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Gene: CHMP3 |
Gene summary for CHMP3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | CHMP3 | Gene ID | 51652 |
Gene name | charged multivesicular body protein 3 | |
Gene Alias | CGI-149 | |
Cytomap | 2p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | Q9Y3E7 |
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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 |
51652 | CHMP3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.05e-34 | 7.46e-01 | 0.0155 |
51652 | CHMP3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.00e-31 | 1.08e+00 | -0.1808 |
51652 | CHMP3 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.69e-05 | 6.60e-01 | 0.0216 |
51652 | CHMP3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.72e-33 | 1.28e+00 | -0.0811 |
51652 | CHMP3 | HTA11_78_2000001011 | Human | Colorectum | AD | 4.39e-32 | 1.23e+00 | -0.1088 |
51652 | CHMP3 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.07e-65 | 1.44e+00 | -0.1954 |
51652 | CHMP3 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.06e-10 | 1.62e+00 | -0.2602 |
51652 | CHMP3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.10e-10 | 1.14e+00 | -0.2196 |
51652 | CHMP3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.00e-13 | 7.38e-01 | -0.1207 |
51652 | CHMP3 | HTA11_83_2000001011 | Human | Colorectum | SER | 4.73e-22 | 1.19e+00 | -0.1526 |
51652 | CHMP3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.06e-52 | 9.70e-01 | -0.1464 |
51652 | CHMP3 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.05e-36 | 7.79e-01 | -0.1001 |
51652 | CHMP3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.53e-38 | 1.20e+00 | -0.059 |
51652 | CHMP3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.13e-21 | 1.28e+00 | -0.1706 |
51652 | CHMP3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.27e-21 | 1.24e+00 | -0.2061 |
51652 | CHMP3 | HTA11_5216_2000001011 | Human | Colorectum | SER | 5.68e-14 | 1.01e+00 | -0.1462 |
51652 | CHMP3 | HTA11_546_2000001011 | Human | Colorectum | AD | 3.50e-17 | 9.44e-01 | -0.0842 |
51652 | CHMP3 | HTA11_9341_2000001011 | Human | Colorectum | SER | 4.60e-04 | 7.17e-01 | -0.00410000000000005 |
51652 | CHMP3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 8.84e-11 | 7.75e-01 | -0.0179 |
51652 | CHMP3 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.36e-24 | 8.07e-01 | 0.096 |
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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:006195215 | Thyroid | ATC | midbody abscission | 14/6293 | 17/18723 | 5.14e-05 | 3.99e-04 | 14 |
GO:000709811 | Thyroid | ATC | centrosome cycle | 65/6293 | 130/18723 | 7.95e-05 | 5.97e-04 | 65 |
GO:004532421 | Thyroid | ATC | late endosome to vacuole transport | 18/6293 | 25/18723 | 9.87e-05 | 7.19e-04 | 18 |
GO:001906821 | Thyroid | ATC | virion assembly | 23/6293 | 35/18723 | 1.03e-04 | 7.41e-04 | 23 |
GO:000690612 | Thyroid | ATC | vesicle fusion | 54/6293 | 106/18723 | 1.67e-04 | 1.14e-03 | 54 |
GO:009017412 | Thyroid | ATC | organelle membrane fusion | 55/6293 | 110/18723 | 2.72e-04 | 1.74e-03 | 55 |
GO:006102511 | Thyroid | ATC | membrane fusion | 76/6293 | 163/18723 | 3.68e-04 | 2.27e-03 | 76 |
GO:003246511 | Thyroid | ATC | regulation of cytokinesis | 47/6293 | 92/18723 | 3.95e-04 | 2.39e-03 | 47 |
GO:003970215 | Thyroid | ATC | viral budding via host ESCRT complex | 15/6293 | 21/18723 | 4.45e-04 | 2.64e-03 | 15 |
GO:000704012 | Thyroid | ATC | lysosome organization | 39/6293 | 74/18723 | 5.41e-04 | 3.13e-03 | 39 |
GO:008017112 | Thyroid | ATC | lytic vacuole organization | 39/6293 | 74/18723 | 5.41e-04 | 3.13e-03 | 39 |
GO:00513027 | Thyroid | ATC | regulation of cell division | 80/6293 | 177/18723 | 8.54e-04 | 4.68e-03 | 80 |
GO:004675515 | Thyroid | ATC | viral budding | 17/6293 | 26/18723 | 9.13e-04 | 4.92e-03 | 17 |
GO:190218821 | Thyroid | ATC | positive regulation of viral release from host cell | 9/6293 | 11/18723 | 1.46e-03 | 7.47e-03 | 9 |
GO:190390221 | Thyroid | ATC | positive regulation of viral life cycle | 18/6293 | 29/18723 | 1.58e-03 | 7.98e-03 | 18 |
GO:001907621 | Thyroid | ATC | viral release from host cell | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:003589021 | Thyroid | ATC | exit from host | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:003589121 | Thyroid | ATC | exit from host cell | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:000833311 | Thyroid | ATC | endosome to lysosome transport | 29/6293 | 55/18723 | 2.65e-03 | 1.22e-02 | 29 |
GO:004390327 | Thyroid | ATC | regulation of biological process involved in symbiotic interaction | 36/6293 | 72/18723 | 2.91e-03 | 1.32e-02 | 36 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa041441 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa041442 | Colorectum | SER | Endocytosis | 81/1580 | 251/8465 | 1.14e-07 | 2.36e-06 | 1.71e-06 | 81 |
hsa04217 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
hsa041443 | Colorectum | SER | Endocytosis | 81/1580 | 251/8465 | 1.14e-07 | 2.36e-06 | 1.71e-06 | 81 |
hsa042171 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
hsa041444 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa041445 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
hsa0414420 | Endometrium | AEH | Endocytosis | 56/1197 | 251/8465 | 2.58e-04 | 2.15e-03 | 1.57e-03 | 56 |
hsa04144110 | Endometrium | AEH | Endocytosis | 56/1197 | 251/8465 | 2.58e-04 | 2.15e-03 | 1.57e-03 | 56 |
hsa0414424 | Endometrium | EEC | Endocytosis | 57/1237 | 251/8465 | 3.34e-04 | 2.82e-03 | 2.10e-03 | 57 |
hsa0414434 | Endometrium | EEC | Endocytosis | 57/1237 | 251/8465 | 3.34e-04 | 2.82e-03 | 2.10e-03 | 57 |
hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
hsa0414413 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
hsa0414422 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
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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 |
CHMP3 | SNV | Missense_Mutation | c.83N>A | p.Arg28Lys | p.R28K | Q9Y3E7 | protein_coding | deleterious(0.02) | benign(0.146) | TCGA-BH-A0B0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
CHMP3 | insertion | In_Frame_Ins | novel | c.11_12insCCCACATCTCAGCTCTGTGATCTC | p.Phe4_Gly5insProHisLeuSerSerValIleSer | p.F4_G5insPHLSSVIS | Q9Y3E7 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
CHMP3 | SNV | Missense_Mutation | c.83N>A | p.Arg28Lys | p.R28K | Q9Y3E7 | protein_coding | deleterious(0.02) | benign(0.146) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHMP3 | SNV | Missense_Mutation | rs368950086 | c.287N>T | p.Ala96Val | p.A96V | Q9Y3E7 | protein_coding | deleterious(0.03) | possibly_damaging(0.858) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
CHMP3 | SNV | Missense_Mutation | novel | c.554C>A | p.Thr185Asn | p.T185N | Q9Y3E7 | protein_coding | deleterious(0.04) | possibly_damaging(0.817) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CHMP3 | SNV | Missense_Mutation | novel | c.63N>T | p.Leu21Phe | p.L21F | Q9Y3E7 | protein_coding | tolerated(0.7) | benign(0.138) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CHMP3 | SNV | Missense_Mutation | c.466N>A | p.Glu156Lys | p.E156K | Q9Y3E7 | protein_coding | deleterious(0.04) | benign(0.195) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
CHMP3 | SNV | Missense_Mutation | novel | c.201N>T | p.Met67Ile | p.M67I | Q9Y3E7 | protein_coding | tolerated(1) | benign(0.003) | TCGA-B5-A11N-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CHMP3 | SNV | Missense_Mutation | novel | c.337N>A | p.Ala113Thr | p.A113T | Q9Y3E7 | protein_coding | tolerated(0.05) | benign(0.222) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CHMP3 | SNV | Missense_Mutation | novel | c.578C>A | p.Pro193His | p.P193H | Q9Y3E7 | protein_coding | deleterious(0.03) | benign(0.379) | TCGA-56-8629-01 | Lung | lung squamous cell carcinoma | Male | <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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