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Gene: APEX1 |
Gene summary for APEX1 |
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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 |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
328 | APEX1 | GSM4909285 | Human | Breast | IDC | 1.63e-09 | 4.12e-01 | 0.21 |
328 | APEX1 | GSM4909286 | Human | Breast | IDC | 7.32e-03 | 2.18e-01 | 0.1081 |
328 | APEX1 | GSM4909291 | Human | Breast | IDC | 4.85e-15 | 6.07e-01 | 0.1753 |
328 | APEX1 | GSM4909293 | Human | Breast | IDC | 5.95e-09 | 3.84e-01 | 0.1581 |
328 | APEX1 | GSM4909296 | Human | Breast | IDC | 5.46e-07 | -1.99e-01 | 0.1524 |
328 | APEX1 | GSM4909297 | Human | Breast | IDC | 9.89e-09 | -1.36e-01 | 0.1517 |
328 | APEX1 | GSM4909305 | Human | Breast | IDC | 5.01e-04 | 2.97e-01 | 0.0436 |
328 | APEX1 | GSM4909311 | Human | Breast | IDC | 1.20e-26 | -3.58e-01 | 0.1534 |
328 | APEX1 | GSM4909312 | Human | Breast | IDC | 6.98e-09 | 4.26e-03 | 0.1552 |
328 | APEX1 | GSM4909319 | Human | Breast | IDC | 2.61e-29 | -3.42e-01 | 0.1563 |
328 | APEX1 | GSM4909320 | Human | Breast | IDC | 5.68e-03 | -2.18e-01 | 0.1575 |
328 | APEX1 | GSM4909321 | Human | Breast | IDC | 2.23e-10 | 4.03e-03 | 0.1559 |
328 | APEX1 | brca2 | Human | Breast | Precancer | 1.49e-05 | 2.10e-01 | -0.024 |
328 | APEX1 | brca3 | Human | Breast | Precancer | 1.63e-05 | 2.17e-01 | -0.0263 |
328 | APEX1 | NCCBC14 | Human | Breast | DCIS | 6.62e-05 | -1.20e-01 | 0.2021 |
328 | APEX1 | NCCBC3 | Human | Breast | DCIS | 4.00e-04 | 3.05e-01 | 0.1198 |
328 | APEX1 | NCCBC5 | Human | Breast | DCIS | 8.68e-06 | -2.11e-01 | 0.2046 |
328 | APEX1 | P1 | Human | Breast | IDC | 1.22e-14 | -2.73e-01 | 0.1527 |
328 | APEX1 | DCIS2 | Human | Breast | DCIS | 1.71e-69 | 2.43e-01 | 0.0085 |
328 | APEX1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.44e-06 | 3.54e-01 | 0.0155 |
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∗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 |
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Tissue | Disease Stage | Enriched GO biological Processes |
Liver | Cyst | ![]() |
Lung | IAC | ![]() |
Lung | AIS | ![]() |
Lung | AAH | ![]() |
Lung | MIAC | ![]() |
∗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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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 |
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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 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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. |
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Somatic mutation of malignant transformation related genes |
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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 |
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(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 |
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