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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 |
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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 |
| 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. |
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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:0045216 | Colorectum | AD | cell-cell junction organization | 80/3918 | 200/18723 | 5.57e-10 | 4.58e-08 | 80 |
| GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0010810 | Colorectum | AD | regulation of cell-substrate adhesion | 81/3918 | 221/18723 | 4.80e-08 | 2.55e-06 | 81 |
| GO:0007043 | Colorectum | AD | cell-cell junction assembly | 57/3918 | 146/18723 | 4.18e-07 | 1.61e-05 | 57 |
| GO:0031589 | Colorectum | AD | cell-substrate adhesion | 116/3918 | 363/18723 | 4.68e-07 | 1.76e-05 | 116 |
| GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
| GO:0010563 | Colorectum | AD | negative regulation of phosphorus metabolic process | 130/3918 | 442/18723 | 1.26e-05 | 2.76e-04 | 130 |
| GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
| GO:0045936 | Colorectum | AD | negative regulation of phosphate metabolic process | 129/3918 | 441/18723 | 1.81e-05 | 3.76e-04 | 129 |
| GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
| GO:0051348 | Colorectum | AD | negative regulation of transferase activity | 85/3918 | 268/18723 | 2.07e-05 | 4.19e-04 | 85 |
| 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:0007409 | Colorectum | AD | axonogenesis | 122/3918 | 418/18723 | 3.36e-05 | 6.15e-04 | 122 |
| GO:0097581 | Colorectum | AD | lamellipodium organization | 35/3918 | 90/18723 | 7.39e-05 | 1.18e-03 | 35 |
| GO:0042326 | Colorectum | AD | negative regulation of phosphorylation | 112/3918 | 385/18723 | 8.02e-05 | 1.27e-03 | 112 |
| GO:0061564 | Colorectum | AD | axon development | 132/3918 | 467/18723 | 8.40e-05 | 1.31e-03 | 132 |
| GO:0001933 | Colorectum | AD | negative regulation of protein phosphorylation | 101/3918 | 342/18723 | 9.39e-05 | 1.42e-03 | 101 |
| GO:0060070 | Colorectum | AD | canonical Wnt signaling pathway | 90/3918 | 303/18723 | 1.76e-04 | 2.38e-03 | 90 |
| 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 |
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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 |
| PTPRO | SNV | Missense_Mutation | rs201019396 | c.839N>A | p.Ser280Tyr | p.S280Y | Q16827 | protein_coding | deleterious_low_confidence(0) | benign(0.365) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPRO | SNV | Missense_Mutation | c.2599G>A | p.Glu867Lys | p.E867K | Q16827 | protein_coding | deleterious(0.01) | possibly_damaging(0.836) | TCGA-AG-A00Y-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PTPRO | SNV | Missense_Mutation | c.2390N>A | p.Ser797Asn | p.S797N | Q16827 | protein_coding | deleterious(0.01) | probably_damaging(0.979) | TCGA-EI-6507-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PTPRO | SNV | Missense_Mutation | novel | c.1378T>G | p.Tyr460Asp | p.Y460D | Q16827 | protein_coding | tolerated(0.1) | benign(0.061) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| PTPRO | SNV | Missense_Mutation | c.204N>A | p.Phe68Leu | p.F68L | Q16827 | protein_coding | tolerated_low_confidence(0.37) | benign(0.005) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PTPRO | SNV | Missense_Mutation | novel | c.2071N>A | p.Leu691Ile | p.L691I | Q16827 | protein_coding | tolerated(0.13) | benign(0.052) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PTPRO | deletion | Frame_Shift_Del | c.2743_2746delNNNN | p.Asn916ArgfsTer29 | p.N916Rfs*29 | Q16827 | protein_coding | TCGA-AD-6901-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |||
| PTPRO | SNV | Missense_Mutation | novel | c.610A>G | p.Thr204Ala | p.T204A | Q16827 | protein_coding | tolerated_low_confidence(0.32) | benign(0.021) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PTPRO | SNV | Missense_Mutation | c.1088T>A | p.Ile363Asn | p.I363N | Q16827 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.897) | TCGA-A5-A0GB-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTPRO | SNV | Missense_Mutation | rs773532368 | c.691C>T | p.Arg231Cys | p.R231C | Q16827 | protein_coding | deleterious_low_confidence(0) | benign(0.226) | TCGA-A5-A0GP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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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