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Gene: PTN |
Gene summary for PTN |
Gene summary. |
Gene information | Species | Human | Gene symbol | PTN | Gene ID | 5764 |
Gene name | pleiotrophin | |
Gene Alias | HARP | |
Cytomap | 7q33 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024R778 |
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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 |
5764 | PTN | GSM4909281 | Human | Breast | IDC | 4.32e-06 | -6.65e-02 | 0.21 |
5764 | PTN | GSM4909282 | Human | Breast | IDC | 2.50e-03 | -3.02e-01 | -0.0288 |
5764 | PTN | GSM4909285 | Human | Breast | IDC | 7.79e-05 | -3.03e-01 | 0.21 |
5764 | PTN | GSM4909286 | Human | Breast | IDC | 1.72e-05 | -3.12e-01 | 0.1081 |
5764 | PTN | GSM4909290 | Human | Breast | IDC | 2.64e-02 | -3.12e-01 | 0.2096 |
5764 | PTN | GSM4909299 | Human | Breast | IDC | 8.68e-87 | 1.66e+00 | 0.035 |
5764 | PTN | GSM4909300 | Human | Breast | IDC | 1.71e-17 | 1.10e+00 | 0.0334 |
5764 | PTN | GSM4909301 | Human | Breast | IDC | 7.79e-05 | -3.12e-01 | 0.1577 |
5764 | PTN | GSM4909304 | Human | Breast | IDC | 7.79e-05 | -3.09e-01 | 0.1636 |
5764 | PTN | GSM4909305 | Human | Breast | IDC | 8.54e-16 | 8.27e-01 | 0.0436 |
5764 | PTN | GSM4909309 | Human | Breast | IDC | 1.48e-62 | 1.54e+00 | 0.0483 |
5764 | PTN | GSM4909312 | Human | Breast | IDC | 1.72e-05 | -3.12e-01 | 0.1552 |
5764 | PTN | GSM4909313 | Human | Breast | IDC | 1.63e-23 | 9.90e-01 | 0.0391 |
5764 | PTN | GSM4909315 | Human | Breast | IDC | 7.79e-05 | -3.12e-01 | 0.21 |
5764 | PTN | GSM4909319 | Human | Breast | IDC | 7.79e-05 | -3.12e-01 | 0.1563 |
5764 | PTN | GSM4909321 | Human | Breast | IDC | 3.66e-05 | -3.12e-01 | 0.1559 |
5764 | PTN | NCCBC3 | Human | Breast | DCIS | 4.12e-54 | 1.23e+00 | 0.1198 |
5764 | PTN | DCIS2 | Human | Breast | DCIS | 7.06e-135 | 1.97e+00 | 0.0085 |
5764 | PTN | AEH-subject1 | Human | Endometrium | AEH | 7.30e-22 | -5.82e-01 | -0.3059 |
5764 | PTN | AEH-subject2 | Human | Endometrium | AEH | 6.64e-25 | -5.74e-01 | -0.2525 |
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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:190165412 | Liver | Cirrhotic | response to ketone | 86/4634 | 194/18723 | 1.82e-09 | 7.73e-08 | 86 |
GO:003166712 | Liver | Cirrhotic | response to nutrient levels | 174/4634 | 474/18723 | 3.08e-09 | 1.27e-07 | 174 |
GO:004300111 | Liver | Cirrhotic | Golgi to plasma membrane protein transport | 27/4634 | 40/18723 | 1.43e-08 | 5.36e-07 | 27 |
GO:007149612 | Liver | Cirrhotic | cellular response to external stimulus | 123/4634 | 320/18723 | 3.27e-08 | 1.10e-06 | 123 |
GO:00004225 | Liver | Cirrhotic | autophagy of mitochondrion | 43/4634 | 81/18723 | 4.02e-08 | 1.31e-06 | 43 |
GO:00617265 | Liver | Cirrhotic | mitochondrion disassembly | 43/4634 | 81/18723 | 4.02e-08 | 1.31e-06 | 43 |
GO:000836012 | Liver | Cirrhotic | regulation of cell shape | 69/4634 | 154/18723 | 4.21e-08 | 1.36e-06 | 69 |
GO:19054755 | Liver | Cirrhotic | regulation of protein localization to membrane | 76/4634 | 175/18723 | 4.55e-08 | 1.45e-06 | 76 |
GO:000941012 | Liver | Cirrhotic | response to xenobiotic stimulus | 165/4634 | 462/18723 | 6.82e-08 | 2.09e-06 | 165 |
GO:000689211 | Liver | Cirrhotic | post-Golgi vesicle-mediated transport | 51/4634 | 104/18723 | 7.12e-08 | 2.15e-06 | 51 |
GO:00072494 | Liver | Cirrhotic | I-kappaB kinase/NF-kappaB signaling | 108/4634 | 281/18723 | 2.21e-07 | 5.64e-06 | 108 |
GO:00070301 | Liver | Cirrhotic | Golgi organization | 68/4634 | 157/18723 | 2.57e-07 | 6.41e-06 | 68 |
GO:190303611 | Liver | Cirrhotic | positive regulation of response to wounding | 38/4634 | 72/18723 | 2.98e-07 | 7.18e-06 | 38 |
GO:004873212 | Liver | Cirrhotic | gland development | 154/4634 | 436/18723 | 4.03e-07 | 9.42e-06 | 154 |
GO:00316686 | Liver | Cirrhotic | cellular response to extracellular stimulus | 96/4634 | 246/18723 | 4.55e-07 | 1.05e-05 | 96 |
GO:001081012 | Liver | Cirrhotic | regulation of cell-substrate adhesion | 88/4634 | 221/18723 | 4.89e-07 | 1.10e-05 | 88 |
GO:00619515 | Liver | Cirrhotic | establishment of protein localization to plasma membrane | 33/4634 | 60/18723 | 5.09e-07 | 1.14e-05 | 33 |
GO:00316695 | Liver | Cirrhotic | cellular response to nutrient levels | 85/4634 | 215/18723 | 1.08e-06 | 2.20e-05 | 85 |
GO:009887611 | Liver | Cirrhotic | vesicle-mediated transport to the plasma membrane | 59/4634 | 136/18723 | 1.46e-06 | 2.88e-05 | 59 |
GO:00704827 | Liver | Cirrhotic | response to oxygen levels | 125/4634 | 347/18723 | 1.55e-06 | 3.02e-05 | 125 |
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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 |
PTN | SDC1 | PTN_SDC1 | PTN | Breast | DCIS |
PTN | SDC2 | PTN_SDC2 | PTN | Breast | DCIS |
PTN | SDC3 | PTN_SDC3 | PTN | Breast | DCIS |
PTN | SDC4 | PTN_SDC4 | PTN | Breast | DCIS |
PTN | NCL | PTN_NCL | PTN | Breast | DCIS |
PTN | SDC1 | PTN_SDC1 | PTN | Breast | Healthy |
PTN | SDC2 | PTN_SDC2 | PTN | Breast | Healthy |
PTN | SDC4 | PTN_SDC4 | PTN | Breast | Healthy |
PTN | NCL | PTN_NCL | PTN | Breast | Healthy |
PTN | SDC1 | PTN_SDC1 | PTN | Cervix | ADJ |
PTN | SDC2 | PTN_SDC2 | PTN | Cervix | ADJ |
PTN | SDC4 | PTN_SDC4 | PTN | Cervix | ADJ |
PTN | NCL | PTN_NCL | PTN | Cervix | ADJ |
PTN | PTPRZ1 | PTN_PTPRZ1 | PTN | Cervix | CC |
PTN | SDC1 | PTN_SDC1 | PTN | Cervix | CC |
PTN | SDC2 | PTN_SDC2 | PTN | Cervix | CC |
PTN | SDC3 | PTN_SDC3 | PTN | Cervix | CC |
PTN | SDC4 | PTN_SDC4 | PTN | Cervix | CC |
PTN | NCL | PTN_NCL | PTN | Cervix | CC |
PTN | SDC1 | PTN_SDC1 | PTN | Cervix | Precancer |
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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 |
PTN | SNV | Missense_Mutation | c.51N>A | p.Phe17Leu | p.F17L | P21246 | protein_coding | tolerated(0.72) | benign(0) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PTN | SNV | Missense_Mutation | rs559496875 | c.388G>A | p.Glu130Lys | p.E130K | P21246 | protein_coding | deleterious(0.03) | benign(0.18) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
PTN | SNV | Missense_Mutation | rs760057615 | c.413C>T | p.Ser138Phe | p.S138F | P21246 | protein_coding | deleterious(0) | probably_damaging(0.939) | TCGA-C8-A8HP-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
PTN | SNV | Missense_Mutation | novel | c.157N>T | p.Ser53Cys | p.S53C | P21246 | protein_coding | deleterious(0.05) | probably_damaging(0.985) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD |
PTN | insertion | Frame_Shift_Ins | novel | c.155_156insTGTGTGTGTGTGTGTGTGTGTGT | p.Trp52CysfsTer9 | p.W52Cfs*9 | P21246 | protein_coding | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | ||
PTN | SNV | Missense_Mutation | c.340N>T | p.Ala114Ser | p.A114S | P21246 | protein_coding | tolerated(0.06) | benign(0.203) | TCGA-A6-5657-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Ancillary | leucovorin | SD | |
PTN | SNV | Missense_Mutation | c.438G>T | p.Lys146Asn | p.K146N | P21246 | protein_coding | tolerated(0.11) | probably_damaging(0.995) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PTN | SNV | Missense_Mutation | c.160N>T | p.Val54Leu | p.V54L | P21246 | protein_coding | tolerated(0.29) | possibly_damaging(0.825) | TCGA-AA-3986-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PTN | SNV | Missense_Mutation | c.454G>A | p.Glu152Lys | p.E152K | P21246 | protein_coding | tolerated(0.59) | probably_damaging(0.973) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
PTN | SNV | Missense_Mutation | c.359N>T | p.Gly120Val | p.G120V | P21246 | protein_coding | deleterious(0) | possibly_damaging(0.903) | TCGA-AG-A02G-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | PD |
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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 |
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