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Gene: APEX1 |
Gene summary for APEX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | APEX1 | Gene ID | 328 |
| Gene name | apurinic/apyrimidinic endodeoxyribonuclease 1 | |
| Gene Alias | APE | |
| Cytomap | 14q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000082 | UniProtAcc | P27695 |
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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 |
| 328 | APEX1 | P2_S3_AK | Human | Skin | AK | 1.37e-05 | 1.99e-01 | -0.3287 |
| 328 | APEX1 | P4_S8_cSCC | Human | Skin | cSCC | 3.62e-10 | 2.09e-01 | -0.3095 |
| 328 | APEX1 | P5_S10_cSCC | Human | Skin | cSCC | 8.08e-18 | 2.28e-01 | -0.299 |
| 328 | APEX1 | P1_cSCC | Human | Skin | cSCC | 1.56e-46 | 1.65e+00 | 0.0292 |
| 328 | APEX1 | P2_cSCC | Human | Skin | cSCC | 2.38e-62 | 1.31e+00 | -0.024 |
| 328 | APEX1 | P4_cSCC | Human | Skin | cSCC | 5.30e-62 | 1.21e+00 | -0.00290000000000005 |
| 328 | APEX1 | P10_cSCC | Human | Skin | cSCC | 2.36e-49 | 1.50e+00 | 0.1017 |
| 328 | APEX1 | cSCC_p1 | Human | Skin | cSCC | 1.71e-06 | 2.04e-01 | -0.1916 |
| 328 | APEX1 | cSCC_p4 | Human | Skin | cSCC | 1.61e-05 | 9.68e-02 | -0.2022 |
| 328 | APEX1 | cSCC_p8 | Human | Skin | cSCC | 3.88e-11 | 1.72e-01 | -0.1971 |
| 328 | APEX1 | cSCC_p9 | Human | Skin | cSCC | 1.90e-12 | 1.68e-01 | -0.1991 |
| 328 | APEX1 | male-WTA | Human | Thyroid | PTC | 1.80e-53 | 3.21e-01 | 0.1037 |
| 328 | APEX1 | PTC01 | Human | Thyroid | PTC | 1.16e-19 | 5.45e-01 | 0.1899 |
| 328 | APEX1 | PTC04 | Human | Thyroid | PTC | 2.28e-07 | 2.72e-01 | 0.1927 |
| 328 | APEX1 | PTC05 | Human | Thyroid | PTC | 2.28e-19 | 1.20e+00 | 0.2065 |
| 328 | APEX1 | PTC06 | Human | Thyroid | PTC | 8.76e-47 | 1.33e+00 | 0.2057 |
| 328 | APEX1 | PTC07 | Human | Thyroid | PTC | 1.30e-63 | 1.14e+00 | 0.2044 |
| 328 | APEX1 | ATC08 | Human | Thyroid | ATC | 1.36e-04 | -9.73e-02 | 0.0541 |
| 328 | APEX1 | ATC11 | Human | Thyroid | ATC | 7.66e-04 | 9.28e-01 | 0.3386 |
| 328 | APEX1 | ATC12 | Human | Thyroid | ATC | 5.31e-15 | 5.21e-01 | 0.34 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| 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 | ||
| 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:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
| GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
| GO:00003029 | Breast | Precancer | response to reactive oxygen species | 38/1080 | 222/18723 | 1.47e-09 | 1.23e-07 | 38 |
| GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
| GO:00425429 | Breast | Precancer | response to hydrogen peroxide | 26/1080 | 146/18723 | 2.52e-07 | 1.26e-05 | 26 |
| GO:19033118 | Breast | Precancer | regulation of mRNA metabolic process | 38/1080 | 288/18723 | 1.63e-06 | 5.97e-05 | 38 |
| GO:00454548 | Breast | Precancer | cell redox homeostasis | 11/1080 | 35/18723 | 2.59e-06 | 8.65e-05 | 11 |
| GO:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
| GO:00064028 | Breast | Precancer | mRNA catabolic process | 31/1080 | 232/18723 | 1.12e-05 | 2.93e-04 | 31 |
| GO:00346149 | Breast | Precancer | cellular response to reactive oxygen species | 23/1080 | 155/18723 | 2.82e-05 | 6.31e-04 | 23 |
| GO:00064018 | Breast | Precancer | RNA catabolic process | 34/1080 | 278/18723 | 2.88e-05 | 6.39e-04 | 34 |
| GO:00007238 | Breast | Precancer | telomere maintenance | 20/1080 | 131/18723 | 6.10e-05 | 1.25e-03 | 20 |
| GO:00346558 | Breast | Precancer | nucleobase-containing compound catabolic process | 42/1080 | 407/18723 | 1.91e-04 | 3.06e-03 | 42 |
| GO:00467007 | Breast | Precancer | heterocycle catabolic process | 44/1080 | 445/18723 | 3.49e-04 | 4.88e-03 | 44 |
| GO:00094108 | Breast | Precancer | response to xenobiotic stimulus | 45/1080 | 462/18723 | 4.17e-04 | 5.56e-03 | 45 |
| GO:00442708 | Breast | Precancer | cellular nitrogen compound catabolic process | 44/1080 | 451/18723 | 4.64e-04 | 6.12e-03 | 44 |
| GO:00322003 | Breast | Precancer | telomere organization | 20/1080 | 159/18723 | 8.45e-04 | 9.82e-03 | 20 |
| GO:00194397 | Breast | Precancer | aromatic compound catabolic process | 44/1080 | 467/18723 | 9.55e-04 | 1.07e-02 | 44 |
| GO:19013617 | Breast | Precancer | organic cyclic compound catabolic process | 45/1080 | 495/18723 | 1.73e-03 | 1.74e-02 | 45 |
| GO:00434888 | Breast | Precancer | regulation of mRNA stability | 19/1080 | 158/18723 | 1.92e-03 | 1.86e-02 | 19 |
| 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 39 40 41 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa034104 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
| hsa0341011 | Esophagus | ESCC | Base excision repair | 38/4205 | 44/8465 | 3.59e-07 | 2.62e-06 | 1.34e-06 | 38 |
| 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 |
| APEX1 | pDC | Lung | MIAC | GPR82,ZBTB46,SLC25A19, etc. | 4.54e-03 |  |
| APEX1 | cDC | Lung | MIAC | GPR82,ZBTB46,SLC25A19, etc. | 3.63e-03 | |
| ∗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 |
| APEX1 | SNV | Missense_Mutation | c.14N>C | p.Gly5Ala | p.G5A | P27695 | protein_coding | tolerated(0.29) | benign(0.007) | TCGA-A8-A0A2-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| APEX1 | SNV | Missense_Mutation | c.865N>T | p.His289Tyr | p.H289Y | P27695 | protein_coding | deleterious(0) | benign(0.125) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| APEX1 | SNV | Missense_Mutation | rs765234188 | c.553N>T | p.Arg185Trp | p.R185W | P27695 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A8OS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| APEX1 | SNV | Missense_Mutation | rs751223947 | c.841N>T | p.Arg281Cys | p.R281C | P27695 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| APEX1 | SNV | Missense_Mutation | novel | c.20N>G | p.Lys7Arg | p.K7R | P27695 | protein_coding | tolerated(0.26) | benign(0.337) | TCGA-ZJ-AAXJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| APEX1 | SNV | Missense_Mutation | c.689C>A | p.Ala230Asp | p.A230D | P27695 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| APEX1 | SNV | Missense_Mutation | c.389G>A | p.Gly130Asp | p.G130D | P27695 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| APEX1 | SNV | Missense_Mutation | novel | c.813N>T | p.Met271Ile | p.M271I | P27695 | protein_coding | tolerated(0.4) | benign(0.376) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| APEX1 | SNV | Missense_Mutation | rs778698391 | c.662N>A | p.Arg221His | p.R221H | P27695 | protein_coding | tolerated(0.09) | possibly_damaging(0.653) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
| APEX1 | SNV | Missense_Mutation | c.688G>A | p.Ala230Thr | p.A230T | P27695 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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 |
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | CARMINE | CARMINE | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | DOPAMINE HYDROCHLORIDE | DOPAMINE HYDROCHLORIDE | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | BENZOQUINONE | BENZOQUINONE | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | 3-METHOXYCATECHOL | 3-METHOXYCATECHOL | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | IRIGENOL | IRIGENOL | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | SURAMIN HEXASODIUM | SURAMIN HEXASODIUM | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | ARACHIDONOYL GLYCINE | ARACHIDONOYL GLYCINE | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | SENNOSIDE A | SENNOSIDE A | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | QUERCETIN | QUERCETIN | ||
| 328 | APEX1 | DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, DRUGGABLE GENOME | CEFAMANDOLE SODIUM | CEFAMANDOLE SODIUM |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
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