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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 | CA_HPV_1 | Human | Cervix | CC | 2.61e-05 | 7.68e-02 | 0.0264 |
1106 | CHD2 | CCI_2 | Human | Cervix | CC | 1.15e-03 | 7.06e-01 | 0.5249 |
1106 | CHD2 | CCI_3 | Human | Cervix | CC | 4.45e-08 | 7.91e-01 | 0.516 |
1106 | CHD2 | T1 | Human | Cervix | CC | 1.66e-02 | 2.75e-01 | 0.0918 |
1106 | CHD2 | AEH-subject1 | Human | Endometrium | AEH | 2.61e-29 | 6.75e-01 | -0.3059 |
1106 | CHD2 | AEH-subject2 | Human | Endometrium | AEH | 8.27e-05 | 3.44e-01 | -0.2525 |
1106 | CHD2 | AEH-subject3 | Human | Endometrium | AEH | 1.43e-09 | 3.08e-01 | -0.2576 |
1106 | CHD2 | AEH-subject4 | Human | Endometrium | AEH | 1.97e-20 | 7.31e-01 | -0.2657 |
1106 | CHD2 | AEH-subject5 | Human | Endometrium | AEH | 7.30e-36 | 8.60e-01 | -0.2953 |
1106 | CHD2 | EEC-subject1 | Human | Endometrium | EEC | 1.09e-37 | 7.29e-01 | -0.2682 |
1106 | CHD2 | EEC-subject2 | Human | Endometrium | EEC | 4.34e-13 | 4.62e-01 | -0.2607 |
1106 | CHD2 | EEC-subject3 | Human | Endometrium | EEC | 1.86e-18 | 3.56e-01 | -0.2525 |
1106 | CHD2 | EEC-subject4 | Human | Endometrium | EEC | 5.38e-20 | 5.63e-01 | -0.2571 |
1106 | CHD2 | EEC-subject5 | Human | Endometrium | EEC | 8.58e-22 | 6.40e-01 | -0.249 |
1106 | CHD2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.12e-12 | 7.81e-02 | -0.1869 |
1106 | CHD2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 6.40e-12 | -5.28e-02 | -0.1875 |
1106 | CHD2 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 6.89e-15 | 5.05e-02 | -0.1883 |
1106 | CHD2 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.38e-09 | 4.45e-02 | -0.1934 |
1106 | CHD2 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.67e-25 | 9.18e-02 | -0.1917 |
1106 | CHD2 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 1.01e-19 | 8.51e-02 | -0.1916 |
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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: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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
∗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 |
CHD2 | insertion | Frame_Shift_Ins | novel | c.2806_2807insCTCT | p.Asp936AlafsTer30 | p.D936Afs*30 | O14647 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | 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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