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Gene: CHD4 |
Gene summary for CHD4 |
Gene summary. |
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 |
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 |
1108 | CHD4 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.08e-05 | 6.48e-01 | 0.2585 |
1108 | CHD4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.77e-20 | 8.19e-01 | 0.3005 |
1108 | CHD4 | A015-C-104 | Human | Colorectum | FAP | 7.83e-05 | 1.36e-01 | -0.1899 |
1108 | CHD4 | A002-C-116 | Human | Colorectum | FAP | 1.59e-02 | -5.47e-02 | -0.0452 |
1108 | CHD4 | LZE2D | Human | Esophagus | HGIN | 5.38e-05 | 5.27e-01 | 0.0642 |
1108 | CHD4 | LZE2T | Human | Esophagus | ESCC | 1.99e-03 | 7.54e-01 | 0.082 |
1108 | CHD4 | LZE4T | Human | Esophagus | ESCC | 8.32e-09 | 3.57e-01 | 0.0811 |
1108 | CHD4 | LZE5T | Human | Esophagus | ESCC | 1.42e-06 | 5.17e-01 | 0.0514 |
1108 | CHD4 | LZE7T | Human | Esophagus | ESCC | 1.57e-12 | 7.41e-01 | 0.0667 |
1108 | CHD4 | LZE8T | Human | Esophagus | ESCC | 4.19e-09 | 5.52e-01 | 0.067 |
1108 | CHD4 | LZE20T | Human | Esophagus | ESCC | 2.47e-04 | 2.11e-01 | 0.0662 |
1108 | CHD4 | LZE22D1 | Human | Esophagus | HGIN | 1.09e-03 | 9.68e-02 | 0.0595 |
1108 | CHD4 | LZE24T | Human | Esophagus | ESCC | 4.08e-13 | 4.57e-01 | 0.0596 |
1108 | CHD4 | LZE21T | Human | Esophagus | ESCC | 2.06e-04 | 4.79e-01 | 0.0655 |
1108 | CHD4 | P1T-E | Human | Esophagus | ESCC | 2.48e-09 | 6.98e-01 | 0.0875 |
1108 | CHD4 | P2T-E | Human | Esophagus | ESCC | 2.93e-49 | 1.05e+00 | 0.1177 |
1108 | CHD4 | P4T-E | Human | Esophagus | ESCC | 5.04e-29 | 8.00e-01 | 0.1323 |
1108 | CHD4 | P5T-E | Human | Esophagus | ESCC | 7.53e-16 | 4.90e-01 | 0.1327 |
1108 | CHD4 | P8T-E | Human | Esophagus | ESCC | 3.20e-30 | 6.51e-01 | 0.0889 |
1108 | CHD4 | P9T-E | Human | Esophagus | ESCC | 3.36e-10 | 2.52e-01 | 0.1131 |
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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: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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Enriched KEGG pathways. |
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 |
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 |
CHD4 | SNV | Missense_Mutation | novel | c.1156G>A | p.Asp386Asn | p.D386N | Q14839 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
CHD4 | SNV | Missense_Mutation | c.266N>T | p.Gly89Val | p.G89V | Q14839 | protein_coding | tolerated_low_confidence(0.05) | benign(0.115) | TCGA-A1-A0SK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
CHD4 | SNV | Missense_Mutation | c.3184C>G | p.Leu1062Val | p.L1062V | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A2-A0CL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
CHD4 | SNV | Missense_Mutation | novel | c.3048N>C | p.Lys1016Asn | p.K1016N | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
CHD4 | SNV | Missense_Mutation | c.2458N>A | p.Glu820Lys | p.E820K | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
CHD4 | SNV | Missense_Mutation | novel | c.800N>T | p.Gly267Val | p.G267V | Q14839 | protein_coding | deleterious(0.02) | probably_damaging(1) | TCGA-A2-A4S2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR |
CHD4 | SNV | Missense_Mutation | c.2629N>T | p.Arg877Trp | p.R877W | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A7-A5ZX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
CHD4 | SNV | Missense_Mutation | c.4007N>A | p.Gly1336Glu | p.G1336E | Q14839 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
CHD4 | SNV | Missense_Mutation | c.3967N>C | p.Glu1323Gln | p.E1323Q | Q14839 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
CHD4 | SNV | Missense_Mutation | c.2630N>A | p.Arg877Gln | p.R877Q | Q14839 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AQ-A1H3-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | 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 |
1108 | CHD4 | ENZYME, CLINICALLY ACTIONABLE | vorinostat | VORINOSTAT | 26296641 |
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