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Gene: MBD4 |
Gene summary for MBD4 |
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Gene information | Species | Human | Gene symbol | MBD4 | Gene ID | 8930 |
Gene name | methyl-CpG binding domain 4, DNA glycosylase | |
Gene Alias | MED1 | |
Cytomap | 3q21.3 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | O95243 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
8930 | MBD4 | LZE2D | Human | Esophagus | HGIN | 1.16e-02 | 1.65e-01 | 0.0642 |
8930 | MBD4 | LZE2T | Human | Esophagus | ESCC | 1.30e-05 | 9.10e-01 | 0.082 |
8930 | MBD4 | LZE4T | Human | Esophagus | ESCC | 5.29e-15 | 5.38e-01 | 0.0811 |
8930 | MBD4 | LZE5T | Human | Esophagus | ESCC | 1.48e-04 | 3.58e-01 | 0.0514 |
8930 | MBD4 | LZE7T | Human | Esophagus | ESCC | 2.30e-12 | 1.12e+00 | 0.0667 |
8930 | MBD4 | LZE8T | Human | Esophagus | ESCC | 5.61e-11 | 2.29e-01 | 0.067 |
8930 | MBD4 | LZE20T | Human | Esophagus | ESCC | 3.49e-04 | 1.14e-01 | 0.0662 |
8930 | MBD4 | LZE22T | Human | Esophagus | ESCC | 1.09e-02 | 3.82e-01 | 0.068 |
8930 | MBD4 | LZE24T | Human | Esophagus | ESCC | 7.05e-18 | 4.97e-01 | 0.0596 |
8930 | MBD4 | LZE6T | Human | Esophagus | ESCC | 3.79e-04 | 4.70e-01 | 0.0845 |
8930 | MBD4 | P1T-E | Human | Esophagus | ESCC | 3.09e-17 | 7.30e-01 | 0.0875 |
8930 | MBD4 | P2T-E | Human | Esophagus | ESCC | 9.97e-73 | 1.24e+00 | 0.1177 |
8930 | MBD4 | P4T-E | Human | Esophagus | ESCC | 3.12e-41 | 8.77e-01 | 0.1323 |
8930 | MBD4 | P5T-E | Human | Esophagus | ESCC | 9.04e-26 | 5.55e-01 | 0.1327 |
8930 | MBD4 | P8T-E | Human | Esophagus | ESCC | 1.45e-31 | 6.00e-01 | 0.0889 |
8930 | MBD4 | P9T-E | Human | Esophagus | ESCC | 2.09e-21 | 5.03e-01 | 0.1131 |
8930 | MBD4 | P10T-E | Human | Esophagus | ESCC | 1.11e-41 | 7.81e-01 | 0.116 |
8930 | MBD4 | P11T-E | Human | Esophagus | ESCC | 1.72e-14 | 5.70e-01 | 0.1426 |
8930 | MBD4 | P12T-E | Human | Esophagus | ESCC | 2.34e-22 | 4.67e-01 | 0.1122 |
8930 | MBD4 | P15T-E | Human | Esophagus | ESCC | 3.04e-28 | 6.14e-01 | 0.1149 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:003465519 | Esophagus | HGIN | nucleobase-containing compound catabolic process | 98/2587 | 407/18723 | 1.44e-08 | 8.94e-07 | 98 |
GO:004670017 | Esophagus | HGIN | heterocycle catabolic process | 103/2587 | 445/18723 | 5.44e-08 | 2.99e-06 | 103 |
GO:004427018 | Esophagus | HGIN | cellular nitrogen compound catabolic process | 103/2587 | 451/18723 | 1.10e-07 | 5.56e-06 | 103 |
GO:001943917 | Esophagus | HGIN | aromatic compound catabolic process | 105/2587 | 467/18723 | 1.89e-07 | 9.31e-06 | 105 |
GO:190136117 | Esophagus | HGIN | organic cyclic compound catabolic process | 106/2587 | 495/18723 | 1.94e-06 | 7.13e-05 | 106 |
GO:00196924 | Esophagus | HGIN | deoxyribose phosphate metabolic process | 16/2587 | 42/18723 | 7.90e-05 | 1.76e-03 | 16 |
GO:00092624 | Esophagus | HGIN | deoxyribonucleotide metabolic process | 16/2587 | 44/18723 | 1.51e-04 | 2.97e-03 | 16 |
GO:00093944 | Esophagus | HGIN | 2'-deoxyribonucleotide metabolic process | 15/2587 | 40/18723 | 1.62e-04 | 3.16e-03 | 15 |
GO:00092643 | Esophagus | HGIN | deoxyribonucleotide catabolic process | 12/2587 | 30/18723 | 3.62e-04 | 5.68e-03 | 12 |
GO:00463863 | Esophagus | HGIN | deoxyribose phosphate catabolic process | 12/2587 | 31/18723 | 5.17e-04 | 7.46e-03 | 12 |
GO:000911720 | Esophagus | HGIN | nucleotide metabolic process | 92/2587 | 489/18723 | 1.11e-03 | 1.36e-02 | 92 |
GO:000675320 | Esophagus | HGIN | nucleoside phosphate metabolic process | 93/2587 | 497/18723 | 1.25e-03 | 1.49e-02 | 93 |
GO:00092233 | Esophagus | HGIN | pyrimidine deoxyribonucleotide catabolic process | 8/2587 | 19/18723 | 2.40e-03 | 2.41e-02 | 8 |
GO:0006285 | Esophagus | HGIN | base-excision repair, AP site formation | 6/2587 | 12/18723 | 3.03e-03 | 2.88e-02 | 6 |
GO:00092193 | Esophagus | HGIN | pyrimidine deoxyribonucleotide metabolic process | 9/2587 | 24/18723 | 3.33e-03 | 3.12e-02 | 9 |
GO:00062442 | Esophagus | HGIN | pyrimidine nucleotide catabolic process | 8/2587 | 21/18723 | 5.00e-03 | 4.19e-02 | 8 |
GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa034104 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
hsa0341011 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
hsa03410 | Oral cavity | OSCC | Base excision repair | 32/3704 | 44/8465 | 9.11e-05 | 3.25e-04 | 1.65e-04 | 32 |
hsa034101 | Oral cavity | OSCC | Base excision repair | 32/3704 | 44/8465 | 9.11e-05 | 3.25e-04 | 1.65e-04 | 32 |
hsa034102 | Oral cavity | LP | Base excision repair | 23/2418 | 44/8465 | 7.66e-04 | 3.75e-03 | 2.42e-03 | 23 |
hsa034103 | Oral cavity | LP | Base excision repair | 23/2418 | 44/8465 | 7.66e-04 | 3.75e-03 | 2.42e-03 | 23 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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∗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 |
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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 |
MBD4 | SNV | Missense_Mutation | novel | c.661G>C | p.Asp221His | p.D221H | O95243 | protein_coding | tolerated(0.25) | benign(0) | TCGA-CV-7446-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
MBD4 | SNV | Missense_Mutation | c.1318C>A | p.Pro440Thr | p.P440T | O95243 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-8296-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Chemotherapy | etoposide | PD | |
MBD4 | SNV | Missense_Mutation | rs757487617 | c.350N>C | p.Lys117Thr | p.K117T | O95243 | protein_coding | deleterious(0) | possibly_damaging(0.484) | TCGA-BR-8368-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
MBD4 | SNV | Missense_Mutation | c.187N>T | p.Pro63Ser | p.P63S | O95243 | protein_coding | tolerated(0.25) | benign(0.013) | TCGA-BR-8369-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
MBD4 | SNV | Missense_Mutation | c.967N>G | p.Phe323Val | p.F323V | O95243 | protein_coding | tolerated(0.16) | benign(0.084) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR | |
MBD4 | SNV | Missense_Mutation | novel | c.182N>A | p.Cys61Tyr | p.C61Y | O95243 | protein_coding | deleterious(0.02) | possibly_damaging(0.687) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
8930 | MBD4 | DNA REPAIR | PD1 INHIBITOR | 29760383 |
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