|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TOM1 |
Gene summary for TOM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TOM1 | Gene ID | 10043 |
| Gene name | target of myb1 membrane trafficking protein | |
| Gene Alias | IMD85 | |
| Cytomap | 22q12.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | B3KUF5 |
Top |
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 |
| 10043 | TOM1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.16e-07 | 4.15e-01 | -0.1808 |
| 10043 | TOM1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 7.05e-07 | 3.10e-01 | -0.0811 |
| 10043 | TOM1 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.73e-09 | 2.84e-01 | -0.1954 |
| 10043 | TOM1 | HTA11_411_2000001011 | Human | Colorectum | SER | 3.64e-03 | 6.62e-01 | -0.2602 |
| 10043 | TOM1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.03e-04 | 3.26e-01 | -0.1207 |
| 10043 | TOM1 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.35e-07 | 2.84e-01 | -0.1464 |
| 10043 | TOM1 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.05e-02 | 1.59e-01 | -0.1001 |
| 10043 | TOM1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.37e-11 | 4.71e-01 | -0.059 |
| 10043 | TOM1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.29e-02 | 1.55e-01 | 0.096 |
| 10043 | TOM1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.01e-07 | 4.10e-01 | 0.3859 |
| 10043 | TOM1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.23e-06 | 4.18e-01 | 0.2585 |
| 10043 | TOM1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.47e-04 | 1.55e-01 | 0.3005 |
| 10043 | TOM1 | LZE4T | Human | Esophagus | ESCC | 3.05e-07 | 2.63e-01 | 0.0811 |
| 10043 | TOM1 | LZE5T | Human | Esophagus | ESCC | 1.20e-02 | 2.45e-01 | 0.0514 |
| 10043 | TOM1 | LZE7T | Human | Esophagus | ESCC | 1.52e-02 | 3.04e-01 | 0.0667 |
| 10043 | TOM1 | LZE8T | Human | Esophagus | ESCC | 2.60e-04 | 1.59e-01 | 0.067 |
| 10043 | TOM1 | LZE20T | Human | Esophagus | ESCC | 6.59e-07 | 2.79e-01 | 0.0662 |
| 10043 | TOM1 | LZE24T | Human | Esophagus | ESCC | 4.21e-15 | 3.99e-01 | 0.0596 |
| 10043 | TOM1 | LZE6T | Human | Esophagus | ESCC | 4.51e-03 | 2.33e-01 | 0.0845 |
| 10043 | TOM1 | P1T-E | Human | Esophagus | ESCC | 2.64e-09 | 7.38e-01 | 0.0875 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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 |
| ∗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. |
Top |
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:00467772 | Colorectum | MSS | protein autophosphorylation | 63/3467 | 227/18723 | 3.96e-04 | 4.91e-03 | 63 |
| GO:00073461 | Colorectum | MSS | regulation of mitotic cell cycle | 108/3467 | 457/18723 | 3.30e-03 | 2.50e-02 | 108 |
| GO:01400141 | Colorectum | MSS | mitotic nuclear division | 70/3467 | 287/18723 | 7.48e-03 | 4.72e-02 | 70 |
| GO:00106393 | Colorectum | FAP | negative regulation of organelle organization | 80/2622 | 348/18723 | 3.62e-06 | 1.27e-04 | 80 |
| GO:00467773 | Colorectum | FAP | protein autophosphorylation | 52/2622 | 227/18723 | 1.88e-04 | 2.76e-03 | 52 |
| GO:00458604 | Colorectum | FAP | positive regulation of protein kinase activity | 77/2622 | 386/18723 | 7.31e-04 | 7.81e-03 | 77 |
| GO:00336744 | Colorectum | FAP | positive regulation of kinase activity | 89/2622 | 467/18723 | 1.33e-03 | 1.22e-02 | 89 |
| GO:00073462 | Colorectum | FAP | regulation of mitotic cell cycle | 85/2622 | 457/18723 | 3.41e-03 | 2.48e-02 | 85 |
| GO:00106394 | Colorectum | CRC | negative regulation of organelle organization | 63/2078 | 348/18723 | 6.09e-05 | 1.35e-03 | 63 |
| GO:00458605 | Colorectum | CRC | positive regulation of protein kinase activity | 67/2078 | 386/18723 | 1.34e-04 | 2.55e-03 | 67 |
| GO:00336745 | Colorectum | CRC | positive regulation of kinase activity | 77/2078 | 467/18723 | 2.42e-04 | 4.00e-03 | 77 |
| GO:00467774 | Colorectum | CRC | protein autophosphorylation | 42/2078 | 227/18723 | 6.08e-04 | 8.10e-03 | 42 |
| GO:001063920 | Esophagus | HGIN | negative regulation of organelle organization | 79/2587 | 348/18723 | 4.12e-06 | 1.37e-04 | 79 |
| GO:000734610 | Esophagus | HGIN | regulation of mitotic cell cycle | 98/2587 | 457/18723 | 4.39e-06 | 1.42e-04 | 98 |
| GO:01400146 | Esophagus | HGIN | mitotic nuclear division | 61/2587 | 287/18723 | 3.38e-04 | 5.55e-03 | 61 |
| GO:00459305 | Esophagus | HGIN | negative regulation of mitotic cell cycle | 49/2587 | 235/18723 | 1.88e-03 | 2.01e-02 | 49 |
| GO:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
| GO:000734615 | Esophagus | ESCC | regulation of mitotic cell cycle | 293/8552 | 457/18723 | 8.00e-16 | 5.64e-14 | 293 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| TOM1 | SNV | Missense_Mutation | rs201539247 | c.128N>T | p.Thr43Met | p.T43M | O60784 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A7-A26E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD |
| TOM1 | SNV | Missense_Mutation | novel | c.5N>G | p.Asp2Gly | p.D2G | O60784 | protein_coding | deleterious(0) | possibly_damaging(0.461) | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD |
| TOM1 | SNV | Missense_Mutation | c.1163C>T | p.Ala388Val | p.A388V | O60784 | protein_coding | deleterious(0.01) | benign(0.234) | TCGA-EW-A1P8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | fluorouracil | PD | |
| TOM1 | insertion | Frame_Shift_Ins | novel | c.566_567insAGGGAAG | p.Asp190GlyfsTer20 | p.D190Gfs*20 | O60784 | protein_coding | TCGA-A2-A0CT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | ||
| TOM1 | insertion | Frame_Shift_Ins | novel | c.794_795insAAAATTAGCCAGGCGTGGTG | p.Gln266LysfsTer22 | p.Q266Kfs*22 | O60784 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| TOM1 | insertion | Frame_Shift_Ins | novel | c.1132_1133insGAGGGTACATTATGGTACTGTGGGCACCC | p.Ala378GlyfsTer17 | p.A378Gfs*17 | O60784 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| TOM1 | insertion | Nonsense_Mutation | novel | c.1123_1124insCTTCCCCAGCAGAATCAATGGATAGCGTTTTGACTGTTCTCTAAC | p.Ser375delinsThrSerProAlaGluSerMetAspSerValLeuThrValLeuTerArg | p.S375delinsTSPAESMDSVLTVL*R | O60784 | protein_coding | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| TOM1 | SNV | Missense_Mutation | novel | c.784C>G | p.Arg262Gly | p.R262G | O60784 | protein_coding | deleterious(0) | possibly_damaging(0.551) | TCGA-EK-A2R9-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| TOM1 | SNV | Missense_Mutation | rs371088274 | c.505N>A | p.Val169Met | p.V169M | O60784 | protein_coding | deleterious(0.05) | possibly_damaging(0.872) | TCGA-EK-A2RL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | taxol | PD |
| TOM1 | SNV | Missense_Mutation | rs371791801 | c.283N>A | p.Val95Met | p.V95M | O60784 | protein_coding | deleterious(0.03) | probably_damaging(0.993) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |