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Gene: COMMD1 |
Gene summary for COMMD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | COMMD1 | Gene ID | 150684 |
| Gene name | copper metabolism domain containing 1 | |
| Gene Alias | C2orf5 | |
| Cytomap | 2p15 | |
| Gene Type | protein-coding | GO ID | GO:0002028 | UniProtAcc | Q8N668 |
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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 |
| 150684 | COMMD1 | cirrhotic1 | Human | Liver | Cirrhotic | 2.40e-09 | 2.14e-01 | 0.0202 |
| 150684 | COMMD1 | cirrhotic2 | Human | Liver | Cirrhotic | 1.40e-03 | -1.76e-02 | 0.0201 |
| 150684 | COMMD1 | cirrhotic3 | Human | Liver | Cirrhotic | 1.22e-03 | -3.91e-02 | 0.0215 |
| 150684 | COMMD1 | HCC1 | Human | Liver | HCC | 5.02e-03 | 3.11e+00 | 0.5336 |
| 150684 | COMMD1 | HCC2 | Human | Liver | HCC | 3.94e-03 | 3.47e+00 | 0.5341 |
| 150684 | COMMD1 | HCC5 | Human | Liver | HCC | 8.42e-05 | 1.67e+00 | 0.4932 |
| 150684 | COMMD1 | Pt13.b | Human | Liver | HCC | 5.79e-11 | -4.89e-02 | 0.0251 |
| 150684 | COMMD1 | Pt13.c | Human | Liver | HCC | 2.41e-03 | -3.52e-01 | 0.0076 |
| 150684 | COMMD1 | S014 | Human | Liver | HCC | 6.94e-04 | 5.16e-01 | 0.2254 |
| 150684 | COMMD1 | S015 | Human | Liver | HCC | 4.60e-05 | 5.92e-01 | 0.2375 |
| 150684 | COMMD1 | S016 | Human | Liver | HCC | 2.84e-03 | 4.39e-01 | 0.2243 |
| 150684 | COMMD1 | S027 | Human | Liver | HCC | 4.70e-02 | 6.16e-01 | 0.2446 |
| 150684 | COMMD1 | S028 | Human | Liver | HCC | 4.44e-02 | 4.41e-01 | 0.2503 |
| 150684 | COMMD1 | S029 | Human | Liver | HCC | 5.38e-05 | 6.04e-01 | 0.2581 |
| 150684 | COMMD1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 9.93e-11 | 5.18e-01 | -0.2116 |
| 150684 | COMMD1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 1.50e-02 | 5.13e-01 | -0.2107 |
| 150684 | COMMD1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 1.86e-03 | 3.44e-01 | -0.2119 |
| 150684 | COMMD1 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 3.61e-19 | 6.86e-01 | -0.0166 |
| 150684 | COMMD1 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.69e-23 | 6.93e-01 | -0.0132 |
| 150684 | COMMD1 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 5.12e-23 | 6.69e-01 | -0.013 |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
| GO:1903362 | Colorectum | AD | regulation of cellular protein catabolic process | 109/3918 | 255/18723 | 2.14e-15 | 6.08e-13 | 109 |
| GO:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
| GO:1903050 | Colorectum | AD | regulation of proteolysis involved in cellular protein catabolic process | 92/3918 | 221/18723 | 2.04e-12 | 3.19e-10 | 92 |
| GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
| GO:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0061136 | Colorectum | AD | regulation of proteasomal protein catabolic process | 75/3918 | 187/18723 | 1.65e-09 | 1.20e-07 | 75 |
| GO:2000058 | Colorectum | AD | regulation of ubiquitin-dependent protein catabolic process | 68/3918 | 164/18723 | 1.82e-09 | 1.31e-07 | 68 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:1903320 | Colorectum | AD | regulation of protein modification by small protein conjugation or removal | 86/3918 | 242/18723 | 9.43e-08 | 4.65e-06 | 86 |
| GO:0006892 | Colorectum | AD | post-Golgi vesicle-mediated transport | 45/3918 | 104/18723 | 2.22e-07 | 9.26e-06 | 45 |
| GO:0032434 | Colorectum | AD | regulation of proteasomal ubiquitin-dependent protein catabolic process | 54/3918 | 134/18723 | 2.51e-07 | 1.02e-05 | 54 |
| GO:0055076 | Colorectum | AD | transition metal ion homeostasis | 53/3918 | 138/18723 | 1.89e-06 | 5.65e-05 | 53 |
| GO:0031396 | Colorectum | AD | regulation of protein ubiquitination | 72/3918 | 210/18723 | 4.50e-06 | 1.21e-04 | 72 |
| GO:0006893 | Colorectum | AD | Golgi to plasma membrane transport | 27/3918 | 60/18723 | 2.41e-05 | 4.66e-04 | 27 |
| GO:0002028 | Colorectum | AD | regulation of sodium ion transport | 36/3918 | 90/18723 | 2.89e-05 | 5.37e-04 | 36 |
| GO:1902305 | Colorectum | AD | regulation of sodium ion transmembrane transport | 27/3918 | 68/18723 | 3.19e-04 | 3.80e-03 | 27 |
| GO:1903828 | Colorectum | AD | negative regulation of cellular protein localization | 39/3918 | 117/18723 | 1.18e-03 | 1.06e-02 | 39 |
| GO:0034394 | Colorectum | AD | protein localization to cell surface | 24/3918 | 68/18723 | 4.33e-03 | 2.97e-02 | 24 |
| GO:2000009 | Colorectum | AD | negative regulation of protein localization to cell surface | 7/3918 | 12/18723 | 5.09e-03 | 3.38e-02 | 7 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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 |
| COMMD1 | SNV | Missense_Mutation | c.409N>G | p.Gln137Glu | p.Q137E | Q8N668 | protein_coding | deleterious(0.02) | benign(0.009) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| COMMD1 | SNV | Missense_Mutation | novel | c.443A>G | p.Glu148Gly | p.E148G | Q8N668 | protein_coding | deleterious(0) | probably_damaging(0.965) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| COMMD1 | SNV | Missense_Mutation | rs779213025 | c.340N>T | p.Arg114Cys | p.R114C | Q8N668 | protein_coding | tolerated(0.14) | benign(0.041) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| COMMD1 | SNV | Missense_Mutation | novel | c.157N>A | p.Ala53Thr | p.A53T | Q8N668 | protein_coding | tolerated(0.43) | benign(0.187) | TCGA-EY-A1GU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| COMMD1 | SNV | Missense_Mutation | novel | c.88A>G | p.Ile30Val | p.I30V | Q8N668 | protein_coding | tolerated(0.25) | benign(0.006) | TCGA-86-A4D0-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | etoposide | CR |
| COMMD1 | SNV | Missense_Mutation | novel | c.353G>C | p.Gly118Ala | p.G118A | Q8N668 | protein_coding | tolerated(0.8) | benign(0.02) | TCGA-99-7458-01 | Lung | lung adenocarcinoma | Female | >=65 | III/IV | Targeted Molecular therapy | tarceva | SD |
| COMMD1 | SNV | Missense_Mutation | novel | c.508N>A | p.Gln170Lys | p.Q170K | Q8N668 | protein_coding | tolerated(0.14) | benign(0.294) | TCGA-63-A5MW-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| COMMD1 | SNV | Missense_Mutation | c.433N>G | p.Ile145Val | p.I145V | Q8N668 | protein_coding | tolerated(1) | benign(0) | TCGA-66-2771-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | CR | |
| COMMD1 | SNV | Missense_Mutation | c.425N>C | p.Val142Ala | p.V142A | Q8N668 | protein_coding | tolerated(0.07) | benign(0.318) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
| COMMD1 | insertion | Nonsense_Mutation | novel | c.260_261insTTGAGGTT | p.Ser88Ter | p.S88* | Q8N668 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | SD |
| 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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