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Gene: SMCO4 |
Gene summary for SMCO4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMCO4 | Gene ID | 56935 |
| Gene name | single-pass membrane protein with coiled-coil domains 4 | |
| Gene Alias | C11orf75 | |
| Cytomap | 11q21 | |
| Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | A0A024R3A3 |
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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 |
| 56935 | SMCO4 | GSM4909281 | Human | Breast | IDC | 4.79e-05 | 2.78e-01 | 0.21 |
| 56935 | SMCO4 | GSM4909282 | Human | Breast | IDC | 1.46e-22 | 5.72e-01 | -0.0288 |
| 56935 | SMCO4 | GSM4909285 | Human | Breast | IDC | 1.37e-12 | 3.33e-01 | 0.21 |
| 56935 | SMCO4 | GSM4909286 | Human | Breast | IDC | 1.85e-03 | 9.34e-02 | 0.1081 |
| 56935 | SMCO4 | GSM4909290 | Human | Breast | IDC | 2.70e-07 | 4.09e-01 | 0.2096 |
| 56935 | SMCO4 | GSM4909296 | Human | Breast | IDC | 2.95e-02 | -7.79e-02 | 0.1524 |
| 56935 | SMCO4 | GSM4909297 | Human | Breast | IDC | 6.40e-05 | -1.77e-01 | 0.1517 |
| 56935 | SMCO4 | GSM4909301 | Human | Breast | IDC | 8.76e-04 | -1.93e-01 | 0.1577 |
| 56935 | SMCO4 | GSM4909302 | Human | Breast | IDC | 2.00e-02 | -1.71e-01 | 0.1545 |
| 56935 | SMCO4 | GSM4909311 | Human | Breast | IDC | 1.79e-06 | -1.97e-01 | 0.1534 |
| 56935 | SMCO4 | GSM4909312 | Human | Breast | IDC | 5.49e-07 | -1.97e-01 | 0.1552 |
| 56935 | SMCO4 | GSM4909319 | Human | Breast | IDC | 2.34e-10 | -2.10e-01 | 0.1563 |
| 56935 | SMCO4 | GSM4909320 | Human | Breast | IDC | 4.28e-02 | -2.14e-01 | 0.1575 |
| 56935 | SMCO4 | GSM4909321 | Human | Breast | IDC | 1.75e-09 | -2.14e-01 | 0.1559 |
| 56935 | SMCO4 | brca2 | Human | Breast | Precancer | 3.46e-02 | 9.12e-02 | -0.024 |
| 56935 | SMCO4 | NCCBC5 | Human | Breast | DCIS | 1.49e-03 | 3.41e-02 | 0.2046 |
| 56935 | SMCO4 | P1 | Human | Breast | IDC | 1.55e-07 | -2.14e-01 | 0.1527 |
| 56935 | SMCO4 | DCIS2 | Human | Breast | DCIS | 6.20e-68 | 5.38e-01 | 0.0085 |
| 56935 | SMCO4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.67e-10 | 5.58e-01 | -0.1808 |
| 56935 | SMCO4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.28e-05 | 3.95e-01 | -0.0811 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
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| 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 |
| SMCO4 | SNV | Missense_Mutation | rs140592708 | c.55N>T | p.Arg19Trp | p.R19W | Q9NRQ5 | protein_coding | deleterious(0) | benign(0.433) | TCGA-A5-A0RA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMCO4 | SNV | Missense_Mutation | c.116N>T | p.Ala39Val | p.A39V | Q9NRQ5 | protein_coding | tolerated(0.13) | benign(0) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SMCO4 | SNV | Missense_Mutation | c.26A>G | p.Lys9Arg | p.K9R | Q9NRQ5 | protein_coding | tolerated(0.37) | benign(0) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SMCO4 | SNV | Missense_Mutation | novel | c.136N>A | p.Val46Met | p.V46M | Q9NRQ5 | protein_coding | deleterious(0.01) | benign(0.167) | TCGA-D1-A17Q-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <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 |
| Page: 1 |
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