|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PTPRO |
Gene summary for PTPRO |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPRO | Gene ID | 5800 |
| Gene name | protein tyrosine phosphatase receptor type O | |
| Gene Alias | GLEPP1 | |
| Cytomap | 12p12.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q16827 |
Top |
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 |
| 5800 | PTPRO | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.61e-11 | -5.17e-01 | 0.0155 |
| 5800 | PTPRO | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.37e-10 | -5.88e-01 | -0.1808 |
| 5800 | PTPRO | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.90e-04 | -5.34e-01 | -0.0811 |
| 5800 | PTPRO | HTA11_78_2000001011 | Human | Colorectum | AD | 2.13e-09 | -5.56e-01 | -0.1088 |
| 5800 | PTPRO | HTA11_3361_2000001011 | Human | Colorectum | AD | 6.55e-06 | -5.60e-01 | -0.1207 |
| 5800 | PTPRO | HTA11_83_2000001011 | Human | Colorectum | SER | 1.12e-04 | -5.67e-01 | -0.1526 |
| 5800 | PTPRO | HTA11_696_2000001011 | Human | Colorectum | AD | 1.29e-07 | -4.12e-01 | -0.1464 |
| 5800 | PTPRO | HTA11_866_2000001011 | Human | Colorectum | AD | 1.85e-03 | -3.86e-01 | -0.1001 |
| 5800 | PTPRO | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.92e-09 | -5.21e-01 | -0.059 |
| 5800 | PTPRO | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.92e-06 | -5.45e-01 | 0.0338 |
| 5800 | PTPRO | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.85e-05 | -3.78e-01 | 0.0674 |
| 5800 | PTPRO | F007 | Human | Colorectum | FAP | 4.25e-09 | -5.41e-01 | 0.1176 |
| 5800 | PTPRO | A002-C-010 | Human | Colorectum | FAP | 2.63e-05 | -4.67e-01 | 0.242 |
| 5800 | PTPRO | A001-C-207 | Human | Colorectum | FAP | 2.19e-10 | -5.16e-01 | 0.1278 |
| 5800 | PTPRO | A015-C-203 | Human | Colorectum | FAP | 1.81e-13 | -3.98e-01 | -0.1294 |
| 5800 | PTPRO | A015-C-204 | Human | Colorectum | FAP | 1.48e-11 | -5.53e-01 | -0.0228 |
| 5800 | PTPRO | A002-C-201 | Human | Colorectum | FAP | 2.75e-15 | -5.18e-01 | 0.0324 |
| 5800 | PTPRO | A002-C-203 | Human | Colorectum | FAP | 1.86e-14 | -5.16e-01 | 0.2786 |
| 5800 | PTPRO | A001-C-108 | Human | Colorectum | FAP | 1.19e-15 | -5.03e-01 | -0.0272 |
| 5800 | PTPRO | A002-C-205 | Human | Colorectum | FAP | 3.74e-13 | -4.71e-01 | -0.1236 |
| Page: 1 2 |
| 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 |
| ∗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. |
Top |
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:00975814 | Colorectum | FAP | lamellipodium organization | 29/2622 | 90/18723 | 8.11e-06 | 2.40e-04 | 29 |
| GO:00513484 | Colorectum | FAP | negative regulation of transferase activity | 63/2622 | 268/18723 | 1.82e-05 | 4.57e-04 | 63 |
| GO:00508083 | Colorectum | FAP | synapse organization | 91/2622 | 426/18723 | 1.90e-05 | 4.74e-04 | 91 |
| GO:00070434 | Colorectum | FAP | cell-cell junction assembly | 39/2622 | 146/18723 | 3.74e-05 | 8.09e-04 | 39 |
| GO:00019334 | Colorectum | FAP | negative regulation of protein phosphorylation | 75/2622 | 342/18723 | 4.02e-05 | 8.53e-04 | 75 |
| GO:00459364 | Colorectum | FAP | negative regulation of phosphate metabolic process | 92/2622 | 441/18723 | 4.43e-05 | 9.26e-04 | 92 |
| GO:00105634 | Colorectum | FAP | negative regulation of phosphorus metabolic process | 92/2622 | 442/18723 | 4.84e-05 | 9.91e-04 | 92 |
| GO:00064693 | Colorectum | FAP | negative regulation of protein kinase activity | 51/2622 | 212/18723 | 5.82e-05 | 1.15e-03 | 51 |
| GO:00423264 | Colorectum | FAP | negative regulation of phosphorylation | 81/2622 | 385/18723 | 9.16e-05 | 1.59e-03 | 81 |
| GO:00508784 | Colorectum | FAP | regulation of body fluid levels | 79/2622 | 379/18723 | 1.52e-04 | 2.35e-03 | 79 |
| GO:00336733 | Colorectum | FAP | negative regulation of kinase activity | 54/2622 | 237/18723 | 1.66e-04 | 2.51e-03 | 54 |
| GO:00720732 | Colorectum | FAP | kidney epithelium development | 35/2622 | 136/18723 | 2.03e-04 | 2.92e-03 | 35 |
| GO:00300322 | Colorectum | FAP | lamellipodium assembly | 22/2622 | 72/18723 | 2.31e-04 | 3.25e-03 | 22 |
| GO:00313453 | Colorectum | FAP | negative regulation of cell projection organization | 44/2622 | 186/18723 | 2.69e-04 | 3.64e-03 | 44 |
| GO:00016551 | Colorectum | FAP | urogenital system development | 70/2622 | 338/18723 | 4.26e-04 | 5.11e-03 | 70 |
| GO:0072001 | Colorectum | FAP | renal system development | 63/2622 | 302/18723 | 6.59e-04 | 7.19e-03 | 63 |
| GO:0001822 | Colorectum | FAP | kidney development | 61/2622 | 293/18723 | 8.38e-04 | 8.72e-03 | 61 |
| GO:00109772 | Colorectum | FAP | negative regulation of neuron projection development | 33/2622 | 137/18723 | 1.07e-03 | 1.04e-02 | 33 |
| GO:00508071 | Colorectum | FAP | regulation of synapse organization | 46/2622 | 211/18723 | 1.30e-03 | 1.20e-02 | 46 |
| GO:0032835 | Colorectum | FAP | glomerulus development | 18/2622 | 62/18723 | 1.60e-03 | 1.42e-02 | 18 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| PTPRO | SNV | Missense_Mutation | c.295N>C | p.Val99Leu | p.V99L | Q16827 | protein_coding | tolerated_low_confidence(0.22) | benign(0.005) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD | |
| PTPRO | SNV | Missense_Mutation | rs761583283 | c.128C>T | p.Ser43Leu | p.S43L | Q16827 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.456) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR |
| PTPRO | SNV | Missense_Mutation | novel | c.2467N>C | p.Ile823Leu | p.I823L | Q16827 | protein_coding | deleterious(0.01) | benign(0.13) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PTPRO | SNV | Missense_Mutation | c.1798C>A | p.Pro600Thr | p.P600T | Q16827 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-AR-A1AH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | PD | ||
| PTPRO | SNV | Missense_Mutation | c.1810N>C | p.Tyr604His | p.Y604H | Q16827 | protein_coding | deleterious(0.03) | possibly_damaging(0.853) | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PTPRO | SNV | Missense_Mutation | c.1444N>C | p.Glu482Gln | p.E482Q | Q16827 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-LD-A74U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | taxotere | SD | |
| PTPRO | insertion | In_Frame_Ins | novel | c.1004_1005insGTTCATGGAAGAGGTGATAATGGAACTGCTATTTGAAGAACAAGT | p.Ser335_Gly336insPheMetGluGluValIleMetGluLeuLeuPheGluGluGlnVal | p.S335_G336insFMEEVIMELLFEEQV | Q16827 | protein_coding | TCGA-BH-A0B8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
| PTPRO | SNV | Missense_Mutation | rs763453061 | c.214N>C | p.Glu72Gln | p.E72Q | Q16827 | protein_coding | tolerated_low_confidence(0.24) | benign(0.01) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPRO | SNV | Missense_Mutation | rs724159880 | c.1444N>A | p.Glu482Lys | p.E482K | Q16827 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPRO | SNV | Missense_Mutation | c.2730G>T | p.Lys910Asn | p.K910N | Q16827 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |