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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_2487_2000001011 | Human | Colorectum | SER | 8.95e-11 | 6.88e-01 | -0.1808 |
128866 | CHMP4B | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.56e-16 | 8.06e-01 | -0.0811 |
128866 | CHMP4B | HTA11_78_2000001011 | Human | Colorectum | AD | 4.62e-03 | 3.58e-01 | -0.1088 |
128866 | CHMP4B | HTA11_347_2000001011 | Human | Colorectum | AD | 3.59e-24 | 7.42e-01 | -0.1954 |
128866 | CHMP4B | HTA11_411_2000001011 | Human | Colorectum | SER | 6.15e-06 | 1.01e+00 | -0.2602 |
128866 | CHMP4B | HTA11_2112_2000001011 | Human | Colorectum | SER | 4.13e-09 | 1.10e+00 | -0.2196 |
128866 | CHMP4B | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.27e-11 | 7.05e-01 | -0.1207 |
128866 | CHMP4B | HTA11_83_2000001011 | Human | Colorectum | SER | 5.50e-07 | 6.11e-01 | -0.1526 |
128866 | CHMP4B | HTA11_696_2000001011 | Human | Colorectum | AD | 2.42e-19 | 7.06e-01 | -0.1464 |
128866 | CHMP4B | HTA11_866_2000001011 | Human | Colorectum | AD | 5.60e-04 | 3.80e-01 | -0.1001 |
128866 | CHMP4B | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.04e-19 | 7.60e-01 | -0.059 |
128866 | CHMP4B | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.56e-08 | 8.82e-01 | -0.1706 |
128866 | CHMP4B | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.49e-13 | 1.18e+00 | -0.2061 |
128866 | CHMP4B | HTA11_546_2000001011 | Human | Colorectum | AD | 4.89e-04 | 4.43e-01 | -0.0842 |
128866 | CHMP4B | HTA11_7862_2000001011 | Human | Colorectum | AD | 5.18e-05 | 4.98e-01 | -0.0179 |
128866 | CHMP4B | HTA11_866_3004761011 | Human | Colorectum | AD | 3.04e-21 | 7.88e-01 | 0.096 |
128866 | CHMP4B | HTA11_8622_2000001021 | Human | Colorectum | SER | 8.16e-03 | 4.47e-01 | 0.0528 |
128866 | CHMP4B | HTA11_7663_2000001011 | Human | Colorectum | SER | 4.98e-06 | 8.20e-01 | 0.0131 |
128866 | CHMP4B | HTA11_10623_2000001011 | Human | Colorectum | AD | 2.57e-03 | 4.66e-01 | -0.0177 |
128866 | CHMP4B | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.69e-03 | 3.71e-01 | 0.0674 |
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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:00070324 | Colorectum | CRC | endosome organization | 18/2078 | 82/18723 | 3.37e-03 | 2.88e-02 | 18 |
GO:00105073 | Colorectum | CRC | negative regulation of autophagy | 18/2078 | 85/18723 | 5.04e-03 | 3.87e-02 | 18 |
GO:00362573 | Colorectum | CRC | multivesicular body organization | 9/2078 | 31/18723 | 5.21e-03 | 3.97e-02 | 9 |
GO:00070513 | Colorectum | CRC | spindle organization | 32/2078 | 184/18723 | 6.70e-03 | 4.77e-02 | 32 |
GO:001603216 | Endometrium | AEH | viral process | 110/2100 | 415/18723 | 1.99e-18 | 1.09e-15 | 110 |
GO:001905816 | Endometrium | AEH | viral life cycle | 86/2100 | 317/18723 | 2.53e-15 | 7.58e-13 | 86 |
GO:004440316 | Endometrium | AEH | biological process involved in symbiotic interaction | 70/2100 | 290/18723 | 3.26e-10 | 3.55e-08 | 70 |
GO:007259410 | Endometrium | AEH | establishment of protein localization to organelle | 89/2100 | 422/18723 | 2.41e-09 | 1.90e-07 | 89 |
GO:005170116 | Endometrium | AEH | biological process involved in interaction with host | 53/2100 | 203/18723 | 2.48e-09 | 1.93e-07 | 53 |
GO:005212616 | Endometrium | AEH | movement in host environment | 46/2100 | 175/18723 | 2.20e-08 | 1.31e-06 | 46 |
GO:000660516 | Endometrium | AEH | protein targeting | 68/2100 | 314/18723 | 6.30e-08 | 3.38e-06 | 68 |
GO:00516568 | Endometrium | AEH | establishment of organelle localization | 77/2100 | 390/18723 | 4.89e-07 | 1.94e-05 | 77 |
GO:005125816 | Endometrium | AEH | protein polymerization | 62/2100 | 297/18723 | 9.04e-07 | 3.19e-05 | 62 |
GO:000690015 | Endometrium | AEH | vesicle budding from membrane | 21/2100 | 61/18723 | 1.43e-06 | 4.60e-05 | 21 |
GO:00709727 | Endometrium | AEH | protein localization to endoplasmic reticulum | 23/2100 | 74/18723 | 3.44e-06 | 9.24e-05 | 23 |
GO:00009108 | Endometrium | AEH | cytokinesis | 40/2100 | 173/18723 | 6.01e-06 | 1.49e-04 | 40 |
GO:003133016 | Endometrium | AEH | negative regulation of cellular catabolic process | 53/2100 | 262/18723 | 1.40e-05 | 2.99e-04 | 53 |
GO:000989515 | Endometrium | AEH | negative regulation of catabolic process | 60/2100 | 320/18723 | 4.32e-05 | 7.28e-04 | 60 |
GO:009015010 | Endometrium | AEH | establishment of protein localization to membrane | 51/2100 | 260/18723 | 4.74e-05 | 7.85e-04 | 51 |
GO:000189410 | Endometrium | AEH | tissue homeostasis | 50/2100 | 268/18723 | 2.04e-04 | 2.54e-03 | 50 |
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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 |
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 |
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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 |
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 |
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