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Gene: SCMH1 |
Gene summary for SCMH1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SCMH1 | Gene ID | 22955 |
Gene name | Scm polycomb group protein homolog 1 | |
Gene Alias | Scml3 | |
Cytomap | 1p34.2 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q96GD3 |
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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 |
22955 | SCMH1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 4.86e-03 | 5.18e-01 | -0.2107 |
22955 | SCMH1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 5.16e-07 | 5.14e-01 | -0.2119 |
22955 | SCMH1 | RNA-P3T-P3T-1 | Human | Lung | IAC | 1.18e-02 | 4.63e-01 | 0.1829 |
22955 | SCMH1 | RNA-P3T-P3T-2 | Human | Lung | IAC | 8.61e-06 | 5.78e-01 | 0.1835 |
22955 | SCMH1 | RNA-P3T-P3T-4 | Human | Lung | IAC | 8.91e-10 | 7.56e-01 | 0.1859 |
22955 | SCMH1 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 5.30e-17 | 6.04e-01 | -0.0166 |
22955 | SCMH1 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 7.82e-25 | 7.37e-01 | -0.0132 |
22955 | SCMH1 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 3.05e-26 | 7.32e-01 | -0.013 |
22955 | SCMH1 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 1.29e-18 | 6.58e-01 | -0.0121 |
22955 | SCMH1 | RNA-P7T1-P7T1-1 | Human | Lung | AIS | 1.97e-03 | 5.36e-01 | -0.0961 |
22955 | SCMH1 | RNA-P7T1-P7T1-2 | Human | Lung | AIS | 8.51e-04 | 5.48e-01 | -0.0876 |
22955 | SCMH1 | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 4.33e-02 | 4.96e-01 | -0.0822 |
22955 | SCMH1 | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 2.01e-03 | 5.00e-01 | -0.0809 |
22955 | SCMH1 | HTA12-23-1 | Human | Pancreas | PDAC | 5.51e-18 | 1.31e+00 | 0.3405 |
22955 | SCMH1 | HTA12-25-1 | Human | Pancreas | PDAC | 1.09e-06 | 6.62e-01 | 0.313 |
22955 | SCMH1 | HTA12-26-1 | Human | Pancreas | PDAC | 3.03e-14 | 7.86e-01 | 0.3728 |
22955 | SCMH1 | HTA12-29-1 | Human | Pancreas | PDAC | 3.32e-50 | 1.00e+00 | 0.3722 |
22955 | SCMH1 | HTA12-30-1 | Human | Pancreas | PDAC | 1.84e-04 | 1.30e+00 | 0.3671 |
22955 | SCMH1 | 047563_1562-all-cells | Human | Prostate | BPH | 1.35e-18 | 5.53e-01 | 0.0791 |
22955 | SCMH1 | 048752_1579-all-cells | Human | Prostate | BPH | 9.06e-63 | 1.03e+00 | 0.1008 |
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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:00063257 | Cervix | CC | chromatin organization | 78/2311 | 409/18723 | 5.40e-05 | 8.02e-04 | 78 |
GO:00063381 | Cervix | CC | chromatin remodeling | 45/2311 | 255/18723 | 8.33e-03 | 4.30e-02 | 45 |
GO:0006325 | Colorectum | AD | chromatin organization | 119/3918 | 409/18723 | 4.85e-05 | 8.33e-04 | 119 |
GO:0006338 | Colorectum | AD | chromatin remodeling | 70/3918 | 255/18723 | 7.44e-03 | 4.53e-02 | 70 |
GO:00063251 | Colorectum | SER | chromatin organization | 89/2897 | 409/18723 | 4.15e-04 | 6.17e-03 | 89 |
GO:00063252 | Colorectum | MSS | chromatin organization | 107/3467 | 409/18723 | 7.22e-05 | 1.21e-03 | 107 |
GO:00063253 | Colorectum | FAP | chromatin organization | 84/2622 | 409/18723 | 1.62e-04 | 2.47e-03 | 84 |
GO:0009952 | Colorectum | FAP | anterior/posterior pattern specification | 41/2622 | 201/18723 | 7.82e-03 | 4.63e-02 | 41 |
GO:00063254 | Colorectum | CRC | chromatin organization | 74/2078 | 409/18723 | 1.48e-05 | 4.61e-04 | 74 |
GO:00099521 | Colorectum | CRC | anterior/posterior pattern specification | 36/2078 | 201/18723 | 2.56e-03 | 2.40e-02 | 36 |
GO:00063258 | Endometrium | AEH | chromatin organization | 64/2100 | 409/18723 | 3.69e-03 | 2.52e-02 | 64 |
GO:000632513 | Endometrium | EEC | chromatin organization | 65/2168 | 409/18723 | 4.98e-03 | 3.14e-02 | 65 |
GO:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
GO:00063255 | Liver | NAFLD | chromatin organization | 64/1882 | 409/18723 | 2.31e-04 | 3.89e-03 | 64 |
GO:000632511 | Liver | HCC | chromatin organization | 206/7958 | 409/18723 | 7.23e-04 | 4.41e-03 | 206 |
GO:00063256 | Lung | IAC | chromatin organization | 69/2061 | 409/18723 | 2.01e-04 | 3.53e-03 | 69 |
GO:000632512 | Lung | AIS | chromatin organization | 62/1849 | 409/18723 | 4.24e-04 | 7.29e-03 | 62 |
GO:00063259 | Prostate | BPH | chromatin organization | 101/3107 | 409/18723 | 1.52e-05 | 1.94e-04 | 101 |
GO:00063382 | Prostate | BPH | chromatin remodeling | 62/3107 | 255/18723 | 9.47e-04 | 5.97e-03 | 62 |
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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 |
SCMH1 | NK | Endometrium | EEC | LDB2,DIAPH3,LINC01572, etc. | 2.51e-02 |
∗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 |
SCMH1 | SNV | Missense_Mutation | novel | c.869C>T | p.Ser290Phe | p.S290F | Q96GD3 | protein_coding | deleterious(0.05) | benign(0.017) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
SCMH1 | SNV | Missense_Mutation | novel | c.1702A>C | p.Asn568His | p.N568H | Q96GD3 | protein_coding | tolerated(0.22) | benign(0.001) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SCMH1 | SNV | Missense_Mutation | c.833N>A | p.Gly278Glu | p.G278E | Q96GD3 | protein_coding | deleterious(0.05) | probably_damaging(0.96) | TCGA-AO-A0JC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD | |
SCMH1 | SNV | Missense_Mutation | c.1681N>G | p.Met561Val | p.M561V | Q96GD3 | protein_coding | tolerated(0.57) | benign(0) | TCGA-C8-A27B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
SCMH1 | insertion | Nonsense_Mutation | novel | c.157_158insTATTACAGTGAGTCTCAATGGGGGACCGAGAGAGTTA | p.Pro53LeufsTer4 | p.P53Lfs*4 | Q96GD3 | protein_coding | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
SCMH1 | deletion | Frame_Shift_Del | novel | c.668delG | p.Gly223AlafsTer5 | p.G223Afs*5 | Q96GD3 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
SCMH1 | deletion | Frame_Shift_Del | novel | c.1160delC | p.Pro387GlnfsTer92 | p.P387Qfs*92 | Q96GD3 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
SCMH1 | SNV | Missense_Mutation | novel | c.1157G>A | p.Gly386Glu | p.G386E | Q96GD3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A8XH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
SCMH1 | SNV | Missense_Mutation | c.1621T>G | p.Ser541Ala | p.S541A | Q96GD3 | protein_coding | tolerated(0.17) | benign(0.001) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
SCMH1 | SNV | Missense_Mutation | c.286G>A | p.Asp96Asn | p.D96N | Q96GD3 | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | 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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