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Gene: TMCO4 |
Gene summary for TMCO4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | TMCO4 | Gene ID | 255104 |
Gene name | transmembrane and coiled-coil domains 4 | |
Gene Alias | TMCO4 | |
Cytomap | 1p36.13 | |
Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q5TGY1 |
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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 |
255104 | TMCO4 | HTA11_347_2000001011 | Human | Colorectum | AD | 8.91e-12 | 5.29e-01 | -0.1954 |
255104 | TMCO4 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.31e-08 | 5.37e-01 | -0.1464 |
255104 | TMCO4 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.67e-06 | 4.81e-01 | -0.1001 |
255104 | TMCO4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.90e-04 | 4.57e-01 | -0.059 |
255104 | TMCO4 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.13e-03 | 5.43e-01 | -0.0842 |
255104 | TMCO4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.24e-02 | 3.01e-01 | 0.0674 |
255104 | TMCO4 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.54e-04 | 6.87e-01 | 0.0112 |
255104 | TMCO4 | A015-C-203 | Human | Colorectum | FAP | 9.18e-09 | -1.06e-01 | -0.1294 |
255104 | TMCO4 | A001-C-108 | Human | Colorectum | FAP | 6.43e-04 | -4.30e-02 | -0.0272 |
255104 | TMCO4 | A002-C-021 | Human | Colorectum | FAP | 1.11e-05 | 2.59e-01 | 0.1171 |
255104 | TMCO4 | A002-C-205 | Human | Colorectum | FAP | 1.81e-06 | -2.75e-02 | -0.1236 |
255104 | TMCO4 | A015-C-006 | Human | Colorectum | FAP | 5.04e-04 | -1.74e-01 | -0.0994 |
255104 | TMCO4 | A002-C-114 | Human | Colorectum | FAP | 1.53e-05 | -1.98e-01 | -0.1561 |
255104 | TMCO4 | A015-C-104 | Human | Colorectum | FAP | 3.43e-08 | -9.63e-02 | -0.1899 |
255104 | TMCO4 | A002-C-016 | Human | Colorectum | FAP | 8.51e-08 | -1.60e-01 | 0.0521 |
255104 | TMCO4 | A015-C-002 | Human | Colorectum | FAP | 3.76e-03 | -2.48e-01 | -0.0763 |
255104 | TMCO4 | A002-C-116 | Human | Colorectum | FAP | 5.01e-12 | -8.42e-02 | -0.0452 |
255104 | TMCO4 | A014-C-008 | Human | Colorectum | FAP | 1.10e-02 | -1.45e-01 | -0.191 |
255104 | TMCO4 | A018-E-020 | Human | Colorectum | FAP | 1.56e-05 | -1.02e-01 | -0.2034 |
255104 | TMCO4 | F034 | Human | Colorectum | FAP | 7.49e-07 | -1.12e-01 | -0.0665 |
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Transcriptomic changes along malignancy continuum. |
∗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 |
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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 |
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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. |
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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 |
TMCO4 | SNV | Missense_Mutation | c.1774N>A | p.Glu592Lys | p.E592K | Q5TGY1 | protein_coding | tolerated_low_confidence(0.05) | benign(0.06) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
TMCO4 | SNV | Missense_Mutation | novel | c.232N>C | p.Glu78Gln | p.E78Q | Q5TGY1 | protein_coding | tolerated(0.09) | possibly_damaging(0.462) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
TMCO4 | SNV | Missense_Mutation | rs535945007 | c.1348N>A | p.Val450Met | p.V450M | Q5TGY1 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-D8-A1X7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | ChemotherapyHormone Therapy | doxorubicine+cyclophosphamide+tamoxifen | SD |
TMCO4 | insertion | In_Frame_Ins | novel | c.1813_1814insATG | p.Pro605delinsHisAla | p.P605delinsHA | Q5TGY1 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
TMCO4 | insertion | Frame_Shift_Ins | novel | c.1812_1813insACACAACTAACAGAGCATGGTGAATA | p.Pro605ThrfsTer85 | p.P605Tfs*85 | Q5TGY1 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
TMCO4 | SNV | Missense_Mutation | novel | c.1208N>C | p.Phe403Ser | p.F403S | Q5TGY1 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
TMCO4 | SNV | Missense_Mutation | rs534456252 | c.37N>A | p.Gln13Lys | p.Q13K | Q5TGY1 | protein_coding | tolerated_low_confidence(0.41) | benign(0) | TCGA-EK-A2RC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
TMCO4 | SNV | Missense_Mutation | novel | c.373N>A | p.Leu125Ile | p.L125I | Q5TGY1 | protein_coding | tolerated(0.18) | probably_damaging(0.987) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
TMCO4 | SNV | Missense_Mutation | rs376327918 | c.121N>A | p.Ala41Thr | p.A41T | Q5TGY1 | protein_coding | tolerated(0.08) | benign(0.009) | TCGA-PN-A8MA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
TMCO4 | SNV | Missense_Mutation | rs745651024 | c.1702N>A | p.Gly568Arg | p.G568R | Q5TGY1 | protein_coding | tolerated_low_confidence(0.56) | benign(0) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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