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Gene: SMIM3 |
Gene summary for SMIM3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMIM3 | Gene ID | 85027 |
| Gene name | small integral membrane protein 3 | |
| Gene Alias | C5orf62 | |
| Cytomap | 5q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q9BZL3 |
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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 |
| 85027 | SMIM3 | LZE4T | Human | Esophagus | ESCC | 7.92e-08 | -2.88e-01 | 0.0811 |
| 85027 | SMIM3 | LZE8T | Human | Esophagus | ESCC | 7.80e-05 | -4.12e-01 | 0.067 |
| 85027 | SMIM3 | LZE20T | Human | Esophagus | ESCC | 9.91e-07 | -3.77e-01 | 0.0662 |
| 85027 | SMIM3 | LZE24T | Human | Esophagus | ESCC | 2.29e-14 | -2.72e-01 | 0.0596 |
| 85027 | SMIM3 | LZE6T | Human | Esophagus | ESCC | 6.12e-03 | -1.54e-01 | 0.0845 |
| 85027 | SMIM3 | P1T-E | Human | Esophagus | ESCC | 2.32e-04 | -3.44e-01 | 0.0875 |
| 85027 | SMIM3 | P2T-E | Human | Esophagus | ESCC | 1.29e-22 | 8.80e-01 | 0.1177 |
| 85027 | SMIM3 | P4T-E | Human | Esophagus | ESCC | 3.64e-10 | 5.80e-02 | 0.1323 |
| 85027 | SMIM3 | P8T-E | Human | Esophagus | ESCC | 5.49e-04 | -2.62e-01 | 0.0889 |
| 85027 | SMIM3 | P11T-E | Human | Esophagus | ESCC | 3.84e-04 | 6.34e-01 | 0.1426 |
| 85027 | SMIM3 | P12T-E | Human | Esophagus | ESCC | 1.33e-14 | -1.58e-02 | 0.1122 |
| 85027 | SMIM3 | P16T-E | Human | Esophagus | ESCC | 7.27e-10 | 2.95e-01 | 0.1153 |
| 85027 | SMIM3 | P20T-E | Human | Esophagus | ESCC | 2.01e-15 | -1.42e-01 | 0.1124 |
| 85027 | SMIM3 | P21T-E | Human | Esophagus | ESCC | 1.85e-10 | 2.25e-01 | 0.1617 |
| 85027 | SMIM3 | P22T-E | Human | Esophagus | ESCC | 2.50e-04 | -1.29e-01 | 0.1236 |
| 85027 | SMIM3 | P24T-E | Human | Esophagus | ESCC | 1.04e-08 | -1.00e-01 | 0.1287 |
| 85027 | SMIM3 | P26T-E | Human | Esophagus | ESCC | 5.80e-14 | 5.64e-03 | 0.1276 |
| 85027 | SMIM3 | P27T-E | Human | Esophagus | ESCC | 1.09e-10 | 1.99e-01 | 0.1055 |
| 85027 | SMIM3 | P31T-E | Human | Esophagus | ESCC | 1.44e-15 | -3.35e-01 | 0.1251 |
| 85027 | SMIM3 | P32T-E | Human | Esophagus | ESCC | 5.50e-07 | 3.43e-01 | 0.1666 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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 |
| SMIM3 | SNV | Missense_Mutation | rs745884586 | c.152N>A | p.Arg51Gln | p.R51Q | Q9BZL3 | protein_coding | tolerated_low_confidence(0.29) | benign(0.412) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMIM3 | insertion | Frame_Shift_Ins | novel | c.147_148insGTGGTTCAAGTAAGGACTGAATGTGTTAATAGACATA | p.Met50ValfsTer20 | p.M50Vfs*20 | Q9BZL3 | protein_coding | TCGA-BH-A0BM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| SMIM3 | SNV | Missense_Mutation | rs745884586 | c.152G>A | p.Arg51Gln | p.R51Q | Q9BZL3 | protein_coding | tolerated_low_confidence(0.29) | benign(0.412) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SMIM3 | SNV | Missense_Mutation | rs546977535 | c.145N>T | p.Arg49Cys | p.R49C | Q9BZL3 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.833) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SMIM3 | SNV | Missense_Mutation | rs534788836 | c.68N>C | p.Ile23Thr | p.I23T | Q9BZL3 | protein_coding | tolerated_low_confidence(0.13) | benign(0.3) | TCGA-DJ-A3VL-01 | Thyroid | thyroid carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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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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