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Gene: PAPPA |
Gene summary for PAPPA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PAPPA | Gene ID | 5069 |
| Gene name | pappalysin 1 | |
| Gene Alias | ASBABP2 | |
| Cytomap | 9q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | B4DTA8 |
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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 |
| 5069 | PAPPA | PTC06 | Human | Thyroid | PTC | 7.62e-07 | 2.61e-01 | 0.2057 |
| 5069 | PAPPA | PTC07 | Human | Thyroid | PTC | 5.43e-04 | 1.33e-01 | 0.2044 |
| 5069 | PAPPA | ATC11 | Human | Thyroid | ATC | 3.34e-11 | 1.45e+00 | 0.3386 |
| 5069 | PAPPA | ATC12 | Human | Thyroid | ATC | 1.87e-59 | 1.72e+00 | 0.34 |
| 5069 | PAPPA | ATC13 | Human | Thyroid | ATC | 6.99e-29 | 7.84e-01 | 0.34 |
| 5069 | PAPPA | ATC2 | Human | Thyroid | ATC | 5.90e-10 | 8.76e-01 | 0.34 |
| 5069 | PAPPA | ATC3 | Human | Thyroid | ATC | 1.37e-27 | 1.95e+00 | 0.338 |
| 5069 | PAPPA | ATC4 | Human | Thyroid | ATC | 5.27e-70 | 1.95e+00 | 0.34 |
| 5069 | PAPPA | ATC5 | Human | Thyroid | ATC | 1.14e-29 | 9.01e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:0048545113 | Thyroid | PTC | response to steroid hormone | 158/5968 | 339/18723 | 8.10e-09 | 2.00e-07 | 158 |
| GO:0031960111 | Thyroid | PTC | response to corticosteroid | 69/5968 | 167/18723 | 6.18e-03 | 2.74e-02 | 69 |
| GO:0051384111 | Thyroid | PTC | response to glucocorticoid | 62/5968 | 148/18723 | 6.39e-03 | 2.81e-02 | 62 |
| GO:001604927 | Thyroid | ATC | cell growth | 241/6293 | 482/18723 | 4.27e-14 | 2.35e-12 | 241 |
| GO:000155826 | Thyroid | ATC | regulation of cell growth | 201/6293 | 414/18723 | 1.57e-10 | 4.76e-09 | 201 |
| GO:0048545210 | Thyroid | ATC | response to steroid hormone | 168/6293 | 339/18723 | 7.21e-10 | 1.88e-08 | 168 |
| GO:006034813 | Thyroid | ATC | bone development | 102/6293 | 205/18723 | 1.18e-06 | 1.52e-05 | 102 |
| GO:0060349 | Thyroid | ATC | bone morphogenesis | 50/6293 | 93/18723 | 4.87e-05 | 3.88e-04 | 50 |
| GO:00487053 | Thyroid | ATC | skeletal system morphogenesis | 101/6293 | 220/18723 | 9.48e-05 | 6.93e-04 | 101 |
| GO:000697016 | Thyroid | ATC | response to osmotic stress | 45/6293 | 84/18723 | 1.27e-04 | 9.03e-04 | 45 |
| GO:005138427 | Thyroid | ATC | response to glucocorticoid | 65/6293 | 148/18723 | 5.62e-03 | 2.28e-02 | 65 |
| GO:000756517 | Thyroid | ATC | female pregnancy | 82/6293 | 193/18723 | 6.04e-03 | 2.42e-02 | 82 |
| GO:003196027 | Thyroid | ATC | response to corticosteroid | 72/6293 | 167/18723 | 6.39e-03 | 2.55e-02 | 72 |
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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 |
| PAPPA | SNV | Missense_Mutation | rs534133186 | c.1783N>C | p.Glu595Gln | p.E595Q | Q13219 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A3XZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| PAPPA | SNV | Missense_Mutation | novel | c.612N>A | p.Asp204Glu | p.D204E | Q13219 | protein_coding | deleterious(0.05) | possibly_damaging(0.876) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PAPPA | SNV | Missense_Mutation | c.4718N>A | p.Arg1573Gln | p.R1573Q | Q13219 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A0AJ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAPPA | SNV | Missense_Mutation | c.3530N>T | p.Ala1177Val | p.A1177V | Q13219 | protein_coding | deleterious(0) | possibly_damaging(0.842) | TCGA-BH-A0B5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR | |
| PAPPA | SNV | Missense_Mutation | rs138142503 | c.1042C>T | p.Arg348Cys | p.R348C | Q13219 | protein_coding | deleterious(0.05) | probably_damaging(0.997) | TCGA-BH-A0EB-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PAPPA | SNV | Missense_Mutation | c.1564N>A | p.Glu522Lys | p.E522K | Q13219 | protein_coding | tolerated(0.13) | probably_damaging(0.913) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PAPPA | SNV | Missense_Mutation | rs201320991 | c.4564G>A | p.Val1522Met | p.V1522M | Q13219 | protein_coding | tolerated(0.1) | benign(0.175) | TCGA-BH-A1FC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PAPPA | SNV | Missense_Mutation | c.1687N>A | p.Glu563Lys | p.E563K | Q13219 | protein_coding | deleterious(0) | possibly_damaging(0.801) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| PAPPA | SNV | Missense_Mutation | rs570712795 | c.1393C>T | p.Arg465Trp | p.R465W | Q13219 | protein_coding | tolerated(0.18) | benign(0.001) | TCGA-D8-A1Y1-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | PD |
| PAPPA | SNV | Missense_Mutation | rs769226917 | c.1862N>T | p.Thr621Ile | p.T621I | Q13219 | protein_coding | deleterious(0.02) | probably_damaging(0.974) | TCGA-E2-A1L7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
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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 |
| 5069 | PAPPA | DRUGGABLE GENOME, NEUTRAL ZINC METALLOPEPTIDASE, PROTEASE | TRANSFORMING GROWTH FACTOR | 12817760 | ||
| 5069 | PAPPA | DRUGGABLE GENOME, NEUTRAL ZINC METALLOPEPTIDASE, PROTEASE | ANTISERUM | 2475160 | ||
| 5069 | PAPPA | DRUGGABLE GENOME, NEUTRAL ZINC METALLOPEPTIDASE, PROTEASE | TGF | 12817760 |
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