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Gene: CHMP4B |
Gene summary for CHMP4B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHMP4B | Gene ID | 128866 |
| Gene name | charged multivesicular body protein 4B | |
| Gene Alias | C20orf178 | |
| Cytomap | 20q11.22 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9H444 |
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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 |
| 128866 | CHMP4B | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.98e-05 | 4.42e-01 | 0.0588 |
| 128866 | CHMP4B | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.63e-05 | 4.33e-01 | 0.294 |
| 128866 | CHMP4B | HTA11_99999965104_69814 | Human | Colorectum | MSS | 5.71e-10 | 7.12e-01 | 0.281 |
| 128866 | CHMP4B | HTA11_99999971662_82457 | Human | Colorectum | MSS | 6.68e-50 | 1.54e+00 | 0.3859 |
| 128866 | CHMP4B | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.21e-19 | 1.14e+00 | 0.2585 |
| 128866 | CHMP4B | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.12e-27 | 7.68e-01 | 0.3005 |
| 128866 | CHMP4B | A015-C-203 | Human | Colorectum | FAP | 9.83e-09 | -2.33e-01 | -0.1294 |
| 128866 | CHMP4B | A001-C-108 | Human | Colorectum | FAP | 1.00e-03 | -1.13e-01 | -0.0272 |
| 128866 | CHMP4B | A002-C-205 | Human | Colorectum | FAP | 6.32e-03 | -1.62e-01 | -0.1236 |
| 128866 | CHMP4B | A015-C-006 | Human | Colorectum | FAP | 1.51e-02 | -2.59e-01 | -0.0994 |
| 128866 | CHMP4B | A015-C-106 | Human | Colorectum | FAP | 3.45e-03 | -1.42e-01 | -0.0511 |
| 128866 | CHMP4B | A002-C-114 | Human | Colorectum | FAP | 1.00e-03 | -2.22e-01 | -0.1561 |
| 128866 | CHMP4B | A015-C-104 | Human | Colorectum | FAP | 1.52e-06 | -1.80e-01 | -0.1899 |
| 128866 | CHMP4B | A001-C-014 | Human | Colorectum | FAP | 3.53e-02 | -1.34e-01 | 0.0135 |
| 128866 | CHMP4B | A002-C-016 | Human | Colorectum | FAP | 4.24e-05 | -1.73e-01 | 0.0521 |
| 128866 | CHMP4B | A002-C-116 | Human | Colorectum | FAP | 3.40e-09 | -1.99e-01 | -0.0452 |
| 128866 | CHMP4B | A014-C-008 | Human | Colorectum | FAP | 2.23e-02 | -2.45e-01 | -0.191 |
| 128866 | CHMP4B | A018-E-020 | Human | Colorectum | FAP | 3.40e-03 | -1.79e-01 | -0.2034 |
| 128866 | CHMP4B | F034 | Human | Colorectum | FAP | 1.33e-03 | -7.08e-02 | -0.0665 |
| 128866 | CHMP4B | CRC-3-11773 | Human | Colorectum | CRC | 3.98e-03 | 3.06e-01 | 0.2564 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0016032 | Colorectum | AD | viral process | 168/3918 | 415/18723 | 4.67e-20 | 3.66e-17 | 168 |
| GO:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0019058 | Colorectum | AD | viral life cycle | 119/3918 | 317/18723 | 6.18e-12 | 8.23e-10 | 119 |
| GO:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0051258 | Colorectum | AD | protein polymerization | 112/3918 | 297/18723 | 1.85e-11 | 2.27e-09 | 112 |
| GO:0090150 | Colorectum | AD | establishment of protein localization to membrane | 100/3918 | 260/18723 | 6.01e-11 | 6.33e-09 | 100 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0006900 | Colorectum | AD | vesicle budding from membrane | 32/3918 | 61/18723 | 5.38e-08 | 2.81e-06 | 32 |
| GO:0044403 | Colorectum | AD | biological process involved in symbiotic interaction | 99/3918 | 290/18723 | 1.02e-07 | 4.93e-06 | 99 |
| GO:0006605 | Colorectum | AD | protein targeting | 105/3918 | 314/18723 | 1.39e-07 | 6.44e-06 | 105 |
| GO:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0016050 | Colorectum | AD | vesicle organization | 101/3918 | 300/18723 | 1.65e-07 | 7.17e-06 | 101 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:0051701 | Colorectum | AD | biological process involved in interaction with host | 73/3918 | 203/18723 | 5.08e-07 | 1.88e-05 | 73 |
| GO:0070997 | Colorectum | AD | neuron death | 114/3918 | 361/18723 | 1.13e-06 | 3.72e-05 | 114 |
| GO:0052126 | Colorectum | AD | movement in host environment | 63/3918 | 175/18723 | 2.85e-06 | 8.11e-05 | 63 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 |
| 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 |
| hsa03250 | Colorectum | MSS | Viral life cycle - HIV-1 | 23/1875 | 63/8465 | 6.55e-03 | 2.64e-02 | 1.62e-02 | 23 |
| hsa041445 | Colorectum | MSS | Endocytosis | 102/1875 | 251/8465 | 1.85e-11 | 4.43e-10 | 2.71e-10 | 102 |
| hsa032501 | Colorectum | MSS | Viral life cycle - HIV-1 | 23/1875 | 63/8465 | 6.55e-03 | 2.64e-02 | 1.62e-02 | 23 |
| hsa041446 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041447 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041448 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
| hsa041449 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
| 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 |
| hsa0414429 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| hsa04144113 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| Page: 1 2 3 4 |
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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 |
| CHMP4B | SNV | Missense_Mutation | c.559G>A | p.Glu187Lys | p.E187K | Q9H444 | protein_coding | tolerated(0.36) | benign(0.025) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CHMP4B | insertion | Frame_Shift_Ins | novel | c.471_472insTTTGTATGTAG | p.Glu158PhefsTer15 | p.E158Ffs*15 | Q9H444 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CHMP4B | insertion | Frame_Shift_Ins | novel | c.473_474insCCTTGATAGTGCCACCTGTAGG | p.Glu158AspfsTer10 | p.E158Dfs*10 | Q9H444 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| CHMP4B | insertion | Frame_Shift_Ins | novel | c.364_365insT | p.Asn122IlefsTer6 | p.N122Ifs*6 | Q9H444 | protein_coding | TCGA-A8-A085-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CHMP4B | deletion | Frame_Shift_Del | novel | c.367delN | p.Met123TrpfsTer9 | p.M123Wfs*9 | Q9H444 | protein_coding | TCGA-A8-A085-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CHMP4B | SNV | Missense_Mutation | novel | c.202N>A | p.Ala68Thr | p.A68T | Q9H444 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CHMP4B | SNV | Missense_Mutation | novel | c.5C>T | p.Ser2Leu | p.S2L | Q9H444 | protein_coding | deleterious(0) | benign(0) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| CHMP4B | SNV | Missense_Mutation | novel | c.122N>G | p.Glu41Gly | p.E41G | Q9H444 | protein_coding | deleterious(0) | possibly_damaging(0.833) | TCGA-A6-6652-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Targeted Molecular therapy | cetuximab | SD |
| CHMP4B | SNV | Missense_Mutation | rs746089715 | c.497N>T | p.Ala166Val | p.A166V | Q9H444 | protein_coding | tolerated(0.11) | probably_damaging(0.962) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| CHMP4B | deletion | Frame_Shift_Del | c.62delN | p.Gln23ArgfsTer14 | p.Q23Rfs*14 | Q9H444 | protein_coding | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | 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 |
| Page: 1 |
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