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Gene: PAPPA2 |
Gene summary for PAPPA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PAPPA2 | Gene ID | 60676 |
| Gene name | pappalysin 2 | |
| Gene Alias | PAPP-A2 | |
| Cytomap | 1q25.2 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | Q9BXP8 |
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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 |
| 60676 | PAPPA2 | HTA12-26-1 | Human | Pancreas | PDAC | 6.68e-09 | 5.22e-01 | 0.3728 |
| 60676 | PAPPA2 | HTA12-29-1 | Human | Pancreas | PDAC | 2.29e-15 | 5.84e-01 | 0.3722 |
| 60676 | PAPPA2 | ATC11 | Human | Thyroid | ATC | 4.44e-15 | 1.09e+00 | 0.3386 |
| 60676 | PAPPA2 | ATC3 | Human | Thyroid | ATC | 6.82e-19 | 1.02e+00 | 0.338 |
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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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| 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: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 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
| PAPPA2 | SNV | Missense_Mutation | c.2717N>T | p.Ser906Leu | p.S906L | Q9BXP8 | protein_coding | deleterious(0) | probably_damaging(0.909) | TCGA-A1-A0SI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PAPPA2 | SNV | Missense_Mutation | rs758198387 | c.4045N>T | p.Arg1349Trp | p.R1349W | Q9BXP8 | protein_coding | deleterious(0.02) | possibly_damaging(0.513) | TCGA-A7-A13E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | PD |
| PAPPA2 | SNV | Missense_Mutation | rs199857969 | c.3505N>A | p.Pro1169Thr | p.P1169T | Q9BXP8 | protein_coding | deleterious(0.03) | benign(0.104) | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| PAPPA2 | SNV | Missense_Mutation | c.4757N>G | p.Glu1586Gly | p.E1586G | Q9BXP8 | protein_coding | deleterious(0.02) | possibly_damaging(0.826) | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| PAPPA2 | SNV | Missense_Mutation | rs771235887 | c.3235N>A | p.Val1079Met | p.V1079M | Q9BXP8 | protein_coding | tolerated(0.32) | benign(0.003) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| PAPPA2 | SNV | Missense_Mutation | c.1873N>A | p.Asp625Asn | p.D625N | Q9BXP8 | protein_coding | tolerated(0.52) | benign(0.124) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAPPA2 | SNV | Missense_Mutation | c.2975N>C | p.Glu992Ala | p.E992A | Q9BXP8 | protein_coding | tolerated(0.06) | benign(0.028) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PAPPA2 | SNV | Missense_Mutation | c.3316N>G | p.Leu1106Val | p.L1106V | Q9BXP8 | protein_coding | deleterious(0.02) | possibly_damaging(0.677) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PAPPA2 | SNV | Missense_Mutation | novel | c.3173N>G | p.Asp1058Gly | p.D1058G | Q9BXP8 | protein_coding | deleterious(0.02) | benign(0.254) | TCGA-AC-A2BK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | CR |
| PAPPA2 | SNV | Missense_Mutation | c.2965N>C | p.Glu989Gln | p.E989Q | Q9BXP8 | protein_coding | tolerated(0.21) | benign(0.184) | TCGA-AC-A6IW-01 | Breast | breast invasive 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 |
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