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Gene: PTPRS |
Gene summary for PTPRS |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPRS | Gene ID | 5802 |
| Gene name | protein tyrosine phosphatase receptor type S | |
| Gene Alias | PTPSIGMA | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q13332 |
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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 |
| 5802 | PTPRS | P126T-E | Human | Esophagus | ESCC | 5.94e-06 | 3.63e-01 | 0.1125 |
| 5802 | PTPRS | P127T-E | Human | Esophagus | ESCC | 1.47e-12 | 2.28e-01 | 0.0826 |
| 5802 | PTPRS | P128T-E | Human | Esophagus | ESCC | 4.58e-37 | 9.23e-01 | 0.1241 |
| 5802 | PTPRS | P130T-E | Human | Esophagus | ESCC | 6.36e-33 | 5.55e-01 | 0.1676 |
| 5802 | PTPRS | C21 | Human | Oral cavity | OSCC | 2.58e-05 | 6.20e-01 | 0.2678 |
| 5802 | PTPRS | C30 | Human | Oral cavity | OSCC | 2.87e-07 | 7.76e-01 | 0.3055 |
| 5802 | PTPRS | C43 | Human | Oral cavity | OSCC | 9.04e-18 | 7.67e-01 | 0.1704 |
| 5802 | PTPRS | C46 | Human | Oral cavity | OSCC | 1.94e-03 | 4.89e-01 | 0.1673 |
| 5802 | PTPRS | C08 | Human | Oral cavity | OSCC | 6.86e-06 | 4.25e-01 | 0.1919 |
| 5802 | PTPRS | EOLP-1 | Human | Oral cavity | EOLP | 5.79e-06 | 3.60e-01 | -0.0202 |
| 5802 | PTPRS | SYSMH1 | Human | Oral cavity | OSCC | 1.51e-10 | 2.36e-01 | 0.1127 |
| 5802 | PTPRS | SYSMH2 | Human | Oral cavity | OSCC | 2.07e-02 | 1.65e-01 | 0.2326 |
| 5802 | PTPRS | SYSMH6 | Human | Oral cavity | OSCC | 4.82e-08 | 3.94e-02 | 0.1275 |
| 5802 | PTPRS | 048752_1579-all-cells | Human | Prostate | BPH | 1.24e-29 | 5.30e-01 | 0.1008 |
| 5802 | PTPRS | 052095_1628-all-cells | Human | Prostate | BPH | 1.76e-13 | 3.52e-01 | 0.1032 |
| 5802 | PTPRS | 052097_1595-all-cells | Human | Prostate | BPH | 1.65e-11 | 2.94e-01 | 0.0972 |
| 5802 | PTPRS | 052099_1652-all-cells | Human | Prostate | BPH | 8.47e-16 | 4.12e-01 | 0.1038 |
| 5802 | PTPRS | Dong_P1 | Human | Prostate | Tumor | 2.18e-12 | 2.23e-01 | 0.035 |
| 5802 | PTPRS | Dong_P3 | Human | Prostate | Tumor | 3.39e-22 | 4.40e-01 | 0.0278 |
| 5802 | PTPRS | Dong_P4 | Human | Prostate | Tumor | 2.38e-06 | 2.60e-01 | 0.0292 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 |
| ∗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:00027644 | Cervix | CC | immune response-regulating signaling pathway | 97/2311 | 468/18723 | 1.49e-07 | 7.07e-06 | 97 |
| GO:00343298 | Cervix | CC | cell junction assembly | 88/2311 | 420/18723 | 3.42e-07 | 1.38e-05 | 88 |
| GO:00163587 | Cervix | CC | dendrite development | 58/2311 | 243/18723 | 4.52e-07 | 1.76e-05 | 58 |
| GO:19030349 | Cervix | CC | regulation of response to wounding | 44/2311 | 167/18723 | 6.33e-07 | 2.31e-05 | 44 |
| GO:00109757 | Cervix | CC | regulation of neuron projection development | 88/2311 | 445/18723 | 4.26e-06 | 1.09e-04 | 88 |
| GO:00160498 | Cervix | CC | cell growth | 92/2311 | 482/18723 | 1.16e-05 | 2.49e-04 | 92 |
| GO:00064708 | Cervix | CC | protein dephosphorylation | 60/2311 | 281/18723 | 1.33e-05 | 2.68e-04 | 60 |
| GO:00310996 | Cervix | CC | regeneration | 46/2311 | 198/18723 | 1.43e-05 | 2.84e-04 | 46 |
| GO:00609965 | Cervix | CC | dendritic spine development | 28/2311 | 99/18723 | 1.61e-05 | 3.15e-04 | 28 |
| GO:00325359 | Cervix | CC | regulation of cellular component size | 76/2311 | 383/18723 | 1.66e-05 | 3.21e-04 | 76 |
| GO:00615647 | Cervix | CC | axon development | 89/2311 | 467/18723 | 1.71e-05 | 3.27e-04 | 89 |
| GO:00022212 | Cervix | CC | pattern recognition receptor signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
| GO:00074097 | Cervix | CC | axonogenesis | 78/2311 | 418/18723 | 1.14e-04 | 1.43e-03 | 78 |
| GO:00622073 | Cervix | CC | regulation of pattern recognition receptor signaling pathway | 27/2311 | 105/18723 | 1.37e-04 | 1.68e-03 | 27 |
| GO:00015588 | Cervix | CC | regulation of cell growth | 77/2311 | 414/18723 | 1.40e-04 | 1.70e-03 | 77 |
| GO:00609984 | Cervix | CC | regulation of dendritic spine development | 18/2311 | 61/18723 | 2.84e-04 | 3.07e-03 | 18 |
| GO:19021153 | Cervix | CC | regulation of organelle assembly | 40/2311 | 186/18723 | 2.92e-04 | 3.15e-03 | 40 |
| GO:000206410 | Cervix | CC | epithelial cell development | 45/2311 | 220/18723 | 4.14e-04 | 4.21e-03 | 45 |
| GO:00507705 | Cervix | CC | regulation of axonogenesis | 34/2311 | 154/18723 | 4.87e-04 | 4.76e-03 | 34 |
| GO:19018886 | Cervix | CC | regulation of cell junction assembly | 42/2311 | 204/18723 | 5.50e-04 | 5.29e-03 | 42 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa045147 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa0451412 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
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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 |
| PTPRS | SNV | Missense_Mutation | rs758242063 | c.554N>G | p.Lys185Arg | p.K185R | Q13332 | protein_coding | deleterious(0.04) | probably_damaging(0.986) | TCGA-A8-A081-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTPRS | SNV | Missense_Mutation | rs749770933 | c.4976N>A | p.Arg1659His | p.R1659H | Q13332 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-AN-A0FT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPRS | SNV | Missense_Mutation | rs771478606 | c.4886N>G | p.Asn1629Ser | p.N1629S | Q13332 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E9-A1R6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PTPRS | insertion | In_Frame_Ins | novel | c.3570_3571insACCCAAGGCCAGGCTGGT | p.Arg1190_Leu1191insThrGlnGlyGlnAlaGly | p.R1190_L1191insTQGQAG | Q13332 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| PTPRS | insertion | In_Frame_Ins | novel | c.5580_5581insAGAGTC | p.Ile1860_Gly1861insArgVal | p.I1860_G1861insRV | Q13332 | protein_coding | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |||
| PTPRS | insertion | Frame_Shift_Ins | novel | c.5578_5579insGCCCCAAGCTTAGGCTGTCCCATCTGGGCTG | p.Ile1860SerfsTer16 | p.I1860Sfs*16 | Q13332 | protein_coding | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |||
| PTPRS | insertion | In_Frame_Ins | novel | c.3910_3911insAAG | p.Leu1304delinsGlnVal | p.L1304delinsQV | Q13332 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| PTPRS | insertion | Frame_Shift_Ins | novel | c.3909_3910insTTCAACTCAG | p.Leu1304PhefsTer13 | p.L1304Ffs*13 | Q13332 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| PTPRS | deletion | Frame_Shift_Del | novel | c.4210delN | p.Gln1404SerfsTer12 | p.Q1404Sfs*12 | Q13332 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PTPRS | deletion | Frame_Shift_Del | novel | c.3363delN | p.Leu1122SerfsTer36 | p.L1122Sfs*36 | Q13332 | protein_coding | TCGA-D8-A27V-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 15 16 17 18 19 20 |
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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 |
| 5802 | PTPRS | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, KINASE, CLINICALLY ACTIONABLE | inhibitor | 252827507 | ||
| 5802 | PTPRS | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, KINASE, CLINICALLY ACTIONABLE | Etidronic acid | |||
| 5802 | PTPRS | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, KINASE, CLINICALLY ACTIONABLE | inhibitor | 381118819 |
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