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Gene: PTPRD |
Gene summary for PTPRD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPRD | Gene ID | 5789 |
| Gene name | protein tyrosine phosphatase receptor type D | |
| Gene Alias | HPTP | |
| Cytomap | 9p24.1-p23 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q59H90 |
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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 |
| 5789 | PTPRD | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.09e-03 | -2.52e-01 | 0.0155 |
| 5789 | PTPRD | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.59e-07 | -5.81e-01 | -0.1808 |
| 5789 | PTPRD | HTA11_1938_2000001011 | Human | Colorectum | AD | 6.39e-08 | -5.89e-01 | -0.0811 |
| 5789 | PTPRD | HTA11_78_2000001011 | Human | Colorectum | AD | 8.16e-03 | -3.96e-01 | -0.1088 |
| 5789 | PTPRD | HTA11_83_2000001011 | Human | Colorectum | SER | 2.41e-07 | -4.93e-01 | -0.1526 |
| 5789 | PTPRD | HTA11_696_2000001011 | Human | Colorectum | AD | 1.75e-04 | -3.46e-01 | -0.1464 |
| 5789 | PTPRD | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.64e-04 | -6.74e-01 | -0.2061 |
| 5789 | PTPRD | HTA11_5216_2000001011 | Human | Colorectum | SER | 3.01e-09 | -8.13e-01 | -0.1462 |
| 5789 | PTPRD | HTA11_8622_2000001021 | Human | Colorectum | SER | 7.11e-04 | -7.18e-01 | 0.0528 |
| 5789 | PTPRD | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.93e-03 | 5.33e-01 | 0.0588 |
| 5789 | PTPRD | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.08e-16 | -7.65e-01 | 0.281 |
| 5789 | PTPRD | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.44e-06 | -3.37e-01 | 0.3859 |
| 5789 | PTPRD | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.14e-74 | -1.21e+00 | 0.3005 |
| 5789 | PTPRD | A002-C-010 | Human | Colorectum | FAP | 1.72e-07 | 2.50e-01 | 0.242 |
| 5789 | PTPRD | A015-C-203 | Human | Colorectum | FAP | 2.05e-34 | -6.46e-01 | -0.1294 |
| 5789 | PTPRD | A015-C-204 | Human | Colorectum | FAP | 2.75e-09 | -5.11e-01 | -0.0228 |
| 5789 | PTPRD | A002-C-201 | Human | Colorectum | FAP | 2.50e-16 | -4.91e-01 | 0.0324 |
| 5789 | PTPRD | A001-C-119 | Human | Colorectum | FAP | 4.26e-15 | -7.09e-01 | -0.1557 |
| 5789 | PTPRD | A001-C-108 | Human | Colorectum | FAP | 4.91e-15 | -2.80e-01 | -0.0272 |
| 5789 | PTPRD | A002-C-205 | Human | Colorectum | FAP | 1.03e-25 | -5.86e-01 | -0.1236 |
| Page: 1 2 3 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:0022604 | Colorectum | AD | regulation of cell morphogenesis | 109/3918 | 309/18723 | 3.08e-09 | 2.07e-07 | 109 |
| GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0006470 | Colorectum | AD | protein dephosphorylation | 88/3918 | 281/18723 | 2.56e-05 | 4.89e-04 | 88 |
| GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
| GO:0031346 | Colorectum | AD | positive regulation of cell projection organization | 104/3918 | 353/18723 | 8.26e-05 | 1.30e-03 | 104 |
| GO:0071709 | Colorectum | AD | membrane assembly | 22/3918 | 50/18723 | 2.00e-04 | 2.66e-03 | 22 |
| GO:0010769 | Colorectum | AD | regulation of cell morphogenesis involved in differentiation | 35/3918 | 96/18723 | 3.26e-04 | 3.85e-03 | 35 |
| GO:0010770 | Colorectum | AD | positive regulation of cell morphogenesis involved in differentiation | 30/3918 | 79/18723 | 3.81e-04 | 4.38e-03 | 30 |
| GO:0010720 | Colorectum | AD | positive regulation of cell development | 87/3918 | 298/18723 | 4.17e-04 | 4.71e-03 | 87 |
| GO:0044091 | Colorectum | AD | membrane biogenesis | 22/3918 | 55/18723 | 9.88e-04 | 9.28e-03 | 22 |
| GO:1901888 | Colorectum | AD | regulation of cell junction assembly | 61/3918 | 204/18723 | 1.50e-03 | 1.27e-02 | 61 |
| GO:0050767 | Colorectum | AD | regulation of neurogenesis | 99/3918 | 364/18723 | 2.35e-03 | 1.82e-02 | 99 |
| GO:0099173 | Colorectum | AD | postsynapse organization | 51/3918 | 168/18723 | 2.47e-03 | 1.90e-02 | 51 |
| GO:0016358 | Colorectum | AD | dendrite development | 69/3918 | 243/18723 | 3.32e-03 | 2.42e-02 | 69 |
| GO:0050808 | Colorectum | AD | synapse organization | 112/3918 | 426/18723 | 4.25e-03 | 2.92e-02 | 112 |
| GO:0050807 | Colorectum | AD | regulation of synapse organization | 60/3918 | 211/18723 | 5.67e-03 | 3.64e-02 | 60 |
| GO:00226041 | Colorectum | SER | regulation of cell morphogenesis | 89/2897 | 309/18723 | 1.51e-09 | 1.52e-07 | 89 |
| GO:00343291 | Colorectum | SER | cell junction assembly | 100/2897 | 420/18723 | 4.23e-06 | 1.61e-04 | 100 |
| GO:00717091 | Colorectum | SER | membrane assembly | 20/2897 | 50/18723 | 2.45e-05 | 6.84e-04 | 20 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa045146 | Lung | IAC | Cell adhesion molecules | 30/1053 | 157/8465 | 1.03e-02 | 3.83e-02 | 2.54e-02 | 30 |
| hsa0451411 | Lung | IAC | Cell adhesion molecules | 30/1053 | 157/8465 | 1.03e-02 | 3.83e-02 | 2.54e-02 | 30 |
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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 |
| PTPRD | SNV | Missense_Mutation | novel | c.4606N>G | p.Arg1536Gly | p.R1536G | P23468 | protein_coding | deleterious(0.03) | probably_damaging(0.991) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| PTPRD | SNV | Missense_Mutation | rs377557345 | c.2431N>T | p.Arg811Cys | p.R811C | P23468 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-A7-A3IZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| PTPRD | SNV | Missense_Mutation | c.3886N>C | p.Glu1296Gln | p.E1296Q | P23468 | protein_coding | tolerated(0.19) | benign(0.01) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTPRD | SNV | Missense_Mutation | c.646N>G | p.Arg216Gly | p.R216G | P23468 | protein_coding | deleterious(0.01) | probably_damaging(0.974) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| PTPRD | SNV | Missense_Mutation | c.2344N>A | p.Glu782Lys | p.E782K | P23468 | protein_coding | tolerated(0.24) | benign(0.158) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PTPRD | SNV | Missense_Mutation | rs200684369 | c.3299C>T | p.Thr1100Met | p.T1100M | P23468 | protein_coding | deleterious(0.02) | possibly_damaging(0.628) | TCGA-AC-A6IV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPRD | SNV | Missense_Mutation | novel | c.2619N>A | p.Phe873Leu | p.F873L | P23468 | protein_coding | tolerated(0.19) | benign(0.034) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTPRD | SNV | Missense_Mutation | rs868831433 | c.5474G>A | p.Gly1825Asp | p.G1825D | P23468 | protein_coding | deleterious(0) | probably_damaging(0.948) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTPRD | SNV | Missense_Mutation | rs749851220 | c.277N>A | p.Glu93Lys | p.E93K | P23468 | protein_coding | tolerated(0.1) | possibly_damaging(0.514) | TCGA-AO-A0JC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD |
| PTPRD | SNV | Missense_Mutation | c.3073N>G | p.His1025Asp | p.H1025D | P23468 | protein_coding | tolerated(0.24) | benign(0.107) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| 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 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 |
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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 |
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | US9340574, 7 | |||
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | pioglitazone | PIOGLITAZONE | ||
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | verapamil | VERAPAMIL | 26425837 | |
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | CIXUTUMUMAB | CIXUTUMUMAB | 23800680 | |
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | trandolapril | TRANDOLAPRIL | 26425837 | |
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | JSI-124 | 26267899 | ||
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | TEPROTUMUMAB | TEPROTUMUMAB | 23800680 | |
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 381118819 | ||
| 5789 | PTPRD | PROTEIN PHOSPHATASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | Antihypertensives |
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