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Gene: TMEM40 |
Gene summary for TMEM40 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM40 | Gene ID | 55287 |
| Gene name | transmembrane protein 40 | |
| Gene Alias | TMEM40 | |
| Cytomap | 3p25.2 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | B4DXI0 |
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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 |
| 55287 | TMEM40 | LZE4T | Human | Esophagus | ESCC | 1.44e-10 | 3.37e-01 | 0.0811 |
| 55287 | TMEM40 | LZE8T | Human | Esophagus | ESCC | 3.83e-07 | 2.06e-01 | 0.067 |
| 55287 | TMEM40 | LZE24T | Human | Esophagus | ESCC | 1.33e-11 | 4.70e-01 | 0.0596 |
| 55287 | TMEM40 | P1T-E | Human | Esophagus | ESCC | 1.68e-03 | 1.72e-01 | 0.0875 |
| 55287 | TMEM40 | P2T-E | Human | Esophagus | ESCC | 4.16e-02 | 1.43e-01 | 0.1177 |
| 55287 | TMEM40 | P4T-E | Human | Esophagus | ESCC | 1.64e-16 | 6.31e-01 | 0.1323 |
| 55287 | TMEM40 | P5T-E | Human | Esophagus | ESCC | 1.34e-54 | 1.30e+00 | 0.1327 |
| 55287 | TMEM40 | P8T-E | Human | Esophagus | ESCC | 6.68e-11 | 2.54e-01 | 0.0889 |
| 55287 | TMEM40 | P9T-E | Human | Esophagus | ESCC | 4.81e-06 | 1.65e-01 | 0.1131 |
| 55287 | TMEM40 | P10T-E | Human | Esophagus | ESCC | 1.22e-07 | 8.95e-02 | 0.116 |
| 55287 | TMEM40 | P11T-E | Human | Esophagus | ESCC | 1.04e-03 | 5.39e-01 | 0.1426 |
| 55287 | TMEM40 | P12T-E | Human | Esophagus | ESCC | 4.29e-17 | 4.85e-01 | 0.1122 |
| 55287 | TMEM40 | P15T-E | Human | Esophagus | ESCC | 3.33e-08 | 4.25e-01 | 0.1149 |
| 55287 | TMEM40 | P16T-E | Human | Esophagus | ESCC | 1.67e-10 | 2.97e-02 | 0.1153 |
| 55287 | TMEM40 | P20T-E | Human | Esophagus | ESCC | 3.00e-04 | 1.81e-01 | 0.1124 |
| 55287 | TMEM40 | P21T-E | Human | Esophagus | ESCC | 1.89e-02 | 2.01e-01 | 0.1617 |
| 55287 | TMEM40 | P22T-E | Human | Esophagus | ESCC | 5.98e-07 | 7.13e-02 | 0.1236 |
| 55287 | TMEM40 | P23T-E | Human | Esophagus | ESCC | 2.22e-21 | 7.79e-01 | 0.108 |
| 55287 | TMEM40 | P26T-E | Human | Esophagus | ESCC | 3.58e-09 | 3.68e-01 | 0.1276 |
| 55287 | TMEM40 | P27T-E | Human | Esophagus | ESCC | 7.61e-15 | 2.45e-01 | 0.1055 |
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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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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 |
| TMEM40 | SNV | Missense_Mutation | rs758550120 | c.247G>A | p.Gly83Arg | p.G83R | Q8WWA1 | protein_coding | tolerated_low_confidence(0.44) | benign(0.001) | TCGA-AN-A0FZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TMEM40 | insertion | Nonsense_Mutation | novel | c.627_628insGGAATGGCTAAATCAAGCTAATTAACATATGTATCCCTCACA | p.Arg209_Ile210insGlyMetAlaLysSerSerTerLeuThrTyrValSerLeuThr | p.R209_I210insGMAKSS*LTYVSLT | Q8WWA1 | protein_coding | TCGA-A7-A0CG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| TMEM40 | SNV | Missense_Mutation | c.290A>T | p.Asn97Ile | p.N97I | Q8WWA1 | protein_coding | tolerated_low_confidence(0.16) | benign(0.281) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM40 | SNV | Missense_Mutation | rs201284335 | c.490N>A | p.Val164Ile | p.V164I | Q8WWA1 | protein_coding | tolerated(0.1) | benign(0.012) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TMEM40 | SNV | Missense_Mutation | c.557C>A | p.Ser186Tyr | p.S186Y | Q8WWA1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM40 | SNV | Missense_Mutation | c.557N>A | p.Ser186Tyr | p.S186Y | Q8WWA1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM40 | SNV | Missense_Mutation | novel | c.149C>A | p.Ser50Tyr | p.S50Y | Q8WWA1 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.571) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| TMEM40 | SNV | Missense_Mutation | novel | c.81N>T | p.Glu27Asp | p.E27D | Q8WWA1 | protein_coding | tolerated_low_confidence(0.06) | benign(0.011) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TMEM40 | SNV | Missense_Mutation | c.220N>T | p.Asp74Tyr | p.D74Y | Q8WWA1 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.874) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TMEM40 | SNV | Missense_Mutation | novel | c.149C>A | p.Ser50Tyr | p.S50Y | Q8WWA1 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.571) | TCGA-D1-A16X-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 |
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