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Gene: PRAG1 |
Gene summary for PRAG1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRAG1 | Gene ID | 157285 |
| Gene name | PEAK1 related, kinase-activating pseudokinase 1 | |
| Gene Alias | NACK | |
| Cytomap | 8p23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q86YV5 |
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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 |
| 157285 | PRAG1 | CCI_1 | Human | Cervix | CC | 1.27e-04 | 6.14e-01 | 0.528 |
| 157285 | PRAG1 | CCI_2 | Human | Cervix | CC | 2.31e-04 | 5.57e-01 | 0.5249 |
| 157285 | PRAG1 | CCI_3 | Human | Cervix | CC | 1.12e-07 | 5.26e-01 | 0.516 |
| 157285 | PRAG1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.63e-02 | -2.09e-01 | 0.0155 |
| 157285 | PRAG1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.69e-02 | 4.73e-01 | -0.1088 |
| 157285 | PRAG1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.23e-03 | 4.90e-01 | -0.1954 |
| 157285 | PRAG1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.67e-20 | -4.12e-01 | 0.294 |
| 157285 | PRAG1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.09e-08 | -4.12e-01 | 0.281 |
| 157285 | PRAG1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.02e-18 | -4.12e-01 | 0.3859 |
| 157285 | PRAG1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 9.30e-06 | -4.12e-01 | 0.2585 |
| 157285 | PRAG1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.63e-19 | -4.12e-01 | 0.3005 |
| 157285 | PRAG1 | A015-C-203 | Human | Colorectum | FAP | 9.62e-12 | -3.18e-01 | -0.1294 |
| 157285 | PRAG1 | A002-C-201 | Human | Colorectum | FAP | 6.77e-07 | -2.01e-01 | 0.0324 |
| 157285 | PRAG1 | A001-C-119 | Human | Colorectum | FAP | 3.10e-02 | 2.86e-02 | -0.1557 |
| 157285 | PRAG1 | A002-C-205 | Human | Colorectum | FAP | 2.08e-09 | -1.45e-01 | -0.1236 |
| 157285 | PRAG1 | A015-C-005 | Human | Colorectum | FAP | 5.10e-04 | -2.32e-01 | -0.0336 |
| 157285 | PRAG1 | A015-C-006 | Human | Colorectum | FAP | 5.07e-06 | -1.76e-01 | -0.0994 |
| 157285 | PRAG1 | A015-C-106 | Human | Colorectum | FAP | 2.32e-04 | -1.92e-01 | -0.0511 |
| 157285 | PRAG1 | A002-C-114 | Human | Colorectum | FAP | 1.30e-10 | -3.11e-01 | -0.1561 |
| 157285 | PRAG1 | A015-C-104 | Human | Colorectum | FAP | 2.33e-12 | -3.23e-01 | -0.1899 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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 | ||
| 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:002260410 | Cervix | CC | regulation of cell morphogenesis | 84/2311 | 309/18723 | 1.00e-12 | 4.29e-10 | 84 |
| GO:00510566 | Cervix | CC | regulation of small GTPase mediated signal transduction | 75/2311 | 302/18723 | 1.54e-09 | 1.74e-07 | 75 |
| GO:00072656 | Cervix | CC | Ras protein signal transduction | 79/2311 | 337/18723 | 9.49e-09 | 7.77e-07 | 79 |
| GO:00109757 | Cervix | CC | regulation of neuron projection development | 88/2311 | 445/18723 | 4.26e-06 | 1.09e-04 | 88 |
| GO:00072666 | Cervix | CC | Rho protein signal transduction | 35/2311 | 137/18723 | 1.77e-05 | 3.33e-04 | 35 |
| GO:00083608 | Cervix | CC | regulation of cell shape | 38/2311 | 154/18723 | 1.86e-05 | 3.46e-04 | 38 |
| GO:00465785 | Cervix | CC | regulation of Ras protein signal transduction | 44/2311 | 189/18723 | 2.05e-05 | 3.73e-04 | 44 |
| GO:00072194 | Cervix | CC | Notch signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
| GO:00085933 | Cervix | CC | regulation of Notch signaling pathway | 25/2311 | 95/18723 | 1.61e-04 | 1.93e-03 | 25 |
| GO:00313456 | Cervix | CC | negative regulation of cell projection organization | 39/2311 | 186/18723 | 5.86e-04 | 5.57e-03 | 39 |
| GO:00350235 | Cervix | CC | regulation of Rho protein signal transduction | 22/2311 | 86/18723 | 5.93e-04 | 5.60e-03 | 22 |
| GO:00109775 | Cervix | CC | negative regulation of neuron projection development | 28/2311 | 137/18723 | 4.74e-03 | 2.83e-02 | 28 |
| GO:0022604 | Colorectum | AD | regulation of cell morphogenesis | 109/3918 | 309/18723 | 3.08e-09 | 2.07e-07 | 109 |
| GO:0008360 | Colorectum | AD | regulation of cell shape | 56/3918 | 154/18723 | 7.01e-06 | 1.73e-04 | 56 |
| GO:0007265 | Colorectum | AD | Ras protein signal transduction | 104/3918 | 337/18723 | 1.01e-05 | 2.35e-04 | 104 |
| GO:0051056 | Colorectum | AD | regulation of small GTPase mediated signal transduction | 94/3918 | 302/18723 | 1.81e-05 | 3.76e-04 | 94 |
| GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
| GO:0031345 | Colorectum | AD | negative regulation of cell projection organization | 58/3918 | 186/18723 | 6.37e-04 | 6.58e-03 | 58 |
| GO:0010977 | Colorectum | AD | negative regulation of neuron projection development | 43/3918 | 137/18723 | 2.60e-03 | 1.97e-02 | 43 |
| GO:0046578 | Colorectum | AD | regulation of Ras protein signal transduction | 56/3918 | 189/18723 | 2.85e-03 | 2.14e-02 | 56 |
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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. |
| 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 |
| PRAG1 | SNV | Missense_Mutation | novel | c.314G>A | p.Ser105Asn | p.S105N | Q86YV5 | protein_coding | tolerated(1) | benign(0.018) | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| PRAG1 | SNV | Missense_Mutation | novel | c.149N>A | p.Arg50Lys | p.R50K | Q86YV5 | protein_coding | tolerated(0.48) | benign(0.155) | TCGA-AR-A2LH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| PRAG1 | SNV | Missense_Mutation | novel | c.1163N>A | p.Ser388Asn | p.S388N | Q86YV5 | protein_coding | tolerated(0.23) | benign(0.007) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PRAG1 | SNV | Missense_Mutation | novel | c.4196N>T | p.Ser1399Leu | p.S1399L | Q86YV5 | protein_coding | deleterious(0) | benign(0.09) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD |
| PRAG1 | SNV | Missense_Mutation | rs868616357 | c.189N>T | p.Arg63Ser | p.R63S | Q86YV5 | protein_coding | deleterious(0.04) | possibly_damaging(0.844) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PRAG1 | SNV | Missense_Mutation | novel | c.1876N>G | p.Pro626Ala | p.P626A | Q86YV5 | protein_coding | tolerated(0.15) | probably_damaging(0.926) | TCGA-E2-A150-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| PRAG1 | SNV | Missense_Mutation | novel | c.1036G>A | p.Gly346Ser | p.G346S | Q86YV5 | protein_coding | tolerated_low_confidence(0.5) | probably_damaging(0.934) | TCGA-PE-A5DD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | |
| PRAG1 | insertion | Nonsense_Mutation | novel | c.311_312insCTCTGTCCCTTTAGGCTAA | p.Ala106ValfsTer5 | p.A106Vfs*5 | Q86YV5 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| PRAG1 | insertion | Frame_Shift_Ins | novel | c.4008_4009insA | p.Val1337SerfsTer111 | p.V1337Sfs*111 | Q86YV5 | protein_coding | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD | ||
| PRAG1 | insertion | Frame_Shift_Ins | novel | c.4007_4008insTGGAAGCACCCATGTCTCCCTGGGAAATGGTACAGATGACTGG | p.Val1337GlyfsTer125 | p.V1337Gfs*125 | Q86YV5 | protein_coding | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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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