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Gene: CHD7 |
Gene summary for CHD7 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHD7 | Gene ID | 55636 |
| Gene name | chromodomain helicase DNA binding protein 7 | |
| Gene Alias | CRG | |
| Cytomap | 8q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9P2D1 |
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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 |
| 55636 | CHD7 | CCI_1 | Human | Cervix | CC | 8.23e-03 | 5.69e-01 | 0.528 |
| 55636 | CHD7 | CCI_2 | Human | Cervix | CC | 8.73e-03 | 7.12e-01 | 0.5249 |
| 55636 | CHD7 | CCI_3 | Human | Cervix | CC | 5.80e-06 | 5.65e-01 | 0.516 |
| 55636 | CHD7 | HTA11_3410_2000001011 | Human | Colorectum | AD | 7.20e-29 | -7.03e-01 | 0.0155 |
| 55636 | CHD7 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.04e-12 | -6.76e-01 | -0.1808 |
| 55636 | CHD7 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.50e-02 | -6.16e-01 | 0.0216 |
| 55636 | CHD7 | HTA11_2112_2000001011 | Human | Colorectum | SER | 9.97e-04 | -7.56e-01 | -0.2196 |
| 55636 | CHD7 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.11e-06 | -6.13e-01 | -0.1207 |
| 55636 | CHD7 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.22e-03 | -2.97e-01 | -0.1464 |
| 55636 | CHD7 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.14e-04 | -3.45e-01 | -0.1001 |
| 55636 | CHD7 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.49e-05 | -6.98e-01 | -0.1706 |
| 55636 | CHD7 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.24e-03 | -6.69e-01 | -0.2061 |
| 55636 | CHD7 | HTA11_9341_2000001011 | Human | Colorectum | SER | 3.95e-03 | -8.56e-01 | -0.00410000000000005 |
| 55636 | CHD7 | HTA11_7862_2000001011 | Human | Colorectum | AD | 9.85e-09 | -7.97e-01 | -0.0179 |
| 55636 | CHD7 | HTA11_866_3004761011 | Human | Colorectum | AD | 6.63e-03 | -3.26e-01 | 0.096 |
| 55636 | CHD7 | HTA11_4255_2000001011 | Human | Colorectum | SER | 2.01e-02 | -6.69e-01 | 0.0446 |
| 55636 | CHD7 | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.10e-04 | -6.47e-01 | 0.0528 |
| 55636 | CHD7 | HTA11_6801_2000001011 | Human | Colorectum | SER | 8.77e-03 | -7.02e-01 | 0.0171 |
| 55636 | CHD7 | HTA11_10711_2000001011 | Human | Colorectum | AD | 7.83e-06 | -4.65e-01 | 0.0338 |
| 55636 | CHD7 | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.12e-04 | -3.41e-01 | 0.0674 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00421108 | Cervix | CC | T cell activation | 107/2311 | 487/18723 | 1.24e-09 | 1.46e-07 | 107 |
| GO:00512359 | Cervix | CC | maintenance of location | 78/2311 | 327/18723 | 5.18e-09 | 4.92e-07 | 78 |
| GO:005165110 | Cervix | CC | maintenance of location in cell | 55/2311 | 214/18723 | 6.63e-08 | 3.85e-06 | 55 |
| GO:00614588 | Cervix | CC | reproductive system development | 87/2311 | 427/18723 | 1.37e-06 | 4.55e-05 | 87 |
| GO:00486088 | Cervix | CC | reproductive structure development | 86/2311 | 424/18723 | 1.90e-06 | 5.97e-05 | 86 |
| GO:002261310 | Cervix | CC | ribonucleoprotein complex biogenesis | 88/2311 | 463/18723 | 2.11e-05 | 3.82e-04 | 88 |
| GO:004225410 | Cervix | CC | ribosome biogenesis | 62/2311 | 299/18723 | 2.48e-05 | 4.27e-04 | 62 |
| GO:00063257 | Cervix | CC | chromatin organization | 78/2311 | 409/18723 | 5.40e-05 | 8.02e-04 | 78 |
| GO:00017018 | Cervix | CC | in utero embryonic development | 71/2311 | 367/18723 | 7.21e-05 | 1.00e-03 | 71 |
| GO:00605375 | Cervix | CC | muscle tissue development | 76/2311 | 403/18723 | 9.76e-05 | 1.27e-03 | 76 |
| GO:00459277 | Cervix | CC | positive regulation of growth | 53/2311 | 259/18723 | 1.33e-04 | 1.64e-03 | 53 |
| GO:00147064 | Cervix | CC | striated muscle tissue development | 72/2311 | 384/18723 | 1.76e-04 | 2.07e-03 | 72 |
| GO:00302173 | Cervix | CC | T cell differentiation | 51/2311 | 257/18723 | 3.81e-04 | 3.89e-03 | 51 |
| GO:19031314 | Cervix | CC | mononuclear cell differentiation | 76/2311 | 426/18723 | 5.66e-04 | 5.42e-03 | 76 |
| GO:00486386 | Cervix | CC | regulation of developmental growth | 61/2311 | 330/18723 | 7.69e-04 | 6.85e-03 | 61 |
| GO:00519603 | Cervix | CC | regulation of nervous system development | 77/2311 | 443/18723 | 1.13e-03 | 9.30e-03 | 77 |
| GO:00507676 | Cervix | CC | regulation of neurogenesis | 65/2311 | 364/18723 | 1.33e-03 | 1.05e-02 | 65 |
| GO:00487365 | Cervix | CC | appendage development | 35/2311 | 172/18723 | 1.88e-03 | 1.39e-02 | 35 |
| GO:00601735 | Cervix | CC | limb development | 35/2311 | 172/18723 | 1.88e-03 | 1.39e-02 | 35 |
| GO:00323923 | Cervix | CC | DNA geometric change | 21/2311 | 90/18723 | 2.71e-03 | 1.85e-02 | 21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| ∗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 |
| CHD7 | SNV | Missense_Mutation | novel | c.181N>G | p.Gln61Glu | p.Q61E | Q9P2D1 | protein_coding | deleterious_low_confidence(0.03) | benign(0.053) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| CHD7 | SNV | Missense_Mutation | c.4660N>T | p.Asp1554Tyr | p.D1554Y | Q9P2D1 | protein_coding | deleterious(0) | possibly_damaging(0.825) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD | |
| CHD7 | SNV | Missense_Mutation | c.8096T>A | p.Met2699Lys | p.M2699K | Q9P2D1 | protein_coding | tolerated(0.5) | possibly_damaging(0.888) | TCGA-A7-A13G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | PD | |
| CHD7 | SNV | Missense_Mutation | c.6571G>C | p.Glu2191Gln | p.E2191Q | Q9P2D1 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-A7-A26H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD | |
| CHD7 | SNV | Missense_Mutation | c.7756N>T | p.Pro2586Ser | p.P2586S | Q9P2D1 | protein_coding | deleterious(0.02) | benign(0.026) | TCGA-A7-A26I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | |
| CHD7 | SNV | Missense_Mutation | novel | c.1537N>T | p.Thr513Ser | p.T513S | Q9P2D1 | protein_coding | tolerated_low_confidence(0.62) | benign(0) | TCGA-A7-A4SC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CHD7 | SNV | Missense_Mutation | rs368609862 | c.5440N>A | p.Ala1814Thr | p.A1814T | Q9P2D1 | protein_coding | tolerated(0.22) | benign(0.009) | TCGA-A8-A091-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | PD |
| CHD7 | SNV | Missense_Mutation | c.223N>C | p.Tyr75His | p.Y75H | Q9P2D1 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.987) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CHD7 | SNV | Missense_Mutation | rs750047137 | c.6529N>A | p.Glu2177Lys | p.E2177K | Q9P2D1 | protein_coding | tolerated(0.45) | benign(0.003) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| CHD7 | SNV | Missense_Mutation | c.4611G>C | p.Lys1537Asn | p.K1537N | Q9P2D1 | protein_coding | deleterious(0.01) | probably_damaging(0.946) | TCGA-AN-A0G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| 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 32 33 34 35 36 37 38 |
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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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