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Gene: PGAP3 |
Gene summary for PGAP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PGAP3 | Gene ID | 93210 |
| Gene name | post-GPI attachment to proteins phospholipase 3 | |
| Gene Alias | AGLA546 | |
| Cytomap | 17q12 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q96FM1 |
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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 |
| 93210 | PGAP3 | GSM4909289 | Human | Breast | IDC | 2.84e-02 | 2.77e-01 | 0.1064 |
| 93210 | PGAP3 | GSM4909290 | Human | Breast | IDC | 3.86e-35 | 6.86e-01 | 0.2096 |
| 93210 | PGAP3 | GSM4909291 | Human | Breast | IDC | 1.35e-08 | 3.05e-01 | 0.1753 |
| 93210 | PGAP3 | GSM4909292 | Human | Breast | IDC | 8.93e-07 | 6.12e-01 | 0.1236 |
| 93210 | PGAP3 | GSM4909293 | Human | Breast | IDC | 3.95e-52 | 6.53e-01 | 0.1581 |
| 93210 | PGAP3 | GSM4909294 | Human | Breast | IDC | 1.04e-08 | 2.63e-01 | 0.2022 |
| 93210 | PGAP3 | NCCBC14 | Human | Breast | DCIS | 6.80e-03 | 2.87e-01 | 0.2021 |
| 93210 | PGAP3 | NCCBC5 | Human | Breast | DCIS | 4.33e-07 | 4.00e-01 | 0.2046 |
| 93210 | PGAP3 | DCIS2 | Human | Breast | DCIS | 8.67e-03 | 2.01e-02 | 0.0085 |
| 93210 | PGAP3 | LZE4T | Human | Esophagus | ESCC | 4.81e-06 | 9.06e-02 | 0.0811 |
| 93210 | PGAP3 | LZE7T | Human | Esophagus | ESCC | 6.72e-04 | 2.22e-01 | 0.0667 |
| 93210 | PGAP3 | LZE24T | Human | Esophagus | ESCC | 2.30e-07 | 2.49e-01 | 0.0596 |
| 93210 | PGAP3 | P1T-E | Human | Esophagus | ESCC | 7.29e-06 | 1.61e-01 | 0.0875 |
| 93210 | PGAP3 | P2T-E | Human | Esophagus | ESCC | 8.91e-20 | 1.80e-01 | 0.1177 |
| 93210 | PGAP3 | P4T-E | Human | Esophagus | ESCC | 1.47e-13 | 1.09e-01 | 0.1323 |
| 93210 | PGAP3 | P5T-E | Human | Esophagus | ESCC | 7.51e-04 | 3.55e-02 | 0.1327 |
| 93210 | PGAP3 | P8T-E | Human | Esophagus | ESCC | 1.15e-17 | 3.34e-01 | 0.0889 |
| 93210 | PGAP3 | P9T-E | Human | Esophagus | ESCC | 9.72e-09 | 9.44e-02 | 0.1131 |
| 93210 | PGAP3 | P10T-E | Human | Esophagus | ESCC | 2.29e-10 | 1.37e-01 | 0.116 |
| 93210 | PGAP3 | P11T-E | Human | Esophagus | ESCC | 1.68e-08 | 2.05e-01 | 0.1426 |
| Page: 1 2 3 4 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00066433 | Esophagus | ESCC | membrane lipid metabolic process | 130/8552 | 203/18723 | 9.29e-08 | 1.54e-06 | 130 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:00464673 | Esophagus | ESCC | membrane lipid biosynthetic process | 91/8552 | 142/18723 | 7.19e-06 | 7.19e-05 | 91 |
| GO:00421573 | Esophagus | ESCC | lipoprotein metabolic process | 86/8552 | 135/18723 | 1.78e-05 | 1.57e-04 | 86 |
| GO:00064973 | Esophagus | ESCC | protein lipidation | 62/8552 | 92/18723 | 2.08e-05 | 1.80e-04 | 62 |
| GO:00421583 | Esophagus | ESCC | lipoprotein biosynthetic process | 64/8552 | 96/18723 | 2.61e-05 | 2.20e-04 | 64 |
| GO:00065063 | Esophagus | ESCC | GPI anchor biosynthetic process | 26/8552 | 32/18723 | 3.97e-05 | 3.21e-04 | 26 |
| GO:00066505 | Esophagus | ESCC | glycerophospholipid metabolic process | 174/8552 | 306/18723 | 4.92e-05 | 3.85e-04 | 174 |
| GO:00065053 | Esophagus | ESCC | GPI anchor metabolic process | 26/8552 | 33/18723 | 1.06e-04 | 7.43e-04 | 26 |
| GO:00066642 | Esophagus | ESCC | glycolipid metabolic process | 63/8552 | 100/18723 | 3.55e-04 | 2.06e-03 | 63 |
| GO:19035092 | Esophagus | ESCC | liposaccharide metabolic process | 63/8552 | 101/18723 | 5.25e-04 | 2.90e-03 | 63 |
| GO:00464864 | Esophagus | ESCC | glycerolipid metabolic process | 211/8552 | 392/18723 | 6.51e-04 | 3.46e-03 | 211 |
| GO:0009247 | Esophagus | ESCC | glycolipid biosynthetic process | 42/8552 | 68/18723 | 5.48e-03 | 2.05e-02 | 42 |
| GO:00066611 | Esophagus | ESCC | phosphatidylinositol biosynthetic process | 73/8552 | 131/18723 | 1.31e-02 | 4.28e-02 | 73 |
| GO:00066432 | Oral cavity | OSCC | membrane lipid metabolic process | 111/7305 | 203/18723 | 4.02e-06 | 4.69e-05 | 111 |
| GO:00421572 | Oral cavity | OSCC | lipoprotein metabolic process | 77/7305 | 135/18723 | 1.61e-05 | 1.60e-04 | 77 |
| GO:00064972 | Oral cavity | OSCC | protein lipidation | 56/7305 | 92/18723 | 1.77e-05 | 1.72e-04 | 56 |
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| 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 |
| PGAP3 | SNV | Missense_Mutation | rs760427744 | c.194N>A | p.Arg65Gln | p.R65Q | Q96FM1 | protein_coding | tolerated(0.35) | benign(0.011) | TCGA-AO-A0J3-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | SD |
| PGAP3 | insertion | Frame_Shift_Ins | novel | c.944_945insGTGCTCCATAACGCCTGGA | p.Asp315GlufsTer101 | p.D315Efs*101 | Q96FM1 | protein_coding | TCGA-AR-A24U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| PGAP3 | SNV | Missense_Mutation | c.665N>T | p.Gly222Val | p.G222V | Q96FM1 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PGAP3 | SNV | Missense_Mutation | rs532257048 | c.808N>A | p.Glu270Lys | p.E270K | Q96FM1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-VS-A9UP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| PGAP3 | SNV | Missense_Mutation | novel | c.468N>G | p.Phe156Leu | p.F156L | Q96FM1 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-VS-A9V5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| PGAP3 | SNV | Missense_Mutation | c.215G>A | p.Cys72Tyr | p.C72Y | Q96FM1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PGAP3 | SNV | Missense_Mutation | c.665N>A | p.Gly222Asp | p.G222D | Q96FM1 | protein_coding | deleterious(0) | probably_damaging(0.965) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| PGAP3 | SNV | Missense_Mutation | rs369388252 | c.886N>A | p.Val296Ile | p.V296I | Q96FM1 | protein_coding | tolerated(0.41) | benign(0.028) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PGAP3 | SNV | Missense_Mutation | rs752623171 | c.325N>A | p.Val109Met | p.V109M | Q96FM1 | protein_coding | tolerated(0.2) | benign(0.034) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PGAP3 | SNV | Missense_Mutation | c.160C>T | p.Pro54Ser | p.P54S | Q96FM1 | protein_coding | tolerated(0.06) | probably_damaging(0.996) | TCGA-CI-6619-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | 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 |
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