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Gene: CHMP4A |
Gene summary for CHMP4A |
Gene summary. |
Gene information | Species | Human | Gene symbol | CHMP4A | Gene ID | 29082 |
Gene name | charged multivesicular body protein 4A | |
Gene Alias | C14orf123 | |
Cytomap | 14q12 | |
Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9BY43 |
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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 |
29082 | CHMP4A | LZE2T | Human | Esophagus | ESCC | 1.01e-05 | 7.12e-01 | 0.082 |
29082 | CHMP4A | LZE4T | Human | Esophagus | ESCC | 4.91e-30 | 8.18e-01 | 0.0811 |
29082 | CHMP4A | LZE5T | Human | Esophagus | ESCC | 4.13e-15 | 9.58e-01 | 0.0514 |
29082 | CHMP4A | LZE7T | Human | Esophagus | ESCC | 3.71e-10 | 5.25e-01 | 0.0667 |
29082 | CHMP4A | LZE8T | Human | Esophagus | ESCC | 4.50e-15 | 4.37e-01 | 0.067 |
29082 | CHMP4A | LZE20T | Human | Esophagus | ESCC | 1.44e-09 | 3.93e-01 | 0.0662 |
29082 | CHMP4A | LZE22D1 | Human | Esophagus | HGIN | 2.47e-04 | 2.84e-01 | 0.0595 |
29082 | CHMP4A | LZE22T | Human | Esophagus | ESCC | 1.27e-06 | 5.37e-01 | 0.068 |
29082 | CHMP4A | LZE24T | Human | Esophagus | ESCC | 8.95e-36 | 8.39e-01 | 0.0596 |
29082 | CHMP4A | LZE21T | Human | Esophagus | ESCC | 5.20e-09 | 7.18e-01 | 0.0655 |
29082 | CHMP4A | LZE6T | Human | Esophagus | ESCC | 2.15e-14 | 6.26e-01 | 0.0845 |
29082 | CHMP4A | P1T-E | Human | Esophagus | ESCC | 2.23e-11 | 6.59e-01 | 0.0875 |
29082 | CHMP4A | P2T-E | Human | Esophagus | ESCC | 1.81e-22 | 3.49e-01 | 0.1177 |
29082 | CHMP4A | P4T-E | Human | Esophagus | ESCC | 2.11e-31 | 6.62e-01 | 0.1323 |
29082 | CHMP4A | P5T-E | Human | Esophagus | ESCC | 2.56e-42 | 8.12e-01 | 0.1327 |
29082 | CHMP4A | P8T-E | Human | Esophagus | ESCC | 8.71e-38 | 7.39e-01 | 0.0889 |
29082 | CHMP4A | P9T-E | Human | Esophagus | ESCC | 6.45e-20 | 4.54e-01 | 0.1131 |
29082 | CHMP4A | P10T-E | Human | Esophagus | ESCC | 4.31e-33 | 5.74e-01 | 0.116 |
29082 | CHMP4A | P11T-E | Human | Esophagus | ESCC | 1.38e-11 | 4.53e-01 | 0.1426 |
29082 | CHMP4A | P12T-E | Human | Esophagus | ESCC | 1.09e-56 | 9.86e-01 | 0.1122 |
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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:00619525 | Esophagus | HGIN | midbody abscission | 8/2587 | 17/18723 | 9.96e-04 | 1.25e-02 | 8 |
GO:00397027 | Esophagus | HGIN | viral budding via host ESCRT complex | 9/2587 | 21/18723 | 1.10e-03 | 1.35e-02 | 9 |
GO:00325097 | Esophagus | HGIN | endosome transport via multivesicular body sorting pathway | 11/2587 | 31/18723 | 2.02e-03 | 2.12e-02 | 11 |
GO:00070803 | Esophagus | HGIN | mitotic metaphase plate congression | 15/2587 | 50/18723 | 2.35e-03 | 2.39e-02 | 15 |
GO:19024108 | Esophagus | HGIN | mitotic cytokinetic process | 9/2587 | 23/18723 | 2.37e-03 | 2.40e-02 | 9 |
GO:00513103 | Esophagus | HGIN | metaphase plate congression | 18/2587 | 65/18723 | 2.46e-03 | 2.45e-02 | 18 |
GO:000703416 | Esophagus | HGIN | vacuolar transport | 35/2587 | 157/18723 | 2.52e-03 | 2.51e-02 | 35 |
GO:19021162 | Esophagus | HGIN | negative regulation of organelle assembly | 13/2587 | 41/18723 | 2.62e-03 | 2.58e-02 | 13 |
GO:00002816 | Esophagus | HGIN | mitotic cytokinesis | 19/2587 | 71/18723 | 2.90e-03 | 2.81e-02 | 19 |
GO:190121510 | Esophagus | HGIN | negative regulation of neuron death | 43/2587 | 208/18723 | 4.04e-03 | 3.64e-02 | 43 |
GO:00000703 | Esophagus | HGIN | mitotic sister chromatid segregation | 36/2587 | 168/18723 | 4.42e-03 | 3.87e-02 | 36 |
GO:00162422 | Esophagus | HGIN | negative regulation of macroautophagy | 11/2587 | 34/18723 | 4.61e-03 | 3.96e-02 | 11 |
GO:00325066 | Esophagus | HGIN | cytokinetic process | 12/2587 | 39/18723 | 4.97e-03 | 4.18e-02 | 12 |
GO:20007853 | Esophagus | HGIN | regulation of autophagosome assembly | 12/2587 | 39/18723 | 4.97e-03 | 4.18e-02 | 12 |
GO:00467556 | Esophagus | HGIN | viral budding | 9/2587 | 26/18723 | 6.15e-03 | 4.92e-02 | 9 |
GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
GO:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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 |
hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
hsa032509 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
hsa0325014 | Esophagus | ESCC | Viral life cycle - HIV-1 | 54/4205 | 63/8465 | 2.01e-09 | 2.17e-08 | 1.11e-08 | 54 |
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 |
hsa032502 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
hsa0325011 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
hsa032508 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
hsa0325013 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
hsa0414428 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
hsa0325022 | Oral cavity | LP | Viral life cycle - HIV-1 | 32/2418 | 63/8465 | 1.55e-04 | 9.08e-04 | 5.86e-04 | 32 |
hsa0421714 | Oral cavity | LP | Necroptosis | 59/2418 | 159/8465 | 1.15e-02 | 3.91e-02 | 2.52e-02 | 59 |
hsa0414436 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
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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 |
CHMP4A | SNV | Missense_Mutation | rs575738905 | c.346N>A | p.Glu116Lys | p.E116K | Q9BY43 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CHMP4A | SNV | Missense_Mutation | novel | c.618N>T | p.Glu206Asp | p.E206D | Q9BY43 | protein_coding | tolerated(0.44) | possibly_damaging(0.707) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CHMP4A | SNV | Missense_Mutation | c.398N>A | p.Arg133His | p.R133H | Q9BY43 | protein_coding | deleterious(0.02) | probably_damaging(0.99) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHMP4A | SNV | Missense_Mutation | c.569N>A | p.Ser190Tyr | p.S190Y | Q9BY43 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
CHMP4A | SNV | Missense_Mutation | novel | c.341N>T | p.Arg114Ile | p.R114I | Q9BY43 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
CHMP4A | SNV | Missense_Mutation | novel | c.341N>T | p.Arg114Ile | p.R114I | Q9BY43 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CHMP4A | SNV | Missense_Mutation | c.53T>C | p.Met18Thr | p.M18T | Q9BY43 | protein_coding | tolerated_low_confidence(0.07) | benign(0) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
CHMP4A | SNV | Missense_Mutation | c.300N>T | p.Lys100Asn | p.K100N | Q9BY43 | protein_coding | deleterious(0) | possibly_damaging(0.823) | TCGA-D1-A16Y-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
CHMP4A | SNV | Missense_Mutation | novel | c.563N>T | p.Ala188Val | p.A188V | Q9BY43 | protein_coding | tolerated(0.08) | possibly_damaging(0.836) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CHMP4A | SNV | Missense_Mutation | c.569C>T | p.Ser190Phe | p.S190F | Q9BY43 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-EY-A1G8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=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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