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Gene: TMEM59 |
Gene summary for TMEM59 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TMEM59 | Gene ID | 9528 |
| Gene name | transmembrane protein 59 | |
| Gene Alias | C1orf8 | |
| Cytomap | 1p32.3 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | D3DQ48 |
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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 |
| 9528 | TMEM59 | GSM4909280 | Human | Breast | Precancer | 2.06e-02 | -6.36e-01 | 0.0305 |
| 9528 | TMEM59 | GSM4909282 | Human | Breast | IDC | 7.17e-18 | 4.60e-01 | -0.0288 |
| 9528 | TMEM59 | GSM4909285 | Human | Breast | IDC | 1.01e-03 | 2.86e-01 | 0.21 |
| 9528 | TMEM59 | GSM4909293 | Human | Breast | IDC | 1.94e-05 | -1.45e-01 | 0.1581 |
| 9528 | TMEM59 | GSM4909294 | Human | Breast | IDC | 1.12e-11 | -3.60e-01 | 0.2022 |
| 9528 | TMEM59 | GSM4909296 | Human | Breast | IDC | 3.64e-20 | -4.56e-01 | 0.1524 |
| 9528 | TMEM59 | GSM4909297 | Human | Breast | IDC | 1.24e-24 | -7.56e-02 | 0.1517 |
| 9528 | TMEM59 | GSM4909301 | Human | Breast | IDC | 2.23e-03 | -2.35e-01 | 0.1577 |
| 9528 | TMEM59 | GSM4909305 | Human | Breast | IDC | 1.13e-02 | 2.69e-01 | 0.0436 |
| 9528 | TMEM59 | GSM4909306 | Human | Breast | IDC | 1.71e-02 | 2.59e-01 | 0.1564 |
| 9528 | TMEM59 | GSM4909311 | Human | Breast | IDC | 5.58e-51 | -4.41e-01 | 0.1534 |
| 9528 | TMEM59 | GSM4909312 | Human | Breast | IDC | 6.00e-11 | 9.33e-02 | 0.1552 |
| 9528 | TMEM59 | GSM4909316 | Human | Breast | IDC | 1.76e-03 | -1.55e-01 | 0.21 |
| 9528 | TMEM59 | GSM4909319 | Human | Breast | IDC | 3.39e-61 | -5.19e-01 | 0.1563 |
| 9528 | TMEM59 | GSM4909320 | Human | Breast | IDC | 8.30e-12 | -5.78e-01 | 0.1575 |
| 9528 | TMEM59 | GSM4909321 | Human | Breast | IDC | 3.55e-22 | -2.61e-01 | 0.1559 |
| 9528 | TMEM59 | M2 | Human | Breast | IDC | 6.84e-07 | -5.59e-01 | 0.21 |
| 9528 | TMEM59 | NCCBC14 | Human | Breast | DCIS | 3.69e-21 | -2.14e-01 | 0.2021 |
| 9528 | TMEM59 | NCCBC2 | Human | Breast | DCIS | 3.32e-05 | -1.77e-01 | 0.1554 |
| 9528 | TMEM59 | NCCBC3 | Human | Breast | DCIS | 7.78e-03 | 3.68e-02 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 | ||
| 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:00105063 | Colorectum | FAP | regulation of autophagy | 80/2622 | 317/18723 | 6.43e-08 | 4.54e-06 | 80 |
| GO:19030773 | Colorectum | FAP | negative regulation of protein localization to plasma membrane | 11/2622 | 24/18723 | 1.70e-04 | 2.56e-03 | 11 |
| GO:19043762 | Colorectum | FAP | negative regulation of protein localization to cell periphery | 11/2622 | 26/18723 | 4.02e-04 | 4.86e-03 | 11 |
| GO:00064861 | Colorectum | FAP | protein glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
| GO:00434131 | Colorectum | FAP | macromolecule glycosylation | 48/2622 | 226/18723 | 1.85e-03 | 1.57e-02 | 48 |
| GO:00700851 | Colorectum | FAP | glycosylation | 50/2622 | 240/18723 | 2.30e-03 | 1.85e-02 | 50 |
| GO:0009101 | Colorectum | FAP | glycoprotein biosynthetic process | 63/2622 | 317/18723 | 2.31e-03 | 1.86e-02 | 63 |
| GO:19054761 | Colorectum | FAP | negative regulation of protein localization to membrane | 11/2622 | 32/18723 | 3.01e-03 | 2.27e-02 | 11 |
| GO:00458614 | Colorectum | FAP | negative regulation of proteolysis | 68/2622 | 351/18723 | 3.07e-03 | 2.31e-02 | 68 |
| GO:00105081 | Colorectum | FAP | positive regulation of autophagy | 29/2622 | 124/18723 | 3.30e-03 | 2.43e-02 | 29 |
| GO:00726595 | Colorectum | CRC | protein localization to plasma membrane | 80/2078 | 284/18723 | 1.36e-15 | 4.07e-12 | 80 |
| GO:19907785 | Colorectum | CRC | protein localization to cell periphery | 85/2078 | 333/18723 | 8.75e-14 | 1.05e-10 | 85 |
| GO:00098965 | Colorectum | CRC | positive regulation of catabolic process | 102/2078 | 492/18723 | 2.48e-10 | 1.06e-07 | 102 |
| GO:00313315 | Colorectum | CRC | positive regulation of cellular catabolic process | 90/2078 | 427/18723 | 1.19e-09 | 4.20e-07 | 90 |
| GO:19043754 | Colorectum | CRC | regulation of protein localization to cell periphery | 36/2078 | 125/18723 | 4.62e-08 | 5.91e-06 | 36 |
| GO:19054754 | Colorectum | CRC | regulation of protein localization to membrane | 45/2078 | 175/18723 | 4.64e-08 | 5.91e-06 | 45 |
| GO:19030764 | Colorectum | CRC | regulation of protein localization to plasma membrane | 31/2078 | 104/18723 | 1.66e-07 | 1.72e-05 | 31 |
| GO:00105064 | Colorectum | CRC | regulation of autophagy | 62/2078 | 317/18723 | 6.04e-06 | 2.35e-04 | 62 |
| GO:19030774 | Colorectum | CRC | negative regulation of protein localization to plasma membrane | 9/2078 | 24/18723 | 6.92e-04 | 9.05e-03 | 9 |
| GO:19043763 | Colorectum | CRC | negative regulation of protein localization to cell periphery | 9/2078 | 26/18723 | 1.35e-03 | 1.49e-02 | 9 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
| 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 |
| TMEM59 | SNV | Missense_Mutation | c.545C>A | p.Ser182Tyr | p.S182Y | Q9BXS4 | protein_coding | deleterious(0) | possibly_damaging(0.832) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TMEM59 | SNV | Missense_Mutation | c.910N>A | p.Glu304Lys | p.E304K | Q9BXS4 | protein_coding | tolerated(0.24) | benign(0.026) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| TMEM59 | SNV | Missense_Mutation | c.943A>C | p.Lys315Gln | p.K315Q | Q9BXS4 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TMEM59 | SNV | Missense_Mutation | rs776175537 | c.272N>A | p.Arg91Gln | p.R91Q | Q9BXS4 | protein_coding | tolerated(0.57) | benign(0.011) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| TMEM59 | SNV | Missense_Mutation | c.874C>T | p.Pro292Ser | p.P292S | Q9BXS4 | protein_coding | tolerated(0.21) | possibly_damaging(0.863) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| TMEM59 | SNV | Missense_Mutation | rs776175537 | c.272N>A | p.Arg91Gln | p.R91Q | Q9BXS4 | protein_coding | tolerated(0.57) | benign(0.011) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| TMEM59 | SNV | Missense_Mutation | novel | c.664C>A | p.Leu222Ile | p.L222I | Q9BXS4 | protein_coding | tolerated(0.32) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM59 | SNV | Missense_Mutation | rs776175537 | c.272G>A | p.Arg91Gln | p.R91Q | Q9BXS4 | protein_coding | tolerated(0.57) | benign(0.011) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TMEM59 | SNV | Missense_Mutation | novel | c.477N>T | p.Gln159His | p.Q159H | Q9BXS4 | protein_coding | tolerated(0.39) | benign(0.005) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| TMEM59 | SNV | Missense_Mutation | c.655N>G | p.Arg219Gly | p.R219G | Q9BXS4 | protein_coding | tolerated(0.06) | benign(0.007) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
| Page: 1 2 3 4 |
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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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