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Gene: PARP1 |
Gene summary for PARP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PARP1 | Gene ID | 142 |
| Gene name | poly(ADP-ribose) polymerase 1 | |
| Gene Alias | ADPRT | |
| Cytomap | 1q42.12 | |
| Gene Type | protein-coding | GO ID | GO:0000002 | UniProtAcc | A0A024R3T8 |
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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 |
| 142 | PARP1 | GSM4909281 | Human | Breast | IDC | 7.32e-18 | 4.57e-01 | 0.21 |
| 142 | PARP1 | GSM4909282 | Human | Breast | IDC | 8.79e-04 | 2.75e-01 | -0.0288 |
| 142 | PARP1 | GSM4909285 | Human | Breast | IDC | 1.48e-37 | 6.11e-01 | 0.21 |
| 142 | PARP1 | GSM4909286 | Human | Breast | IDC | 6.97e-13 | 3.28e-01 | 0.1081 |
| 142 | PARP1 | GSM4909287 | Human | Breast | IDC | 1.27e-04 | 3.52e-01 | 0.2057 |
| 142 | PARP1 | GSM4909290 | Human | Breast | IDC | 3.16e-04 | 3.44e-01 | 0.2096 |
| 142 | PARP1 | GSM4909293 | Human | Breast | IDC | 2.71e-40 | 6.55e-01 | 0.1581 |
| 142 | PARP1 | GSM4909298 | Human | Breast | IDC | 3.17e-08 | 2.63e-01 | 0.1551 |
| 142 | PARP1 | GSM4909301 | Human | Breast | IDC | 1.67e-02 | 2.40e-01 | 0.1577 |
| 142 | PARP1 | GSM4909306 | Human | Breast | IDC | 5.53e-14 | 3.82e-01 | 0.1564 |
| 142 | PARP1 | GSM4909307 | Human | Breast | IDC | 3.77e-15 | 4.99e-01 | 0.1569 |
| 142 | PARP1 | GSM4909308 | Human | Breast | IDC | 4.28e-25 | 6.54e-01 | 0.158 |
| 142 | PARP1 | GSM4909311 | Human | Breast | IDC | 4.76e-07 | -8.56e-02 | 0.1534 |
| 142 | PARP1 | GSM4909317 | Human | Breast | IDC | 2.37e-02 | 2.31e-01 | 0.1355 |
| 142 | PARP1 | GSM4909319 | Human | Breast | IDC | 1.39e-26 | 1.94e-01 | 0.1563 |
| 142 | PARP1 | brca2 | Human | Breast | Precancer | 2.79e-08 | 2.01e-01 | -0.024 |
| 142 | PARP1 | brca3 | Human | Breast | Precancer | 6.18e-04 | 2.33e-01 | -0.0263 |
| 142 | PARP1 | M2 | Human | Breast | IDC | 3.08e-11 | 7.43e-01 | 0.21 |
| 142 | PARP1 | NCCBC14 | Human | Breast | DCIS | 4.43e-22 | 7.15e-01 | 0.2021 |
| 142 | PARP1 | NCCBC3 | Human | Breast | DCIS | 4.66e-03 | 2.62e-01 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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:000697918 | Prostate | BPH | response to oxidative stress | 142/3107 | 446/18723 | 8.11e-16 | 1.36e-13 | 142 |
| GO:200124218 | Prostate | BPH | regulation of intrinsic apoptotic signaling pathway | 70/3107 | 164/18723 | 2.34e-15 | 3.72e-13 | 70 |
| GO:005109818 | Prostate | BPH | regulation of binding | 121/3107 | 363/18723 | 2.74e-15 | 4.14e-13 | 121 |
| GO:190382918 | Prostate | BPH | positive regulation of cellular protein localization | 98/3107 | 276/18723 | 1.46e-14 | 1.84e-12 | 98 |
| GO:004325418 | Prostate | BPH | regulation of protein-containing complex assembly | 133/3107 | 428/18723 | 5.40e-14 | 6.08e-12 | 133 |
| GO:006219718 | Prostate | BPH | cellular response to chemical stress | 110/3107 | 337/18723 | 2.44e-13 | 2.40e-11 | 110 |
| GO:003450410 | Prostate | BPH | protein localization to nucleus | 98/3107 | 290/18723 | 4.78e-13 | 4.35e-11 | 98 |
| GO:004854518 | Prostate | BPH | response to steroid hormone | 109/3107 | 339/18723 | 9.35e-13 | 8.15e-11 | 109 |
| GO:003009918 | Prostate | BPH | myeloid cell differentiation | 115/3107 | 381/18723 | 2.22e-11 | 1.51e-09 | 115 |
| GO:190018010 | Prostate | BPH | regulation of protein localization to nucleus | 54/3107 | 136/18723 | 1.02e-10 | 6.02e-09 | 54 |
| GO:007138316 | Prostate | BPH | cellular response to steroid hormone stimulus | 71/3107 | 204/18723 | 1.72e-10 | 9.79e-09 | 71 |
| GO:000072314 | Prostate | BPH | telomere maintenance | 52/3107 | 131/18723 | 2.27e-10 | 1.23e-08 | 52 |
| GO:005110118 | Prostate | BPH | regulation of DNA binding | 48/3107 | 118/18723 | 4.13e-10 | 2.15e-08 | 48 |
| GO:003459918 | Prostate | BPH | cellular response to oxidative stress | 90/3107 | 288/18723 | 4.70e-10 | 2.43e-08 | 90 |
| GO:004593618 | Prostate | BPH | negative regulation of phosphate metabolic process | 124/3107 | 441/18723 | 5.95e-10 | 2.90e-08 | 124 |
| GO:19001829 | Prostate | BPH | positive regulation of protein localization to nucleus | 39/3107 | 87/18723 | 6.07e-10 | 2.91e-08 | 39 |
| GO:001056318 | Prostate | BPH | negative regulation of phosphorus metabolic process | 124/3107 | 442/18723 | 6.94e-10 | 3.25e-08 | 124 |
| GO:190165417 | Prostate | BPH | response to ketone | 67/3107 | 194/18723 | 8.10e-10 | 3.74e-08 | 67 |
| GO:000915018 | Prostate | BPH | purine ribonucleotide metabolic process | 107/3107 | 368/18723 | 1.18e-09 | 5.19e-08 | 107 |
| GO:004232617 | Prostate | BPH | negative regulation of phosphorylation | 110/3107 | 385/18723 | 2.08e-09 | 8.35e-08 | 110 |
| 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 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| hsa042108 | Breast | Precancer | Apoptosis | 25/684 | 136/8465 | 7.61e-05 | 6.87e-04 | 5.26e-04 | 25 |
| hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| hsa0421013 | Breast | Precancer | Apoptosis | 25/684 | 136/8465 | 7.61e-05 | 6.87e-04 | 5.26e-04 | 25 |
| hsa0541523 | Breast | IDC | Diabetic cardiomyopathy | 67/867 | 203/8465 | 3.17e-19 | 8.59e-18 | 6.43e-18 | 67 |
| hsa0421022 | Breast | IDC | Apoptosis | 31/867 | 136/8465 | 1.34e-05 | 1.61e-04 | 1.20e-04 | 31 |
| hsa0541533 | Breast | IDC | Diabetic cardiomyopathy | 67/867 | 203/8465 | 3.17e-19 | 8.59e-18 | 6.43e-18 | 67 |
| hsa0421032 | Breast | IDC | Apoptosis | 31/867 | 136/8465 | 1.34e-05 | 1.61e-04 | 1.20e-04 | 31 |
| hsa0541543 | Breast | DCIS | Diabetic cardiomyopathy | 65/846 | 203/8465 | 1.81e-18 | 4.87e-17 | 3.59e-17 | 65 |
| hsa0421041 | Breast | DCIS | Apoptosis | 29/846 | 136/8465 | 5.92e-05 | 5.97e-04 | 4.40e-04 | 29 |
| hsa0541553 | Breast | DCIS | Diabetic cardiomyopathy | 65/846 | 203/8465 | 1.81e-18 | 4.87e-17 | 3.59e-17 | 65 |
| hsa0421051 | Breast | DCIS | Apoptosis | 29/846 | 136/8465 | 5.92e-05 | 5.97e-04 | 4.40e-04 | 29 |
| hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
| hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
| hsa054152 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
| hsa054153 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
| hsa054154 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
| hsa04210 | Colorectum | MSS | Apoptosis | 44/1875 | 136/8465 | 3.66e-03 | 1.66e-02 | 1.01e-02 | 44 |
| hsa054155 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
| hsa042101 | Colorectum | MSS | Apoptosis | 44/1875 | 136/8465 | 3.66e-03 | 1.66e-02 | 1.01e-02 | 44 |
| Page: 1 2 3 4 |
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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 |
| PARP1 | BAS | Lung | Healthy | TM4SF1,KRT19,C3, etc. | 1.00e-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 |
| PARP1 | SNV | Missense_Mutation | rs79529505 | c.1223N>G | p.Val408Gly | p.V408G | P09874 | protein_coding | deleterious(0) | benign(0.367) | TCGA-A2-A0CQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| PARP1 | SNV | Missense_Mutation | rs79529505 | c.1223N>G | p.Val408Gly | p.V408G | P09874 | protein_coding | deleterious(0) | benign(0.367) | TCGA-A2-A0YJ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD |
| PARP1 | SNV | Missense_Mutation | rs377195931 | c.919N>A | p.Asp307Asn | p.D307N | P09874 | protein_coding | tolerated(0.23) | benign(0.189) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| PARP1 | SNV | Missense_Mutation | rs377195931 | c.919G>A | p.Asp307Asn | p.D307N | P09874 | protein_coding | tolerated(0.23) | benign(0.189) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| PARP1 | SNV | Missense_Mutation | rs79529505 | c.1223N>G | p.Val408Gly | p.V408G | P09874 | protein_coding | deleterious(0) | benign(0.367) | TCGA-A8-A06Q-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PARP1 | SNV | Missense_Mutation | c.2032N>C | p.Asp678His | p.D678H | P09874 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR | |
| PARP1 | SNV | Missense_Mutation | c.2524G>A | p.Glu842Lys | p.E842K | P09874 | protein_coding | tolerated(0.18) | benign(0.026) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PARP1 | SNV | Missense_Mutation | novel | c.2971G>C | p.Val991Leu | p.V991L | P09874 | protein_coding | deleterious(0.01) | possibly_damaging(0.796) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PARP1 | SNV | Missense_Mutation | novel | c.1102A>C | p.Thr368Pro | p.T368P | P09874 | protein_coding | tolerated(0.29) | benign(0.079) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PARP1 | SNV | Missense_Mutation | c.268N>A | p.Glu90Lys | p.E90K | P09874 | protein_coding | tolerated(0.09) | possibly_damaging(0.566) | TCGA-B6-A0IJ-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 |
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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 |
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | Quinazolinedione derivative 2 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | inhibitor | 223366069 | RUCAPARIB | |
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | inhibitor | CHEMBL1094636 | NIRAPARIB | |
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | 4-Carboxamido-isoindolinone derivative 2 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | CC-486 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | 3-oxo-2,3-dihydro-1H-indazole-4-carboxamide derivative 5 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | OLAPARIB | OLAPARIB | 28454547,25144364,26650448 | |
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | 4-Carboxamido-isoindolinone derivative 3 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | Phthalazine ketone derivative 3 | |||
| 142 | PARP1 | ENZYME, TRANSCRIPTION FACTOR, DRUGGABLE GENOME, DNA REPAIR, TRANSCRIPTION FACTOR COMPLEX, CLINICALLY ACTIONABLE, DRUG RESISTANCE | RUCAPARIB | RUCAPARIB |
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