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Gene: PTPN1 |
Gene summary for PTPN1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PTPN1 | Gene ID | 5770 |
Gene name | protein tyrosine phosphatase non-receptor type 1 | |
Gene Alias | PTP1B | |
Cytomap | 20q13.13 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | B4DSN5 |
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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 |
5770 | PTPN1 | LZE2T | Human | Esophagus | ESCC | 4.35e-02 | 1.84e-01 | 0.082 |
5770 | PTPN1 | LZE4T | Human | Esophagus | ESCC | 1.52e-18 | 8.84e-01 | 0.0811 |
5770 | PTPN1 | LZE7T | Human | Esophagus | ESCC | 3.34e-06 | 3.47e-01 | 0.0667 |
5770 | PTPN1 | LZE8T | Human | Esophagus | ESCC | 3.14e-11 | 3.28e-01 | 0.067 |
5770 | PTPN1 | LZE20T | Human | Esophagus | ESCC | 9.57e-05 | 2.33e-01 | 0.0662 |
5770 | PTPN1 | LZE24T | Human | Esophagus | ESCC | 6.04e-13 | 3.30e-01 | 0.0596 |
5770 | PTPN1 | LZE6T | Human | Esophagus | ESCC | 4.03e-09 | 1.23e-01 | 0.0845 |
5770 | PTPN1 | P1T-E | Human | Esophagus | ESCC | 2.84e-13 | 5.70e-01 | 0.0875 |
5770 | PTPN1 | P2T-E | Human | Esophagus | ESCC | 1.22e-46 | 9.35e-01 | 0.1177 |
5770 | PTPN1 | P4T-E | Human | Esophagus | ESCC | 6.90e-24 | 5.10e-01 | 0.1323 |
5770 | PTPN1 | P5T-E | Human | Esophagus | ESCC | 9.33e-19 | 4.11e-01 | 0.1327 |
5770 | PTPN1 | P8T-E | Human | Esophagus | ESCC | 4.73e-20 | 2.74e-01 | 0.0889 |
5770 | PTPN1 | P9T-E | Human | Esophagus | ESCC | 3.95e-12 | 1.42e-01 | 0.1131 |
5770 | PTPN1 | P10T-E | Human | Esophagus | ESCC | 2.96e-24 | 3.96e-01 | 0.116 |
5770 | PTPN1 | P11T-E | Human | Esophagus | ESCC | 3.20e-07 | 7.25e-01 | 0.1426 |
5770 | PTPN1 | P12T-E | Human | Esophagus | ESCC | 3.79e-38 | 8.06e-01 | 0.1122 |
5770 | PTPN1 | P15T-E | Human | Esophagus | ESCC | 6.67e-20 | 6.31e-01 | 0.1149 |
5770 | PTPN1 | P16T-E | Human | Esophagus | ESCC | 6.60e-34 | 7.10e-01 | 0.1153 |
5770 | PTPN1 | P17T-E | Human | Esophagus | ESCC | 1.22e-15 | 6.13e-01 | 0.1278 |
5770 | PTPN1 | P20T-E | Human | Esophagus | ESCC | 4.92e-20 | 5.70e-01 | 0.1124 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:001081027 | Skin | cSCC | regulation of cell-substrate adhesion | 88/4864 | 221/18723 | 4.26e-06 | 6.32e-05 | 88 |
GO:004887229 | Skin | cSCC | homeostasis of number of cells | 104/4864 | 272/18723 | 5.34e-06 | 7.71e-05 | 104 |
GO:01404676 | Skin | cSCC | integrated stress response signaling | 16/4864 | 22/18723 | 5.92e-06 | 8.44e-05 | 16 |
GO:005189324 | Skin | cSCC | regulation of focal adhesion assembly | 34/4864 | 66/18723 | 8.09e-06 | 1.09e-04 | 34 |
GO:009010924 | Skin | cSCC | regulation of cell-substrate junction assembly | 34/4864 | 66/18723 | 8.09e-06 | 1.09e-04 | 34 |
GO:003109924 | Skin | cSCC | regeneration | 79/4864 | 198/18723 | 1.18e-05 | 1.51e-04 | 79 |
GO:007084924 | Skin | cSCC | response to epidermal growth factor | 27/4864 | 49/18723 | 1.38e-05 | 1.73e-04 | 27 |
GO:1903573112 | Skin | cSCC | negative regulation of response to endoplasmic reticulum stress | 25/4864 | 44/18723 | 1.40e-05 | 1.74e-04 | 25 |
GO:004232626 | Skin | cSCC | negative regulation of phosphorylation | 137/4864 | 385/18723 | 1.63e-05 | 1.99e-04 | 137 |
GO:004804124 | Skin | cSCC | focal adhesion assembly | 41/4864 | 87/18723 | 1.71e-05 | 2.07e-04 | 41 |
GO:0046825111 | Skin | cSCC | regulation of protein export from nucleus | 19/4864 | 30/18723 | 1.82e-05 | 2.19e-04 | 19 |
GO:003158926 | Skin | cSCC | cell-substrate adhesion | 130/4864 | 363/18723 | 1.87e-05 | 2.23e-04 | 130 |
GO:006145825 | Skin | cSCC | reproductive system development | 149/4864 | 427/18723 | 2.30e-05 | 2.65e-04 | 149 |
GO:007136424 | Skin | cSCC | cellular response to epidermal growth factor stimulus | 25/4864 | 45/18723 | 2.37e-05 | 2.72e-04 | 25 |
GO:004860824 | Skin | cSCC | reproductive structure development | 148/4864 | 424/18723 | 2.40e-05 | 2.74e-04 | 148 |
GO:000717323 | Skin | cSCC | epidermal growth factor receptor signaling pathway | 48/4864 | 108/18723 | 2.42e-05 | 2.76e-04 | 48 |
GO:000193326 | Skin | cSCC | negative regulation of protein phosphorylation | 123/4864 | 342/18723 | 2.48e-05 | 2.82e-04 | 123 |
GO:005134829 | Skin | cSCC | negative regulation of transferase activity | 100/4864 | 268/18723 | 2.60e-05 | 2.94e-04 | 100 |
GO:190198812 | Skin | cSCC | negative regulation of cell cycle phase transition | 94/4864 | 249/18723 | 2.65e-05 | 3.00e-04 | 94 |
GO:001094812 | Skin | cSCC | negative regulation of cell cycle process | 108/4864 | 294/18723 | 2.75e-05 | 3.09e-04 | 108 |
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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 |
hsa0452030 | Esophagus | ESCC | Adherens junction | 69/4205 | 93/8465 | 1.08e-06 | 6.83e-06 | 3.50e-06 | 69 |
hsa049109 | Esophagus | ESCC | Insulin signaling pathway | 89/4205 | 137/8465 | 1.97e-04 | 7.32e-04 | 3.75e-04 | 89 |
hsa049318 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
hsa05208310 | Esophagus | ESCC | Chemical carcinogenesis - reactive oxygen species | 168/4205 | 223/8465 | 1.83e-15 | 6.81e-14 | 3.49e-14 | 168 |
hsa04520114 | Esophagus | ESCC | Adherens junction | 69/4205 | 93/8465 | 1.08e-06 | 6.83e-06 | 3.50e-06 | 69 |
hsa0491014 | Esophagus | ESCC | Insulin signaling pathway | 89/4205 | 137/8465 | 1.97e-04 | 7.32e-04 | 3.75e-04 | 89 |
hsa0493113 | Esophagus | ESCC | Insulin resistance | 69/4205 | 108/8465 | 1.92e-03 | 5.54e-03 | 2.84e-03 | 69 |
hsa0520842 | Liver | HCC | Chemical carcinogenesis - reactive oxygen species | 167/4020 | 223/8465 | 2.85e-17 | 1.91e-15 | 1.06e-15 | 167 |
hsa0491041 | Liver | HCC | Insulin signaling pathway | 95/4020 | 137/8465 | 1.53e-07 | 1.97e-06 | 1.10e-06 | 95 |
hsa0493121 | Liver | HCC | Insulin resistance | 77/4020 | 108/8465 | 3.89e-07 | 4.46e-06 | 2.48e-06 | 77 |
hsa0452042 | Liver | HCC | Adherens junction | 68/4020 | 93/8465 | 3.99e-07 | 4.46e-06 | 2.48e-06 | 68 |
hsa0520852 | Liver | HCC | Chemical carcinogenesis - reactive oxygen species | 167/4020 | 223/8465 | 2.85e-17 | 1.91e-15 | 1.06e-15 | 167 |
hsa0491051 | Liver | HCC | Insulin signaling pathway | 95/4020 | 137/8465 | 1.53e-07 | 1.97e-06 | 1.10e-06 | 95 |
hsa0493131 | Liver | HCC | Insulin resistance | 77/4020 | 108/8465 | 3.89e-07 | 4.46e-06 | 2.48e-06 | 77 |
hsa0452052 | Liver | HCC | Adherens junction | 68/4020 | 93/8465 | 3.99e-07 | 4.46e-06 | 2.48e-06 | 68 |
hsa0452016 | Lung | IAC | Adherens junction | 37/1053 | 93/8465 | 1.99e-11 | 2.16e-09 | 1.43e-09 | 37 |
hsa0520816 | Lung | IAC | Chemical carcinogenesis - reactive oxygen species | 51/1053 | 223/8465 | 8.45e-06 | 2.14e-04 | 1.42e-04 | 51 |
hsa0452017 | Lung | IAC | Adherens junction | 37/1053 | 93/8465 | 1.99e-11 | 2.16e-09 | 1.43e-09 | 37 |
hsa0520817 | Lung | IAC | Chemical carcinogenesis - reactive oxygen species | 51/1053 | 223/8465 | 8.45e-06 | 2.14e-04 | 1.42e-04 | 51 |
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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 |
PTPN1 | SNV | Missense_Mutation | novel | c.255N>T | p.Gln85His | p.Q85H | P18031 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
PTPN1 | SNV | Missense_Mutation | novel | c.1192N>T | p.Asp398Tyr | p.D398Y | P18031 | protein_coding | deleterious(0.02) | benign(0.071) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
PTPN1 | SNV | Missense_Mutation | novel | c.1058N>G | p.Pro353Arg | p.P353R | P18031 | protein_coding | tolerated(0.62) | benign(0.024) | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PTPN1 | insertion | Nonsense_Mutation | novel | c.836_837insGGCTTTTGGCATCTTTATGGAAACAAAATCCTGAAAGTGGTTT | p.Phe280AlafsTer11 | p.F280Afs*11 | P18031 | protein_coding | TCGA-A8-A09X-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
PTPN1 | insertion | Nonsense_Mutation | novel | c.1060_1061insGTTAGAAATGAGGAAGTTTCGGATGGGGC | p.Leu354CysfsTer2 | p.L354Cfs*2 | P18031 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
PTPN1 | deletion | Frame_Shift_Del | c.1125delN | p.Gly377GlufsTer27 | p.G377Efs*27 | P18031 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | |||
PTPN1 | SNV | Missense_Mutation | rs138343840 | c.1123G>A | p.Val375Met | p.V375M | P18031 | protein_coding | tolerated(0.08) | benign(0.031) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
PTPN1 | SNV | Missense_Mutation | novel | c.845N>C | p.Met282Thr | p.M282T | P18031 | protein_coding | deleterious(0.05) | benign(0.041) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
PTPN1 | SNV | Missense_Mutation | c.136T>C | p.Tyr46His | p.Y46H | P18031 | protein_coding | deleterious(0.02) | probably_damaging(0.989) | TCGA-AA-3713-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | PR | |
PTPN1 | SNV | Missense_Mutation | novel | c.1027G>A | p.Asp343Asn | p.D343N | P18031 | protein_coding | tolerated(0.44) | benign(0.014) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | inhibitor | 252827507 | ||
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | OLEANOLIC_ACID | OLEANOLIC_ACID | 21453996 | |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | inhibitor | 384403654 | ||
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | ALLYL ISOTHIOCYANATE | ALLYL ISOTHIOCYANATE | 26338358 | |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | LICOAGRODIN | LICOAGRODIN | 24047800 | |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | REL-HUEAFURANOID A | CHEMBL2207339 | 23141910 | |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | ISIS 113715 | |||
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | TILUDRONATE | TILUDRONIC ACID | ||
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | GLISOFLAVONE | GLISOFLAVONE | 20724155 | |
5770 | PTPN1 | DRUGGABLE GENOME, PROTEIN PHOSPHATASE, ENZYME, KINASE | INSULIN | INSULIN | 8826975 |
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