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Gene: PPFIA1 |
Gene summary for PPFIA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPFIA1 | Gene ID | 8500 |
| Gene name | PTPRF interacting protein alpha 1 | |
| Gene Alias | LIP.1 | |
| Cytomap | 11q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | B3KVS8 |
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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 |
| 8500 | PPFIA1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.13e-20 | -6.63e-01 | 0.0155 |
| 8500 | PPFIA1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.01e-08 | -6.04e-01 | -0.1808 |
| 8500 | PPFIA1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.08e-04 | -5.31e-01 | -0.0811 |
| 8500 | PPFIA1 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.24e-06 | -5.39e-01 | -0.1088 |
| 8500 | PPFIA1 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.13e-05 | -4.17e-01 | -0.1954 |
| 8500 | PPFIA1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.56e-04 | -5.49e-01 | -0.1207 |
| 8500 | PPFIA1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.67e-04 | -5.80e-01 | -0.1526 |
| 8500 | PPFIA1 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.69e-19 | -5.82e-01 | -0.1464 |
| 8500 | PPFIA1 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.96e-21 | -6.02e-01 | -0.1001 |
| 8500 | PPFIA1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.05e-03 | -4.55e-01 | -0.059 |
| 8500 | PPFIA1 | HTA11_546_2000001011 | Human | Colorectum | AD | 6.84e-03 | -5.61e-01 | -0.0842 |
| 8500 | PPFIA1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.64e-14 | -6.05e-01 | 0.096 |
| 8500 | PPFIA1 | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.12e-02 | -6.12e-01 | 0.0528 |
| 8500 | PPFIA1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 3.12e-02 | -6.68e-01 | 0.0131 |
| 8500 | PPFIA1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 1.00e-03 | -6.43e-01 | -0.0177 |
| 8500 | PPFIA1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 6.37e-10 | -6.45e-01 | 0.0338 |
| 8500 | PPFIA1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.50e-20 | -6.22e-01 | 0.0674 |
| 8500 | PPFIA1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 7.57e-05 | -5.72e-01 | 0.0588 |
| 8500 | PPFIA1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.32e-15 | -5.19e-01 | 0.294 |
| 8500 | PPFIA1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.25e-02 | -4.62e-01 | 0.281 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:00514941 | Colorectum | SER | negative regulation of cytoskeleton organization | 48/2897 | 163/18723 | 4.34e-06 | 1.63e-04 | 48 |
| GO:00510171 | Colorectum | SER | actin filament bundle assembly | 46/2897 | 157/18723 | 7.88e-06 | 2.69e-04 | 46 |
| GO:00315891 | Colorectum | SER | cell-substrate adhesion | 86/2897 | 363/18723 | 2.36e-05 | 6.64e-04 | 86 |
| GO:00322311 | Colorectum | SER | regulation of actin filament bundle assembly | 29/2897 | 105/18723 | 1.01e-03 | 1.20e-02 | 29 |
| GO:00300381 | Colorectum | SER | contractile actin filament bundle assembly | 29/2897 | 106/18723 | 1.19e-03 | 1.36e-02 | 29 |
| GO:00431491 | Colorectum | SER | stress fiber assembly | 29/2897 | 106/18723 | 1.19e-03 | 1.36e-02 | 29 |
| GO:00071601 | Colorectum | SER | cell-matrix adhesion | 53/2897 | 233/18723 | 2.10e-03 | 2.06e-02 | 53 |
| GO:00514921 | Colorectum | SER | regulation of stress fiber assembly | 25/2897 | 91/18723 | 2.36e-03 | 2.25e-02 | 25 |
| GO:19038281 | Colorectum | SER | negative regulation of cellular protein localization | 30/2897 | 117/18723 | 2.96e-03 | 2.62e-02 | 30 |
| GO:00310321 | Colorectum | SER | actomyosin structure organization | 45/2897 | 196/18723 | 3.60e-03 | 3.03e-02 | 45 |
| GO:01100201 | Colorectum | SER | regulation of actomyosin structure organization | 26/2897 | 100/18723 | 4.43e-03 | 3.54e-02 | 26 |
| GO:00508081 | Colorectum | SER | synapse organization | 85/2897 | 426/18723 | 7.17e-03 | 4.99e-02 | 85 |
| GO:19030771 | Colorectum | SER | negative regulation of protein localization to plasma membrane | 9/2897 | 24/18723 | 7.19e-03 | 4.99e-02 | 9 |
| GO:00726592 | Colorectum | MSS | protein localization to plasma membrane | 113/3467 | 284/18723 | 3.23e-17 | 1.55e-14 | 113 |
| GO:19907782 | Colorectum | MSS | protein localization to cell periphery | 120/3467 | 333/18723 | 2.02e-14 | 5.47e-12 | 120 |
| GO:00070152 | Colorectum | MSS | actin filament organization | 146/3467 | 442/18723 | 1.16e-13 | 2.67e-11 | 146 |
| GO:00329702 | Colorectum | MSS | regulation of actin filament-based process | 128/3467 | 397/18723 | 2.47e-11 | 3.49e-09 | 128 |
| GO:19054752 | Colorectum | MSS | regulation of protein localization to membrane | 68/3467 | 175/18723 | 2.16e-10 | 2.09e-08 | 68 |
| GO:19029032 | Colorectum | MSS | regulation of supramolecular fiber organization | 121/3467 | 383/18723 | 3.63e-10 | 3.28e-08 | 121 |
| GO:00329562 | Colorectum | MSS | regulation of actin cytoskeleton organization | 113/3467 | 358/18723 | 1.46e-09 | 1.07e-07 | 113 |
| 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 |
| 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 |
| PPFIA1 | SNV | Missense_Mutation | c.113N>C | p.Gln38Pro | p.Q38P | Q13136 | protein_coding | deleterious(0) | possibly_damaging(0.824) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| PPFIA1 | SNV | Missense_Mutation | novel | c.632N>T | p.Asn211Ile | p.N211I | Q13136 | protein_coding | tolerated(0.06) | benign(0.017) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| PPFIA1 | SNV | Missense_Mutation | rs767442340 | c.1912N>A | p.Ala638Thr | p.A638T | Q13136 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-A8-A091-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | PD |
| PPFIA1 | SNV | Missense_Mutation | novel | c.217N>T | p.His73Tyr | p.H73Y | Q13136 | protein_coding | tolerated(0.11) | possibly_damaging(0.709) | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PPFIA1 | SNV | Missense_Mutation | c.136G>A | p.Glu46Lys | p.E46K | Q13136 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PPFIA1 | SNV | Missense_Mutation | c.2240G>C | p.Arg747Thr | p.R747T | Q13136 | protein_coding | deleterious(0.02) | possibly_damaging(0.703) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PPFIA1 | SNV | Missense_Mutation | novel | c.2920N>C | p.Ser974Arg | p.S974R | Q13136 | protein_coding | deleterious(0.01) | possibly_damaging(0.905) | TCGA-AO-A1KT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | SD |
| PPFIA1 | SNV | Missense_Mutation | c.2567N>A | p.Arg856His | p.R856H | Q13136 | protein_coding | deleterious(0.02) | possibly_damaging(0.475) | TCGA-AQ-A04H-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | |
| PPFIA1 | SNV | Missense_Mutation | novel | c.2071A>G | p.Ser691Gly | p.S691G | Q13136 | protein_coding | tolerated(0.38) | benign(0) | TCGA-BH-A0HY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | taxotere | CR |
| PPFIA1 | SNV | Missense_Mutation | c.2513N>T | p.Ser838Leu | p.S838L | Q13136 | protein_coding | tolerated(0.27) | benign(0.013) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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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 |
| Page: 1 |
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