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Gene: TOMM5 |
Gene summary for TOMM5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TOMM5 | Gene ID | 401505 |
| Gene name | translocase of outer mitochondrial membrane 5 | |
| Gene Alias | C9orf105 | |
| Cytomap | 9p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | Q8N4H5 |
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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 |
| 401505 | TOMM5 | GSM4909281 | Human | Breast | IDC | 1.37e-07 | 3.31e-01 | 0.21 |
| 401505 | TOMM5 | GSM4909287 | Human | Breast | IDC | 2.46e-07 | 4.40e-01 | 0.2057 |
| 401505 | TOMM5 | GSM4909290 | Human | Breast | IDC | 3.15e-32 | 8.68e-01 | 0.2096 |
| 401505 | TOMM5 | GSM4909292 | Human | Breast | IDC | 7.31e-07 | 7.85e-01 | 0.1236 |
| 401505 | TOMM5 | GSM4909297 | Human | Breast | IDC | 3.18e-03 | -6.31e-02 | 0.1517 |
| 401505 | TOMM5 | GSM4909304 | Human | Breast | IDC | 5.79e-21 | 5.54e-01 | 0.1636 |
| 401505 | TOMM5 | GSM4909311 | Human | Breast | IDC | 9.50e-14 | 1.61e-01 | 0.1534 |
| 401505 | TOMM5 | GSM4909312 | Human | Breast | IDC | 4.72e-02 | 1.25e-01 | 0.1552 |
| 401505 | TOMM5 | GSM4909319 | Human | Breast | IDC | 4.92e-16 | 1.04e-02 | 0.1563 |
| 401505 | TOMM5 | brca2 | Human | Breast | Precancer | 1.66e-02 | 1.81e-01 | -0.024 |
| 401505 | TOMM5 | P1 | Human | Breast | IDC | 2.71e-04 | -1.49e-01 | 0.1527 |
| 401505 | TOMM5 | DCIS2 | Human | Breast | DCIS | 1.52e-11 | -1.41e-01 | 0.0085 |
| 401505 | TOMM5 | CCII_1 | Human | Cervix | CC | 4.14e-02 | -1.99e-01 | 0.3249 |
| 401505 | TOMM5 | sample1 | Human | Cervix | CC | 1.42e-03 | 4.00e-01 | 0.0959 |
| 401505 | TOMM5 | sample3 | Human | Cervix | CC | 9.43e-27 | 5.62e-01 | 0.1387 |
| 401505 | TOMM5 | L1 | Human | Cervix | CC | 9.18e-04 | 3.64e-01 | 0.0802 |
| 401505 | TOMM5 | T1 | Human | Cervix | CC | 8.71e-08 | 3.84e-01 | 0.0918 |
| 401505 | TOMM5 | T3 | Human | Cervix | CC | 1.31e-28 | 5.98e-01 | 0.1389 |
| 401505 | TOMM5 | LZE2D | Human | Esophagus | HGIN | 1.85e-11 | 8.77e-01 | 0.0642 |
| 401505 | TOMM5 | LZE2T | Human | Esophagus | ESCC | 2.75e-12 | 1.50e+00 | 0.082 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| 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:00068398 | Breast | Precancer | mitochondrial transport | 45/1080 | 254/18723 | 1.37e-11 | 1.88e-09 | 45 |
| GO:00705858 | Breast | Precancer | protein localization to mitochondrion | 21/1080 | 125/18723 | 9.07e-06 | 2.42e-04 | 21 |
| GO:00726558 | Breast | Precancer | establishment of protein localization to mitochondrion | 20/1080 | 120/18723 | 1.66e-05 | 4.03e-04 | 20 |
| GO:00066268 | Breast | Precancer | protein targeting to mitochondrion | 15/1080 | 100/18723 | 5.94e-04 | 7.48e-03 | 15 |
| GO:00066059 | Breast | Precancer | protein targeting | 33/1080 | 314/18723 | 6.50e-04 | 7.99e-03 | 33 |
| GO:00725948 | Breast | Precancer | establishment of protein localization to organelle | 41/1080 | 422/18723 | 7.75e-04 | 9.20e-03 | 41 |
| GO:000683913 | Breast | IDC | mitochondrial transport | 51/1434 | 254/18723 | 1.54e-10 | 1.83e-08 | 51 |
| GO:007058513 | Breast | IDC | protein localization to mitochondrion | 23/1434 | 125/18723 | 6.92e-05 | 1.40e-03 | 23 |
| GO:007265513 | Breast | IDC | establishment of protein localization to mitochondrion | 22/1434 | 120/18723 | 1.04e-04 | 1.97e-03 | 22 |
| GO:000660514 | Breast | IDC | protein targeting | 43/1434 | 314/18723 | 1.44e-04 | 2.53e-03 | 43 |
| GO:007259413 | Breast | IDC | establishment of protein localization to organelle | 51/1434 | 422/18723 | 7.94e-04 | 9.55e-03 | 51 |
| GO:000662613 | Breast | IDC | protein targeting to mitochondrion | 17/1434 | 100/18723 | 1.47e-03 | 1.50e-02 | 17 |
| GO:000683923 | Breast | DCIS | mitochondrial transport | 51/1390 | 254/18723 | 5.04e-11 | 6.79e-09 | 51 |
| GO:007058522 | Breast | DCIS | protein localization to mitochondrion | 23/1390 | 125/18723 | 4.28e-05 | 9.05e-04 | 23 |
| GO:007265522 | Breast | DCIS | establishment of protein localization to mitochondrion | 22/1390 | 120/18723 | 6.60e-05 | 1.31e-03 | 22 |
| GO:000660523 | Breast | DCIS | protein targeting | 43/1390 | 314/18723 | 7.17e-05 | 1.41e-03 | 43 |
| GO:007259423 | Breast | DCIS | establishment of protein localization to organelle | 51/1390 | 422/18723 | 3.91e-04 | 5.40e-03 | 51 |
| GO:000662622 | Breast | DCIS | protein targeting to mitochondrion | 17/1390 | 100/18723 | 1.05e-03 | 1.15e-02 | 17 |
| GO:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
| GO:00068399 | Cervix | CC | mitochondrial transport | 60/2311 | 254/18723 | 4.21e-07 | 1.67e-05 | 60 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| TOMM5 | deletion | Frame_Shift_Del | novel | c.2delN | p.Met1? | p.M1? | Q8N4H5 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TOMM5 | SNV | Missense_Mutation | c.246C>G | p.Cys82Trp | p.C82W | Q8N4H5 | protein_coding | tolerated_low_confidence(0.21) | benign(0.279) | TCGA-A6-3810-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| TOMM5 | SNV | Missense_Mutation | novel | c.202N>A | p.Gly68Ser | p.G68S | Q8N4H5 | protein_coding | tolerated_low_confidence(0.16) | benign(0.082) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TOMM5 | SNV | Missense_Mutation | novel | c.263N>A | p.Gly88Asp | p.G88D | Q8N4H5 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.876) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| TOMM5 | SNV | Missense_Mutation | novel | c.196N>A | p.His66Asn | p.H66N | Q8N4H5 | protein_coding | tolerated_low_confidence(0.11) | benign(0.001) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR |
| Page: 1 |
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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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