation of response to DNA damage stimulus | 49/2897 | 219/18723 | 4.24e-03 | 3.45e-02 | 49 |
GO:00510522 | Colorectum | MSS | regulation of DNA metabolic process | 108/3467 | 359/18723 | 5.86e-08 | 3.10e-06 | 108 |
GO:00510542 | Colorectum | MSS | positive regulation of DNA metabolic process | 69/3467 | 201/18723 | 6.33e-08 | 3.26e-06 | 69 |
GO:20010202 | Colorectum | MSS | regulation of response to DNA damage stimulus | 64/3467 | 219/18723 | 7.20e-05 | 1.21e-03 | 64 |
GO:00063252 | Colorectum | MSS | chromatin organization | 107/3467 | 409/18723 | 7.22e-05 | 1.21e-03 | 107 |
GO:20010221 | Colorectum | MSS | positive regulation of response to DNA damage stimulus | 33/3467 | 105/18723 | 9.83e-04 | 9.86e-03 | 33 |
GO:00062821 | Colorectum | MSS | regulation of DNA repair | 38/3467 | 130/18723 | 1.93e-03 | 1.67e-02 | 38 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SMCHD1 | SNV | Missense_Mutation | c.434N>A | p.Leu145His | p.L145H | A6NHR9 | protein_coding | deleterious(0) | possibly_damaging(0.905) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
SMCHD1 | SNV | Missense_Mutation | c.2974N>G | p.Ile992Val | p.I992V | A6NHR9 | protein_coding | tolerated(1) | benign(0.208) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
SMCHD1 | SNV | Missense_Mutation | c.3784N>C | p.Trp1262Arg | p.W1262R | A6NHR9 | protein_coding | tolerated(0.08) | probably_damaging(0.994) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
SMCHD1 | SNV | Missense_Mutation | rs769623229 | c.4136N>T | p.Ala1379Val | p.A1379V | A6NHR9 | protein_coding | tolerated(0.14) | benign(0.003) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
SMCHD1 | SNV | Missense_Mutation | rs747322089 | c.5936N>T | p.Thr1979Met | p.T1979M | A6NHR9 | protein_coding | tolerated(0.27) | benign(0) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | c.5213N>T | p.Ala1738Val | p.A1738V | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SMCHD1 | SNV | Missense_Mutation | novel | c.1192N>A | p.Asp398Asn | p.D398N | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.5402N>G | p.Phe1801Cys | p.F1801C | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.5525N>T | p.Ala1842Val | p.A1842V | A6NHR9 | protein_coding | deleterious(0.02) | probably_damaging(0.995) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SMCHD1 | SNV | Missense_Mutation | novel | c.5659N>T | p.Arg1887Trp | p.R1887W | A6NHR9 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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