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Gene: PTPN11 |
Gene summary for PTPN11 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPN11 | Gene ID | 5781 |
| Gene name | protein tyrosine phosphatase non-receptor type 11 | |
| Gene Alias | BPTP3 | |
| Cytomap | 12q24.13 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q06124 |
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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 |
| 5781 | PTPN11 | LZE4T | Human | Esophagus | ESCC | 3.57e-07 | 3.43e-01 | 0.0811 |
| 5781 | PTPN11 | LZE7T | Human | Esophagus | ESCC | 1.63e-04 | 5.39e-01 | 0.0667 |
| 5781 | PTPN11 | LZE8T | Human | Esophagus | ESCC | 4.12e-02 | 2.26e-01 | 0.067 |
| 5781 | PTPN11 | LZE22T | Human | Esophagus | ESCC | 4.19e-03 | 2.55e-01 | 0.068 |
| 5781 | PTPN11 | LZE24T | Human | Esophagus | ESCC | 1.62e-14 | 4.91e-01 | 0.0596 |
| 5781 | PTPN11 | LZE21T | Human | Esophagus | ESCC | 1.59e-04 | 3.69e-01 | 0.0655 |
| 5781 | PTPN11 | LZE6T | Human | Esophagus | ESCC | 2.41e-03 | 2.45e-01 | 0.0845 |
| 5781 | PTPN11 | P1T-E | Human | Esophagus | ESCC | 1.63e-04 | 4.45e-01 | 0.0875 |
| 5781 | PTPN11 | P2T-E | Human | Esophagus | ESCC | 6.64e-69 | 1.31e+00 | 0.1177 |
| 5781 | PTPN11 | P4T-E | Human | Esophagus | ESCC | 1.27e-30 | 6.92e-01 | 0.1323 |
| 5781 | PTPN11 | P5T-E | Human | Esophagus | ESCC | 5.87e-22 | 4.40e-01 | 0.1327 |
| 5781 | PTPN11 | P8T-E | Human | Esophagus | ESCC | 4.62e-21 | 5.57e-01 | 0.0889 |
| 5781 | PTPN11 | P9T-E | Human | Esophagus | ESCC | 5.36e-09 | 2.52e-01 | 0.1131 |
| 5781 | PTPN11 | P10T-E | Human | Esophagus | ESCC | 1.80e-26 | 5.38e-01 | 0.116 |
| 5781 | PTPN11 | P11T-E | Human | Esophagus | ESCC | 6.18e-23 | 7.56e-01 | 0.1426 |
| 5781 | PTPN11 | P12T-E | Human | Esophagus | ESCC | 1.87e-28 | 4.70e-01 | 0.1122 |
| 5781 | PTPN11 | P15T-E | Human | Esophagus | ESCC | 2.15e-20 | 5.32e-01 | 0.1149 |
| 5781 | PTPN11 | P16T-E | Human | Esophagus | ESCC | 9.33e-42 | 6.84e-01 | 0.1153 |
| 5781 | PTPN11 | P17T-E | Human | Esophagus | ESCC | 5.76e-07 | 5.29e-01 | 0.1278 |
| 5781 | PTPN11 | P19T-E | Human | Esophagus | ESCC | 4.84e-07 | 6.17e-01 | 0.1662 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:003350018 | Skin | AK | carbohydrate homeostasis | 45/1910 | 259/18723 | 2.60e-04 | 2.82e-03 | 45 |
| GO:00603254 | Skin | AK | face morphogenesis | 10/1910 | 28/18723 | 2.78e-04 | 2.94e-03 | 10 |
| GO:005087016 | Skin | AK | positive regulation of T cell activation | 39/1910 | 216/18723 | 2.94e-04 | 3.06e-03 | 39 |
| GO:00100017 | Skin | AK | glial cell differentiation | 40/1910 | 225/18723 | 3.45e-04 | 3.47e-03 | 40 |
| GO:00480134 | Skin | AK | ephrin receptor signaling pathway | 14/1910 | 51/18723 | 4.29e-04 | 4.05e-03 | 14 |
| GO:00028319 | Skin | AK | regulation of response to biotic stimulus | 53/1910 | 327/18723 | 4.63e-04 | 4.31e-03 | 53 |
| GO:190303917 | Skin | AK | positive regulation of leukocyte cell-cell adhesion | 41/1910 | 239/18723 | 6.22e-04 | 5.45e-03 | 41 |
| GO:00336276 | Skin | AK | cell adhesion mediated by integrin | 17/1910 | 72/18723 | 7.51e-04 | 6.32e-03 | 17 |
| GO:19019884 | Skin | AK | negative regulation of cell cycle phase transition | 42/1910 | 249/18723 | 7.65e-04 | 6.39e-03 | 42 |
| GO:000975517 | Skin | AK | hormone-mediated signaling pathway | 34/1910 | 190/18723 | 8.18e-04 | 6.80e-03 | 34 |
| GO:00101712 | Skin | AK | body morphogenesis | 12/1910 | 43/18723 | 9.25e-04 | 7.53e-03 | 12 |
| GO:00603233 | Skin | AK | head morphogenesis | 10/1910 | 32/18723 | 9.35e-04 | 7.56e-03 | 10 |
| GO:00487084 | Skin | AK | astrocyte differentiation | 18/1910 | 81/18723 | 1.14e-03 | 8.81e-03 | 18 |
| GO:00603243 | Skin | AK | face development | 12/1910 | 44/18723 | 1.16e-03 | 8.88e-03 | 12 |
| GO:000828610 | Skin | AK | insulin receptor signaling pathway | 23/1910 | 116/18723 | 1.36e-03 | 1.01e-02 | 23 |
| GO:003286819 | Skin | AK | response to insulin | 43/1910 | 264/18723 | 1.37e-03 | 1.02e-02 | 43 |
| GO:003461425 | Skin | AK | cellular response to reactive oxygen species | 28/1910 | 155/18723 | 1.95e-03 | 1.32e-02 | 28 |
| GO:000181917 | Skin | AK | positive regulation of cytokine production | 67/1910 | 467/18723 | 2.59e-03 | 1.67e-02 | 67 |
| GO:00000776 | Skin | AK | DNA damage checkpoint | 22/1910 | 115/18723 | 2.74e-03 | 1.74e-02 | 22 |
| GO:00614483 | Skin | AK | connective tissue development | 40/1910 | 252/18723 | 3.17e-03 | 1.95e-02 | 40 |
| 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 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05208211 | Esophagus | ESCC | Chemical carcinogenesis - reactive oxygen species | 168/4205 | 223/8465 | 1.83e-15 | 6.81e-14 | 3.49e-14 | 168 |
| hsa05130211 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
| hsa0522020 | Esophagus | ESCC | Chronic myeloid leukemia | 61/4205 | 76/8465 | 3.20e-08 | 2.68e-07 | 1.37e-07 | 61 |
| hsa0520529 | Esophagus | ESCC | Proteoglycans in cancer | 138/4205 | 205/8465 | 1.79e-07 | 1.40e-06 | 7.15e-07 | 138 |
| hsa046259 | Esophagus | ESCC | C-type lectin receptor signaling pathway | 73/4205 | 104/8465 | 1.57e-05 | 7.98e-05 | 4.09e-05 | 73 |
| hsa0512018 | Esophagus | ESCC | Epithelial cell signaling in Helicobacter pylori infection | 52/4205 | 70/8465 | 2.17e-05 | 1.07e-04 | 5.47e-05 | 52 |
| hsa0521118 | Esophagus | ESCC | Renal cell carcinoma | 51/4205 | 69/8465 | 3.29e-05 | 1.53e-04 | 7.83e-05 | 51 |
| hsa0472225 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa049318 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| hsa052356 | Esophagus | ESCC | PD-L1 expression and PD-1 checkpoint pathway in cancer | 58/4205 | 89/8465 | 2.19e-03 | 6.16e-03 | 3.16e-03 | 58 |
| hsa0436016 | Esophagus | ESCC | Axon guidance | 108/4205 | 182/8465 | 5.13e-03 | 1.30e-02 | 6.67e-03 | 108 |
| hsa05208310 | Esophagus | ESCC | Chemical carcinogenesis - reactive oxygen species | 168/4205 | 223/8465 | 1.83e-15 | 6.81e-14 | 3.49e-14 | 168 |
| hsa05130310 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
| hsa05220110 | Esophagus | ESCC | Chronic myeloid leukemia | 61/4205 | 76/8465 | 3.20e-08 | 2.68e-07 | 1.37e-07 | 61 |
| hsa0520537 | Esophagus | ESCC | Proteoglycans in cancer | 138/4205 | 205/8465 | 1.79e-07 | 1.40e-06 | 7.15e-07 | 138 |
| hsa0462513 | Esophagus | ESCC | C-type lectin receptor signaling pathway | 73/4205 | 104/8465 | 1.57e-05 | 7.98e-05 | 4.09e-05 | 73 |
| hsa0512019 | Esophagus | ESCC | Epithelial cell signaling in Helicobacter pylori infection | 52/4205 | 70/8465 | 2.17e-05 | 1.07e-04 | 5.47e-05 | 52 |
| hsa0521119 | Esophagus | ESCC | Renal cell carcinoma | 51/4205 | 69/8465 | 3.29e-05 | 1.53e-04 | 7.83e-05 | 51 |
| hsa04722111 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa0493113 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
| Page: 1 2 3 4 5 6 7 |
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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 |
| PTPN11 | SNV | Missense_Mutation | c.436N>T | p.Asp146Tyr | p.D146Y | Q06124 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTPN11 | SNV | Missense_Mutation | c.38N>A | p.Gly13Asp | p.G13D | Q06124 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C8-A12L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTPN11 | SNV | Missense_Mutation | novel | c.626T>C | p.Val209Ala | p.V209A | Q06124 | protein_coding | tolerated(0.06) | benign(0.02) | TCGA-C5-A7CG-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PTPN11 | SNV | Missense_Mutation | novel | c.1082N>G | p.Glu361Gly | p.E361G | Q06124 | protein_coding | deleterious(0.01) | possibly_damaging(0.908) | TCGA-C5-A8YT-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| PTPN11 | SNV | Missense_Mutation | rs397507512 | c.211N>C | p.Phe71Leu | p.F71L | Q06124 | protein_coding | deleterious(0) | probably_damaging(0.945) | TCGA-A6-2684-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PTPN11 | SNV | Missense_Mutation | rs397507546 | c.1520N>T | p.Gly507Val | p.G507V | Q06124 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD |
| PTPN11 | SNV | Missense_Mutation | c.207N>T | p.Glu69Asp | p.E69D | Q06124 | protein_coding | tolerated(0.05) | benign(0.135) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PTPN11 | SNV | Missense_Mutation | c.463G>A | p.Asp155Asn | p.D155N | Q06124 | protein_coding | tolerated(0.08) | benign(0.074) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD | |
| PTPN11 | SNV | Missense_Mutation | novel | c.1405N>T | p.Arg469Trp | p.R469W | Q06124 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PTPN11 | SNV | Missense_Mutation | c.1547N>A | p.Arg516Gln | p.R516Q | Q06124 | protein_coding | tolerated(0.12) | benign(0.015) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | II-B08 | 20170098 | ||
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | U0126 | 17942397 | ||
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | 4-HYDRAZINYLBENZENESULFONIC ACID | CHEMBL510966 | 19007293 | |
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | cryptotanshinone | CRYPTOTANSHINONE | 23957426 | |
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | PLX4720 | PLX-4720 | 26351322 | |
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | MESO-2,3-DIMERCAPTOSUCCINIC ACID | CHEMBL28721 | ||
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | OLTIPRAZ | OLTIPRAZ | 20655236 | |
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | Refametinib | REFAMETINIB | ||
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | N/A | 19047918,21901340 | ||
| 5781 | PTPN11 | DRUGGABLE GENOME, KINASE, PROTEIN PHOSPHATASE, ENZYME, CLINICALLY ACTIONABLE | TNO155 |
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