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Gene: SMDT1 |
Gene summary for SMDT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMDT1 | Gene ID | 91689 |
| Gene name | single-pass membrane protein with aspartate rich tail 1 | |
| Gene Alias | C22orf32 | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9H4I9 |
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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 |
| 91689 | SMDT1 | GSM4909282 | Human | Breast | IDC | 1.37e-05 | -3.24e-01 | -0.0288 |
| 91689 | SMDT1 | GSM4909285 | Human | Breast | IDC | 3.45e-23 | -5.36e-01 | 0.21 |
| 91689 | SMDT1 | GSM4909286 | Human | Breast | IDC | 1.67e-03 | 8.29e-02 | 0.1081 |
| 91689 | SMDT1 | GSM4909287 | Human | Breast | IDC | 2.18e-10 | -4.95e-01 | 0.2057 |
| 91689 | SMDT1 | GSM4909288 | Human | Breast | IDC | 5.50e-03 | -3.82e-01 | 0.0988 |
| 91689 | SMDT1 | GSM4909293 | Human | Breast | IDC | 3.23e-06 | -2.31e-01 | 0.1581 |
| 91689 | SMDT1 | GSM4909294 | Human | Breast | IDC | 3.41e-08 | -1.99e-01 | 0.2022 |
| 91689 | SMDT1 | GSM4909296 | Human | Breast | IDC | 3.70e-14 | -7.89e-02 | 0.1524 |
| 91689 | SMDT1 | GSM4909297 | Human | Breast | IDC | 8.37e-26 | -1.34e-01 | 0.1517 |
| 91689 | SMDT1 | GSM4909311 | Human | Breast | IDC | 1.76e-50 | -3.88e-01 | 0.1534 |
| 91689 | SMDT1 | GSM4909312 | Human | Breast | IDC | 2.40e-22 | -3.37e-01 | 0.1552 |
| 91689 | SMDT1 | GSM4909313 | Human | Breast | IDC | 1.72e-04 | 1.16e-01 | 0.0391 |
| 91689 | SMDT1 | GSM4909315 | Human | Breast | IDC | 4.51e-07 | -3.35e-01 | 0.21 |
| 91689 | SMDT1 | GSM4909319 | Human | Breast | IDC | 4.71e-72 | -2.31e-01 | 0.1563 |
| 91689 | SMDT1 | GSM4909320 | Human | Breast | IDC | 1.39e-04 | -2.39e-01 | 0.1575 |
| 91689 | SMDT1 | GSM4909321 | Human | Breast | IDC | 1.30e-26 | -3.26e-01 | 0.1559 |
| 91689 | SMDT1 | brca2 | Human | Breast | Precancer | 3.21e-03 | -9.12e-02 | -0.024 |
| 91689 | SMDT1 | brca3 | Human | Breast | Precancer | 8.09e-06 | -2.31e-01 | -0.0263 |
| 91689 | SMDT1 | M2 | Human | Breast | IDC | 4.25e-02 | -2.23e-01 | 0.21 |
| 91689 | SMDT1 | NCCBC14 | Human | Breast | DCIS | 1.39e-12 | -3.27e-01 | 0.2021 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 |
| 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:000683927 | Skin | cSCC | mitochondrial transport | 124/4864 | 254/18723 | 3.54e-15 | 2.81e-13 | 124 |
| GO:199054224 | Skin | cSCC | mitochondrial transmembrane transport | 43/4864 | 102/18723 | 2.68e-04 | 2.16e-03 | 43 |
| GO:00068396 | Stomach | GC | mitochondrial transport | 42/1159 | 254/18723 | 4.95e-09 | 5.72e-07 | 42 |
| GO:19905424 | Stomach | GC | mitochondrial transmembrane transport | 20/1159 | 102/18723 | 3.71e-06 | 1.49e-04 | 20 |
| GO:000683911 | Stomach | CAG with IM | mitochondrial transport | 42/1050 | 254/18723 | 2.58e-10 | 4.44e-08 | 42 |
| GO:199054211 | Stomach | CAG with IM | mitochondrial transmembrane transport | 20/1050 | 102/18723 | 8.13e-07 | 4.05e-05 | 20 |
| GO:000683921 | Stomach | CSG | mitochondrial transport | 42/1034 | 254/18723 | 1.61e-10 | 2.75e-08 | 42 |
| GO:199054221 | Stomach | CSG | mitochondrial transmembrane transport | 20/1034 | 102/18723 | 6.40e-07 | 3.53e-05 | 20 |
| GO:000683931 | Stomach | CAG | mitochondrial transport | 19/552 | 254/18723 | 2.03e-04 | 4.32e-03 | 19 |
| GO:00068395 | Stomach | SIM | mitochondrial transport | 22/708 | 254/18723 | 2.74e-04 | 5.21e-03 | 22 |
| GO:000683928 | Thyroid | PTC | mitochondrial transport | 150/5968 | 254/18723 | 2.76e-19 | 3.34e-17 | 150 |
| GO:199054225 | Thyroid | PTC | mitochondrial transmembrane transport | 57/5968 | 102/18723 | 4.49e-07 | 7.38e-06 | 57 |
| GO:00068515 | Thyroid | PTC | mitochondrial calcium ion transmembrane transport | 16/5968 | 20/18723 | 1.31e-05 | 1.42e-04 | 16 |
| GO:00515608 | Thyroid | PTC | mitochondrial calcium ion homeostasis | 19/5968 | 26/18723 | 1.93e-05 | 1.98e-04 | 19 |
| GO:00364446 | Thyroid | PTC | calcium import into the mitochondrion | 12/5968 | 14/18723 | 4.96e-05 | 4.42e-04 | 12 |
| GO:000683929 | Thyroid | ATC | mitochondrial transport | 151/6293 | 254/18723 | 2.07e-17 | 2.14e-15 | 151 |
| GO:199054226 | Thyroid | ATC | mitochondrial transmembrane transport | 57/6293 | 102/18723 | 3.05e-06 | 3.49e-05 | 57 |
| GO:000685111 | Thyroid | ATC | mitochondrial calcium ion transmembrane transport | 16/6293 | 20/18723 | 2.79e-05 | 2.36e-04 | 16 |
| GO:005156014 | Thyroid | ATC | mitochondrial calcium ion homeostasis | 19/6293 | 26/18723 | 4.49e-05 | 3.61e-04 | 19 |
| GO:003644412 | Thyroid | ATC | calcium import into the mitochondrion | 12/6293 | 14/18723 | 8.96e-05 | 6.59e-04 | 12 |
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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 |
| SMDT1 | insertion | Frame_Shift_Ins | novel | c.319_320insGCCCTCCTAGT | p.Asp107GlyfsTer63 | p.D107Gfs*63 | Q9H4I9 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SMDT1 | insertion | Nonsense_Mutation | novel | c.321_322insTGGTGCACCCGATTGCCTGTAGGGATTTAAAG | p.Ter108TrpfsTer10 | p.*108Wfs*10 | Q9H4I9 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SMDT1 | SNV | Missense_Mutation | novel | c.137N>T | p.Arg46Met | p.R46M | Q9H4I9 | protein_coding | deleterious(0.02) | probably_damaging(0.983) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMDT1 | SNV | Missense_Mutation | rs139230313 | c.206G>A | p.Arg69His | p.R69H | Q9H4I9 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMDT1 | SNV | Missense_Mutation | novel | c.292N>G | p.Phe98Val | p.F98V | Q9H4I9 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-66-2785-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SMDT1 | SNV | Missense_Mutation | novel | c.188N>C | p.Met63Thr | p.M63T | Q9H4I9 | protein_coding | tolerated(0.85) | benign(0.047) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SMDT1 | SNV | Missense_Mutation | novel | c.34N>T | p.Ala12Ser | p.A12S | Q9H4I9 | protein_coding | tolerated(0.28) | benign(0.036) | TCGA-CG-5723-01 | Stomach | stomach 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 |
| Page: 1 |
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