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Gene: COPS6 |
Gene summary for COPS6 |
Gene summary. |
Gene information | Species | Human | Gene symbol | COPS6 | Gene ID | 10980 |
Gene name | COP9 signalosome subunit 6 | |
Gene Alias | CSN6 | |
Cytomap | 7q22.1 | |
Gene Type | protein-coding | GO ID | GO:0000338 | UniProtAcc | Q7L5N1 |
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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 |
10980 | COPS6 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.65e-03 | 2.35e-01 | -0.1808 |
10980 | COPS6 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.90e-05 | 3.72e-01 | -0.0811 |
10980 | COPS6 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.58e-06 | 2.04e-01 | -0.1954 |
10980 | COPS6 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.91e-03 | 6.37e-01 | -0.2602 |
10980 | COPS6 | HTA11_2112_2000001011 | Human | Colorectum | SER | 4.13e-03 | 4.23e-01 | -0.2196 |
10980 | COPS6 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.25e-05 | 3.83e-01 | -0.1207 |
10980 | COPS6 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.73e-08 | 3.78e-01 | -0.1464 |
10980 | COPS6 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.41e-08 | 3.78e-01 | -0.059 |
10980 | COPS6 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.32e-04 | 3.90e-01 | -0.1706 |
10980 | COPS6 | HTA11_5216_2000001011 | Human | Colorectum | SER | 5.55e-04 | 4.49e-01 | -0.1462 |
10980 | COPS6 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.28e-10 | 4.00e-01 | 0.096 |
10980 | COPS6 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.78e-04 | 4.06e-01 | 0.0131 |
10980 | COPS6 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.13e-11 | 4.46e-01 | 0.0674 |
10980 | COPS6 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.28e-15 | 5.06e-01 | 0.294 |
10980 | COPS6 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.22e-04 | 3.83e-01 | 0.281 |
10980 | COPS6 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.96e-11 | 5.33e-01 | 0.3859 |
10980 | COPS6 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 9.06e-06 | 4.49e-01 | 0.2585 |
10980 | COPS6 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.40e-15 | 5.56e-01 | 0.3005 |
10980 | COPS6 | AEH-subject1 | Human | Endometrium | AEH | 2.81e-32 | -5.53e-01 | -0.3059 |
10980 | COPS6 | AEH-subject2 | Human | Endometrium | AEH | 5.04e-18 | -4.51e-01 | -0.2525 |
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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 |
GO:00003383 | Esophagus | HGIN | protein deneddylation | 6/2587 | 10/18723 | 8.81e-04 | 1.13e-02 | 6 |
GO:00706463 | Esophagus | HGIN | protein modification by small protein removal | 34/2587 | 157/18723 | 4.68e-03 | 4.02e-02 | 34 |
GO:007064612 | Esophagus | ESCC | protein modification by small protein removal | 95/8552 | 157/18723 | 1.25e-04 | 8.56e-04 | 95 |
GO:000033812 | Esophagus | ESCC | protein deneddylation | 10/8552 | 10/18723 | 3.94e-04 | 2.26e-03 | 10 |
GO:0000338 | Liver | Cirrhotic | protein deneddylation | 7/4634 | 10/18723 | 3.29e-03 | 1.83e-02 | 7 |
GO:00706461 | Liver | HCC | protein modification by small protein removal | 91/7958 | 157/18723 | 6.50e-05 | 5.92e-04 | 91 |
GO:00003381 | Liver | HCC | protein deneddylation | 9/7958 | 10/18723 | 2.79e-03 | 1.31e-02 | 9 |
GO:00003382 | Oral cavity | OSCC | protein deneddylation | 10/7305 | 10/18723 | 8.14e-05 | 6.26e-04 | 10 |
GO:00706462 | Oral cavity | OSCC | protein modification by small protein removal | 77/7305 | 157/18723 | 6.55e-03 | 2.43e-02 | 77 |
GO:000033811 | Oral cavity | LP | protein deneddylation | 9/4623 | 10/18723 | 2.64e-05 | 4.21e-04 | 9 |
GO:00003384 | Skin | cSCC | protein deneddylation | 10/4864 | 10/18723 | 1.39e-06 | 2.40e-05 | 10 |
GO:00706464 | Skin | cSCC | protein modification by small protein removal | 55/4864 | 157/18723 | 7.29e-03 | 3.46e-02 | 55 |
GO:00706465 | Thyroid | PTC | protein modification by small protein removal | 71/5968 | 157/18723 | 3.03e-04 | 2.12e-03 | 71 |
GO:007064613 | Thyroid | ATC | protein modification by small protein removal | 71/6293 | 157/18723 | 1.59e-03 | 7.99e-03 | 71 |
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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 |
COPS6 | SNV | Missense_Mutation | c.607G>A | p.Val203Ile | p.V203I | Q7L5N1 | protein_coding | tolerated(0.1) | possibly_damaging(0.596) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
COPS6 | SNV | Missense_Mutation | rs749647179 | c.905N>C | p.Met302Thr | p.M302T | Q7L5N1 | protein_coding | deleterious(0.05) | benign(0.007) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD |
COPS6 | SNV | Missense_Mutation | c.178N>C | p.Ser60Pro | p.S60P | Q7L5N1 | protein_coding | deleterious(0) | possibly_damaging(0.46) | TCGA-QG-A5YX-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
COPS6 | SNV | Missense_Mutation | c.679N>A | p.Ala227Thr | p.A227T | Q7L5N1 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
COPS6 | SNV | Missense_Mutation | novel | c.238A>C | p.Asn80His | p.N80H | Q7L5N1 | protein_coding | tolerated(0.13) | benign(0.026) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
COPS6 | insertion | In_Frame_Ins | novel | c.209_211dupGGG | p.Gly70dup | p.G70dup | Q7L5N1 | protein_coding | TCGA-AG-3883-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
COPS6 | SNV | Missense_Mutation | c.679G>A | p.Ala227Thr | p.A227T | Q7L5N1 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
COPS6 | SNV | Missense_Mutation | novel | c.743N>A | p.Gly248Glu | p.G248E | Q7L5N1 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
COPS6 | SNV | Missense_Mutation | rs766604429 | c.868N>A | p.Ala290Thr | p.A290T | Q7L5N1 | protein_coding | tolerated(1) | benign(0.014) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
COPS6 | SNV | Missense_Mutation | novel | c.962N>T | p.Arg321Ile | p.R321I | Q7L5N1 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
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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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