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Gene: TMEM9 |
Gene summary for TMEM9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM9 | Gene ID | 252839 |
| Gene name | transmembrane protein 9 | |
| Gene Alias | DERM4 | |
| Cytomap | 1q32.1 | |
| Gene Type | protein-coding | GO ID | GO:0006807 | UniProtAcc | A0A024R967 |
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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 |
| 252839 | TMEM9 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.69e-05 | 1.42e-01 | 0.0155 |
| 252839 | TMEM9 | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.76e-08 | 3.29e-01 | -0.0811 |
| 252839 | TMEM9 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.98e-05 | 1.65e-01 | -0.1954 |
| 252839 | TMEM9 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.12e-02 | 2.45e-01 | -0.1207 |
| 252839 | TMEM9 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.97e-11 | 2.51e-01 | -0.1464 |
| 252839 | TMEM9 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.09e-11 | 3.88e-01 | -0.059 |
| 252839 | TMEM9 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.91e-19 | 4.22e-01 | 0.096 |
| 252839 | TMEM9 | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.98e-06 | 4.19e-01 | 0.0446 |
| 252839 | TMEM9 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.09e-05 | 3.12e-01 | 0.0131 |
| 252839 | TMEM9 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.76e-07 | 2.89e-01 | 0.0338 |
| 252839 | TMEM9 | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.60e-09 | 2.43e-01 | 0.0674 |
| 252839 | TMEM9 | HTA11_6818_2000001011 | Human | Colorectum | AD | 6.78e-04 | 2.70e-01 | 0.0112 |
| 252839 | TMEM9 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.38e-11 | 4.67e-01 | 0.0588 |
| 252839 | TMEM9 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.66e-18 | 4.02e-01 | 0.294 |
| 252839 | TMEM9 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.15e-05 | 6.10e-01 | 0.3487 |
| 252839 | TMEM9 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.85e-10 | 3.18e-01 | 0.281 |
| 252839 | TMEM9 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.09e-27 | 6.41e-01 | 0.3859 |
| 252839 | TMEM9 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.00e-13 | 2.93e-01 | 0.3005 |
| 252839 | TMEM9 | AEH-subject1 | Human | Endometrium | AEH | 5.28e-15 | -3.73e-01 | -0.3059 |
| 252839 | TMEM9 | AEH-subject2 | Human | Endometrium | AEH | 2.99e-16 | -3.90e-01 | -0.2525 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:000703313 | Oral cavity | LP | vacuole organization | 79/4623 | 180/18723 | 1.26e-08 | 4.74e-07 | 79 |
| GO:000724917 | Oral cavity | LP | I-kappaB kinase/NF-kappaB signaling | 110/4623 | 281/18723 | 4.94e-08 | 1.70e-06 | 110 |
| GO:000703213 | Oral cavity | LP | endosome organization | 41/4623 | 82/18723 | 6.46e-07 | 1.73e-05 | 41 |
| GO:0045861110 | Oral cavity | LP | negative regulation of proteolysis | 122/4623 | 351/18723 | 1.32e-05 | 2.34e-04 | 122 |
| GO:001648513 | Oral cavity | LP | protein processing | 83/4623 | 225/18723 | 2.87e-05 | 4.52e-04 | 83 |
| GO:190382813 | Oral cavity | LP | negative regulation of cellular protein localization | 49/4623 | 117/18723 | 3.18e-05 | 4.89e-04 | 49 |
| GO:004206313 | Oral cavity | LP | gliogenesis | 104/4623 | 301/18723 | 7.21e-05 | 9.49e-04 | 104 |
| GO:001604918 | Oral cavity | LP | cell growth | 155/4623 | 482/18723 | 1.08e-04 | 1.31e-03 | 155 |
| GO:000704211 | Oral cavity | LP | lysosomal lumen acidification | 9/4623 | 11/18723 | 1.13e-04 | 1.35e-03 | 9 |
| GO:000704011 | Oral cavity | LP | lysosome organization | 33/4623 | 74/18723 | 1.44e-04 | 1.65e-03 | 33 |
| GO:008017111 | Oral cavity | LP | lytic vacuole organization | 33/4623 | 74/18723 | 1.44e-04 | 1.65e-03 | 33 |
| GO:000155817 | Oral cavity | LP | regulation of cell growth | 134/4623 | 414/18723 | 2.25e-04 | 2.41e-03 | 134 |
| GO:00357511 | Oral cavity | LP | regulation of lysosomal lumen pH | 11/4623 | 16/18723 | 2.52e-04 | 2.63e-03 | 11 |
| GO:001000111 | Oral cavity | LP | glial cell differentiation | 78/4623 | 225/18723 | 4.82e-04 | 4.52e-03 | 78 |
| GO:001605515 | Oral cavity | LP | Wnt signaling pathway | 140/4623 | 444/18723 | 5.80e-04 | 5.35e-03 | 140 |
| GO:190331711 | Oral cavity | LP | regulation of protein maturation | 29/4623 | 67/18723 | 6.51e-04 | 5.90e-03 | 29 |
| GO:019873815 | Oral cavity | LP | cell-cell signaling by wnt | 140/4623 | 446/18723 | 7.12e-04 | 6.38e-03 | 140 |
| GO:007061311 | Oral cavity | LP | regulation of protein processing | 28/4623 | 65/18723 | 8.77e-04 | 7.59e-03 | 28 |
| GO:00109551 | Oral cavity | LP | negative regulation of protein processing | 15/4623 | 29/18723 | 1.55e-03 | 1.20e-02 | 15 |
| GO:19033181 | Oral cavity | LP | negative regulation of protein maturation | 15/4623 | 29/18723 | 1.55e-03 | 1.20e-02 | 15 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 |
| 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 |
| 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 |
| TMEM9 | SNV | Missense_Mutation | c.377C>G | p.Thr126Ser | p.T126S | protein_coding | tolerated(1) | benign(0.427) | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TMEM9 | SNV | Missense_Mutation | rs776119463 | c.529A>G | p.Thr177Ala | p.T177A | protein_coding | deleterious(0.04) | probably_damaging(0.983) | TCGA-CK-5914-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| TMEM9 | SNV | Missense_Mutation | novel | c.458N>A | p.Ala153Glu | p.A153E | protein_coding | deleterious(0.01) | possibly_damaging(0.798) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| TMEM9 | SNV | Missense_Mutation | novel | c.532G>T | p.Val178Phe | p.V178F | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM9 | SNV | Missense_Mutation | novel | c.181G>A | p.Val61Met | p.V61M | protein_coding | deleterious(0.04) | possibly_damaging(0.554) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM9 | SNV | Missense_Mutation | c.538G>A | p.Asp180Asn | p.D180N | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | ||
| TMEM9 | SNV | Missense_Mutation | rs746735599 | c.452C>T | p.Pro151Leu | p.P151L | protein_coding | deleterious(0.04) | benign(0.017) | TCGA-B5-A11H-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Hormone Therapy | megace | SD | |
| TMEM9 | SNV | Missense_Mutation | novel | c.238N>A | p.Glu80Lys | p.E80K | protein_coding | tolerated(0.07) | probably_damaging(0.993) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM9 | SNV | Missense_Mutation | novel | c.519G>T | p.Glu173Asp | p.E173D | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-BG-A3EW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TMEM9 | SNV | Missense_Mutation | c.5N>T | p.Lys2Met | p.K2M | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.984) | TCGA-D1-A15X-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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