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Gene: CHD4 |
Gene summary for CHD4 |
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Gene information | Species | Human | Gene symbol | CHD4 | Gene ID | 1108 |
Gene name | chromodomain helicase DNA binding protein 4 | |
Gene Alias | CHD-4 | |
Cytomap | 12p13.31 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q14839 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
1108 | CHD4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.45e-02 | 2.09e-01 | 0.0155 |
1108 | CHD4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.43e-02 | 3.55e-01 | -0.1808 |
1108 | CHD4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.79e-10 | 6.41e-01 | -0.0811 |
1108 | CHD4 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.71e-03 | 3.79e-01 | -0.1088 |
1108 | CHD4 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.13e-15 | 5.77e-01 | -0.1954 |
1108 | CHD4 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.94e-12 | 5.47e-01 | -0.1464 |
1108 | CHD4 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.58e-12 | 5.26e-01 | -0.1001 |
1108 | CHD4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.92e-19 | 8.85e-01 | -0.059 |
1108 | CHD4 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.00e-08 | 6.54e-01 | -0.0842 |
1108 | CHD4 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.01e-16 | 6.90e-01 | 0.096 |
1108 | CHD4 | HTA11_7663_2000001011 | Human | Colorectum | SER | 2.45e-03 | 8.41e-01 | 0.0131 |
1108 | CHD4 | HTA11_6801_2000001011 | Human | Colorectum | SER | 1.63e-05 | 8.31e-01 | 0.0171 |
1108 | CHD4 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.54e-06 | 6.46e-01 | 0.0338 |
1108 | CHD4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.81e-35 | 9.93e-01 | 0.0674 |
1108 | CHD4 | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.43e-02 | 6.23e-01 | 0.0112 |
1108 | CHD4 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.87e-10 | 6.56e-01 | 0.0588 |
1108 | CHD4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 9.51e-23 | 7.84e-01 | 0.294 |
1108 | CHD4 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.10e-05 | 1.25e+00 | 0.3487 |
1108 | CHD4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 4.70e-26 | 1.16e+00 | 0.281 |
1108 | CHD4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.73e-28 | 9.40e-01 | 0.3859 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0006325 | Colorectum | AD | chromatin organization | 119/3918 | 409/18723 | 4.85e-05 | 8.33e-04 | 119 |
GO:0032392 | Colorectum | AD | DNA geometric change | 31/3918 | 90/18723 | 2.02e-03 | 1.63e-02 | 31 |
GO:0006338 | Colorectum | AD | chromatin remodeling | 70/3918 | 255/18723 | 7.44e-03 | 4.53e-02 | 70 |
GO:00063251 | Colorectum | SER | chromatin organization | 89/2897 | 409/18723 | 4.15e-04 | 6.17e-03 | 89 |
GO:00063252 | Colorectum | MSS | chromatin organization | 107/3467 | 409/18723 | 7.22e-05 | 1.21e-03 | 107 |
GO:00323921 | Colorectum | MSS | DNA geometric change | 29/3467 | 90/18723 | 1.26e-03 | 1.20e-02 | 29 |
GO:0032508 | Colorectum | MSS | DNA duplex unwinding | 25/3467 | 84/18723 | 8.27e-03 | 4.99e-02 | 25 |
GO:00063253 | Colorectum | FAP | chromatin organization | 84/2622 | 409/18723 | 1.62e-04 | 2.47e-03 | 84 |
GO:000632516 | Esophagus | HGIN | chromatin organization | 92/2587 | 409/18723 | 1.05e-06 | 4.16e-05 | 92 |
GO:00323926 | Esophagus | HGIN | DNA geometric change | 25/2587 | 90/18723 | 3.77e-04 | 5.85e-03 | 25 |
GO:00325084 | Esophagus | HGIN | DNA duplex unwinding | 22/2587 | 84/18723 | 1.91e-03 | 2.03e-02 | 22 |
GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
GO:0006457110 | Esophagus | ESCC | protein folding | 163/8552 | 212/18723 | 1.13e-20 | 1.74e-18 | 163 |
GO:0006839110 | Esophagus | ESCC | mitochondrial transport | 187/8552 | 254/18723 | 8.35e-20 | 9.81e-18 | 187 |
GO:0033108110 | Esophagus | ESCC | mitochondrial respiratory chain complex assembly | 83/8552 | 93/18723 | 9.56e-19 | 1.05e-16 | 83 |
GO:0072655110 | Esophagus | ESCC | establishment of protein localization to mitochondrion | 97/8552 | 120/18723 | 2.17e-15 | 1.33e-13 | 97 |
GO:0070585110 | Esophagus | ESCC | protein localization to mitochondrion | 100/8552 | 125/18723 | 2.96e-15 | 1.77e-13 | 100 |
GO:001703818 | Esophagus | ESCC | protein import | 149/8552 | 206/18723 | 5.90e-15 | 3.31e-13 | 149 |
GO:0006626110 | Esophagus | ESCC | protein targeting to mitochondrion | 81/8552 | 100/18723 | 3.60e-13 | 1.67e-11 | 81 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa052039 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
hsa0520315 | Esophagus | HGIN | Viral carcinogenesis | 53/1383 | 204/8465 | 2.58e-04 | 2.71e-03 | 2.15e-03 | 53 |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa05165 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
hsa05203 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
hsa051651 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
hsa052031 | Liver | Cirrhotic | Viral carcinogenesis | 76/2530 | 204/8465 | 1.34e-02 | 4.20e-02 | 2.59e-02 | 76 |
hsa051652 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
hsa051653 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
hsa052033 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
hsa051656 | Lung | IAC | Human papillomavirus infection | 71/1053 | 331/8465 | 1.88e-06 | 7.63e-05 | 5.06e-05 | 71 |
hsa052034 | Lung | IAC | Viral carcinogenesis | 43/1053 | 204/8465 | 3.02e-04 | 3.07e-03 | 2.04e-03 | 43 |
hsa0516511 | Lung | IAC | Human papillomavirus infection | 71/1053 | 331/8465 | 1.88e-06 | 7.63e-05 | 5.06e-05 | 71 |
hsa0520311 | Lung | IAC | Viral carcinogenesis | 43/1053 | 204/8465 | 3.02e-04 | 3.07e-03 | 2.04e-03 | 43 |
hsa0516521 | Lung | AIS | Human papillomavirus infection | 64/961 | 331/8465 | 1.03e-05 | 3.04e-04 | 1.95e-04 | 64 |
hsa0520321 | Lung | AIS | Viral carcinogenesis | 37/961 | 204/8465 | 2.49e-03 | 1.49e-02 | 9.55e-03 | 37 |
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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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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 |
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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 |
CHD4 | SNV | Missense_Mutation | novel | c.1591N>A | p.Ser531Thr | p.S531T | Q14839 | protein_coding | tolerated(0.22) | benign(0.369) | TCGA-22-1016-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
CHD4 | SNV | Missense_Mutation | c.3775N>C | p.Asp1259His | p.D1259H | Q14839 | protein_coding | deleterious(0.01) | possibly_damaging(0.695) | TCGA-34-5928-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CHD4 | SNV | Missense_Mutation | c.3319N>C | p.Glu1107Gln | p.E1107Q | Q14839 | protein_coding | deleterious(0.04) | probably_damaging(0.987) | TCGA-39-5019-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
CHD4 | SNV | Missense_Mutation | c.2280G>C | p.Gln760His | p.Q760H | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-43-5668-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Other, specify in notesMAGE3-AS15-NSC-003 | clinical | PD | |
CHD4 | SNV | Missense_Mutation | novel | c.3576N>C | p.Met1192Ile | p.M1192I | Q14839 | protein_coding | deleterious(0) | benign(0.024) | TCGA-56-7822-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | eloxatin | PD |
CHD4 | SNV | Missense_Mutation | novel | c.3548G>A | p.Arg1183His | p.R1183H | Q14839 | protein_coding | deleterious(0.01) | possibly_damaging(0.656) | TCGA-60-2696-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CHD4 | SNV | Missense_Mutation | c.2197N>T | p.Gly733Cys | p.G733C | Q14839 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-63-5131-01 | Lung | lung squamous cell carcinoma | Male | Unknown | I/II | Unknown | Unknown | SD | |
CHD4 | SNV | Missense_Mutation | c.4615N>G | p.Lys1539Glu | p.K1539E | Q14839 | protein_coding | tolerated(0.16) | benign(0.027) | TCGA-66-2777-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
CHD4 | SNV | Missense_Mutation | novel | c.181C>T | p.Arg61Trp | p.R61W | Q14839 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.523) | TCGA-77-7140-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
CHD4 | SNV | Missense_Mutation | rs377488166 | c.1216N>A | p.Glu406Lys | p.E406K | Q14839 | protein_coding | tolerated(0.06) | possibly_damaging(0.557) | TCGA-77-7142-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
1108 | CHD4 | ENZYME, CLINICALLY ACTIONABLE | vorinostat | VORINOSTAT | 26296641 |
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