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Gene: CHD2 |
Gene summary for CHD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHD2 | Gene ID | 1106 |
| Gene name | chromodomain helicase DNA binding protein 2 | |
| Gene Alias | DEE94 | |
| Cytomap | 15q26.1 | |
| Gene Type | protein-coding | GO ID | GO:0002244 | UniProtAcc | O14647 |
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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 |
| 1106 | CHD2 | RNA-P7T1-P7T1-2 | Human | Lung | AIS | 9.18e-09 | 8.23e-01 | -0.0876 |
| 1106 | CHD2 | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 1.02e-06 | 7.75e-01 | -0.0822 |
| 1106 | CHD2 | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 4.07e-12 | 9.42e-01 | -0.0809 |
| 1106 | CHD2 | C04 | Human | Oral cavity | OSCC | 3.10e-04 | 4.36e-01 | 0.2633 |
| 1106 | CHD2 | C21 | Human | Oral cavity | OSCC | 1.60e-13 | 6.32e-01 | 0.2678 |
| 1106 | CHD2 | C30 | Human | Oral cavity | OSCC | 1.80e-09 | 7.10e-01 | 0.3055 |
| 1106 | CHD2 | C43 | Human | Oral cavity | OSCC | 1.01e-08 | 1.42e-01 | 0.1704 |
| 1106 | CHD2 | C51 | Human | Oral cavity | OSCC | 2.30e-06 | 5.81e-01 | 0.2674 |
| 1106 | CHD2 | C57 | Human | Oral cavity | OSCC | 9.36e-05 | 1.59e-01 | 0.1679 |
| 1106 | CHD2 | C08 | Human | Oral cavity | OSCC | 8.38e-05 | 2.44e-01 | 0.1919 |
| 1106 | CHD2 | EOLP-1 | Human | Oral cavity | EOLP | 4.68e-18 | 6.01e-01 | -0.0202 |
| 1106 | CHD2 | EOLP-2 | Human | Oral cavity | EOLP | 9.57e-03 | 3.24e-01 | -0.0203 |
| 1106 | CHD2 | NEOLP-1 | Human | Oral cavity | NEOLP | 3.79e-12 | 5.80e-01 | -0.0194 |
| 1106 | CHD2 | NEOLP-2 | Human | Oral cavity | NEOLP | 3.34e-10 | 4.83e-01 | -0.0196 |
| 1106 | CHD2 | NEOLP-3 | Human | Oral cavity | NEOLP | 3.63e-12 | 5.76e-01 | -0.0191 |
| 1106 | CHD2 | SYSMH1 | Human | Oral cavity | OSCC | 3.13e-07 | 1.64e-01 | 0.1127 |
| 1106 | CHD2 | SYSMH2 | Human | Oral cavity | OSCC | 3.30e-12 | 4.59e-01 | 0.2326 |
| 1106 | CHD2 | SYSMH3 | Human | Oral cavity | OSCC | 4.13e-06 | 3.19e-01 | 0.2442 |
| 1106 | CHD2 | SYSMH4 | Human | Oral cavity | OSCC | 5.49e-08 | -1.20e-01 | 0.1226 |
| 1106 | CHD2 | SYSMH6 | Human | Oral cavity | OSCC | 2.00e-08 | 4.57e-02 | 0.1275 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00460349 | Breast | Precancer | ATP metabolic process | 82/1080 | 277/18723 | 1.94e-36 | 5.19e-33 | 82 |
| GO:00061199 | Breast | Precancer | oxidative phosphorylation | 53/1080 | 141/18723 | 1.15e-29 | 2.04e-26 | 53 |
| GO:00090608 | Breast | Precancer | aerobic respiration | 58/1080 | 189/18723 | 5.69e-27 | 7.62e-24 | 58 |
| GO:00060918 | Breast | Precancer | generation of precursor metabolites and energy | 94/1080 | 490/18723 | 1.54e-25 | 1.64e-22 | 94 |
| GO:00453338 | Breast | Precancer | cellular respiration | 59/1080 | 230/18723 | 5.97e-23 | 5.32e-20 | 59 |
| GO:00159808 | Breast | Precancer | energy derivation by oxidation of organic compounds | 70/1080 | 318/18723 | 8.33e-23 | 6.37e-20 | 70 |
| GO:00427738 | Breast | Precancer | ATP synthesis coupled electron transport | 35/1080 | 95/18723 | 1.08e-19 | 5.76e-17 | 35 |
| GO:00427758 | Breast | Precancer | mitochondrial ATP synthesis coupled electron transport | 35/1080 | 95/18723 | 1.08e-19 | 5.76e-17 | 35 |
| GO:00229048 | Breast | Precancer | respiratory electron transport chain | 35/1080 | 114/18723 | 8.51e-17 | 3.26e-14 | 35 |
| GO:00229008 | Breast | Precancer | electron transport chain | 42/1080 | 175/18723 | 1.37e-15 | 4.59e-13 | 42 |
| GO:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
| GO:00362939 | Breast | Precancer | response to decreased oxygen levels | 53/1080 | 322/18723 | 4.09e-12 | 6.84e-10 | 53 |
| GO:00016669 | Breast | Precancer | response to hypoxia | 51/1080 | 307/18723 | 7.33e-12 | 1.11e-09 | 51 |
| GO:00704829 | Breast | Precancer | response to oxygen levels | 55/1080 | 347/18723 | 7.47e-12 | 1.11e-09 | 55 |
| GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
| GO:00362948 | Breast | Precancer | cellular response to decreased oxygen levels | 31/1080 | 161/18723 | 2.61e-09 | 2.11e-07 | 31 |
| GO:00714538 | Breast | Precancer | cellular response to oxygen levels | 32/1080 | 177/18723 | 7.32e-09 | 5.52e-07 | 32 |
| GO:00714565 | Breast | Precancer | cellular response to hypoxia | 29/1080 | 151/18723 | 8.98e-09 | 6.50e-07 | 29 |
| GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
| GO:00434677 | Breast | Precancer | regulation of generation of precursor metabolites and energy | 22/1080 | 130/18723 | 4.95e-06 | 1.51e-04 | 22 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| CHD2 | CD8TCM | Oral cavity | ADJ | PTPRC,RACK1,ELF1, etc. | 3.91e-01 |  |
| CHD2 | DUCT1 | Pancreas | Healthy | RRBP1,RBM25,LUC7L3, etc. | 4.22e-01 |  |
| CHD2 | CD8TRM | Pancreas | PDAC | LINC01578,HNRNPC,SIK3, etc. | 1.74e-01 |  |
| ∗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. |
| Page: 1 |
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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 |
| CHD2 | SNV | Missense_Mutation | novel | c.4091N>T | p.Ser1364Leu | p.S1364L | O14647 | protein_coding | tolerated(0.06) | benign(0.04) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| CHD2 | SNV | Missense_Mutation | novel | c.2893N>G | p.Lys965Glu | p.K965E | O14647 | protein_coding | deleterious(0) | probably_damaging(0.952) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| CHD2 | SNV | Missense_Mutation | rs769085842 | c.5329C>G | p.Leu1777Val | p.L1777V | O14647 | protein_coding | tolerated_low_confidence(0.11) | benign(0.001) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| CHD2 | SNV | Missense_Mutation | novel | c.362G>A | p.Arg121Gln | p.R121Q | O14647 | protein_coding | deleterious(0.03) | probably_damaging(0.978) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHD2 | SNV | Missense_Mutation | novel | c.1696G>A | p.Gly566Ser | p.G566S | O14647 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHD2 | SNV | Missense_Mutation | c.2855A>G | p.Glu952Gly | p.E952G | O14647 | protein_coding | tolerated(0.07) | benign(0.01) | TCGA-AN-A0AS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| CHD2 | SNV | Missense_Mutation | novel | c.569N>A | p.Arg190His | p.R190H | O14647 | protein_coding | tolerated(0.06) | benign(0.026) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| CHD2 | SNV | Missense_Mutation | novel | c.2125N>T | p.Leu709Phe | p.L709F | O14647 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| CHD2 | SNV | Missense_Mutation | rs748103788 | c.3752G>A | p.Arg1251His | p.R1251H | O14647 | protein_coding | tolerated(0.74) | benign(0.007) | TCGA-D8-A1JL-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHD2 | SNV | Missense_Mutation | novel | c.5372N>T | p.Pro1791Leu | p.P1791L | O14647 | protein_coding | tolerated_low_confidence(0.23) | benign(0.003) | TCGA-LL-A441-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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 |
| Page: 1 |
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