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Gene: PNPLA3 |
Gene summary for PNPLA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PNPLA3 | Gene ID | 80339 |
| Gene name | patatin like phospholipase domain containing 3 | |
| Gene Alias | ADPN | |
| Cytomap | 22q13.31 | |
| Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | Q9NST1 |
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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 |
| 80339 | PNPLA3 | NAFLD1 | Human | Liver | NAFLD | 4.26e-09 | 8.15e-01 | -0.04 |
| 80339 | PNPLA3 | S43 | Human | Liver | Cirrhotic | 3.80e-06 | -2.01e-01 | -0.0187 |
| 80339 | PNPLA3 | HCC1_Meng | Human | Liver | HCC | 2.17e-66 | -5.29e-02 | 0.0246 |
| 80339 | PNPLA3 | HCC2_Meng | Human | Liver | HCC | 1.15e-12 | -1.78e-01 | 0.0107 |
| 80339 | PNPLA3 | cirrhotic1 | Human | Liver | Cirrhotic | 5.33e-05 | -2.33e-01 | 0.0202 |
| 80339 | PNPLA3 | cirrhotic2 | Human | Liver | Cirrhotic | 2.00e-04 | -2.13e-01 | 0.0201 |
| 80339 | PNPLA3 | HCC2 | Human | Liver | HCC | 5.66e-15 | 3.27e+00 | 0.5341 |
| 80339 | PNPLA3 | HCC5 | Human | Liver | HCC | 1.09e-04 | 1.60e+00 | 0.4932 |
| 80339 | PNPLA3 | Pt13.a | Human | Liver | HCC | 5.70e-03 | -2.17e-01 | 0.021 |
| 80339 | PNPLA3 | S029 | Human | Liver | HCC | 2.51e-02 | 5.42e-02 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00066316 | Liver | NAFLD | fatty acid metabolic process | 92/1882 | 390/18723 | 3.38e-15 | 3.29e-12 | 92 |
| GO:00713755 | Liver | NAFLD | cellular response to peptide hormone stimulus | 65/1882 | 290/18723 | 3.95e-10 | 9.62e-08 | 65 |
| GO:00442425 | Liver | NAFLD | cellular lipid catabolic process | 52/1882 | 214/18723 | 1.15e-09 | 2.17e-07 | 52 |
| GO:00550883 | Liver | NAFLD | lipid homeostasis | 44/1882 | 167/18723 | 1.48e-09 | 2.54e-07 | 44 |
| GO:19016536 | Liver | NAFLD | cellular response to peptide | 71/1882 | 359/18723 | 1.82e-08 | 2.09e-06 | 71 |
| GO:00328695 | Liver | NAFLD | cellular response to insulin stimulus | 47/1882 | 203/18723 | 3.60e-08 | 3.63e-06 | 47 |
| GO:00066413 | Liver | NAFLD | triglyceride metabolic process | 29/1882 | 100/18723 | 9.51e-08 | 7.62e-06 | 29 |
| GO:00160426 | Liver | NAFLD | lipid catabolic process | 63/1882 | 320/18723 | 1.35e-07 | 1.02e-05 | 63 |
| GO:00434346 | Liver | NAFLD | response to peptide hormone | 76/1882 | 414/18723 | 1.51e-07 | 1.09e-05 | 76 |
| GO:00328685 | Liver | NAFLD | response to insulin | 53/1882 | 264/18723 | 6.99e-07 | 3.95e-05 | 53 |
| GO:00066392 | Liver | NAFLD | acylglycerol metabolic process | 32/1882 | 128/18723 | 8.82e-07 | 4.60e-05 | 32 |
| GO:00066382 | Liver | NAFLD | neutral lipid metabolic process | 32/1882 | 129/18723 | 1.06e-06 | 5.35e-05 | 32 |
| GO:00464863 | Liver | NAFLD | glycerolipid metabolic process | 66/1882 | 392/18723 | 1.94e-05 | 5.52e-04 | 66 |
| GO:00097437 | Liver | NAFLD | response to carbohydrate | 45/1882 | 253/18723 | 1.07e-04 | 2.11e-03 | 45 |
| GO:00194322 | Liver | NAFLD | triglyceride biosynthetic process | 13/1882 | 42/18723 | 1.60e-04 | 2.94e-03 | 13 |
| GO:00464612 | Liver | NAFLD | neutral lipid catabolic process | 12/1882 | 39/18723 | 3.02e-04 | 4.75e-03 | 12 |
| GO:00464642 | Liver | NAFLD | acylglycerol catabolic process | 12/1882 | 39/18723 | 3.02e-04 | 4.75e-03 | 12 |
| GO:00450174 | Liver | NAFLD | glycerolipid biosynthetic process | 43/1882 | 252/18723 | 3.83e-04 | 5.73e-03 | 43 |
| GO:00016763 | Liver | NAFLD | long-chain fatty acid metabolic process | 23/1882 | 112/18723 | 6.73e-04 | 8.66e-03 | 23 |
| GO:00464601 | Liver | NAFLD | neutral lipid biosynthetic process | 13/1882 | 50/18723 | 1.04e-03 | 1.22e-02 | 13 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa005615 | Liver | HCC | Glycerolipid metabolism | 41/4020 | 63/8465 | 3.59e-03 | 1.12e-02 | 6.22e-03 | 41 |
| hsa0056112 | Liver | HCC | Glycerolipid metabolism | 41/4020 | 63/8465 | 3.59e-03 | 1.12e-02 | 6.22e-03 | 41 |
| 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 |
| PNPLA3 | SNV | Missense_Mutation | novel | c.634C>G | p.Leu212Val | p.L212V | Q9NST1 | protein_coding | tolerated(0.14) | benign(0.023) | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PNPLA3 | SNV | Missense_Mutation | c.140N>T | p.Ser47Leu | p.S47L | Q9NST1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PNPLA3 | SNV | Missense_Mutation | c.943N>C | p.Ser315Arg | p.S315R | Q9NST1 | protein_coding | tolerated(0.37) | benign(0) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PNPLA3 | SNV | Missense_Mutation | c.406N>T | p.Asp136Tyr | p.D136Y | Q9NST1 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PNPLA3 | SNV | Missense_Mutation | c.1220N>T | p.Ser407Phe | p.S407F | Q9NST1 | protein_coding | deleterious(0.03) | probably_damaging(0.996) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PNPLA3 | SNV | Missense_Mutation | rs372035117 | c.334N>A | p.Gly112Ser | p.G112S | Q9NST1 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AA-A01Z-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PNPLA3 | SNV | Missense_Mutation | c.845N>A | p.Ser282Asn | p.S282N | Q9NST1 | protein_coding | tolerated(0.18) | benign(0.1) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PNPLA3 | SNV | Missense_Mutation | c.887N>C | p.Leu296Pro | p.L296P | Q9NST1 | protein_coding | tolerated(0.42) | benign(0) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PNPLA3 | deletion | Frame_Shift_Del | c.681delN | p.Pro229ArgfsTer34 | p.P229Rfs*34 | Q9NST1 | protein_coding | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |||
| PNPLA3 | SNV | Missense_Mutation | rs201682627 | c.1144G>A | p.Asp382Asn | p.D382N | Q9NST1 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-A5-A0GW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | 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 |
| 80339 | PNPLA3 | ENZYME | vincristine | VINCRISTINE | 28744905 | |
| 80339 | PNPLA3 | ENZYME | cyclophosphamide | CYCLOPHOSPHAMIDE | 28744905 | |
| 80339 | PNPLA3 | ENZYME | prednisolone | PREDNISOLONE | 28744905 | |
| 80339 | PNPLA3 | ENZYME | daunorubicin | DAUNORUBICIN | 28744905 | |
| 80339 | PNPLA3 | ENZYME | ethanol | ALCOHOL | 30132178 | |
| 80339 | PNPLA3 | ENZYME | asparaginase | ASPARAGINASE | 28744905 |
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