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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 | S014 | Human | Liver | HCC | 5.16e-30 | 2.44e+00 | 0.2254 |
| 5764 | PTN | S015 | Human | Liver | HCC | 2.82e-29 | 2.18e+00 | 0.2375 |
| 5764 | PTN | S016 | Human | Liver | HCC | 1.35e-43 | 2.49e+00 | 0.2243 |
| 5764 | PTN | C38 | Human | Oral cavity | OSCC | 5.77e-05 | 9.88e-01 | 0.172 |
| 5764 | PTN | C43 | Human | Oral cavity | OSCC | 9.20e-84 | 2.38e+00 | 0.1704 |
| 5764 | PTN | C46 | Human | Oral cavity | OSCC | 1.12e-53 | 1.90e+00 | 0.1673 |
| 5764 | PTN | C57 | Human | Oral cavity | OSCC | 6.15e-03 | 8.96e-01 | 0.1679 |
| 5764 | PTN | C07 | Human | Oral cavity | OSCC | 8.25e-09 | 1.22e-01 | 0.2491 |
| 5764 | PTN | C08 | Human | Oral cavity | OSCC | 2.97e-54 | 2.12e+00 | 0.1919 |
| 5764 | PTN | LN38 | Human | Oral cavity | OSCC | 4.96e-02 | 1.18e+00 | 0.168 |
| 5764 | PTN | LN46 | Human | Oral cavity | OSCC | 3.69e-21 | 1.61e+00 | 0.1666 |
| 5764 | PTN | LP15 | Human | Oral cavity | LP | 1.43e-04 | 1.53e+00 | 0.2174 |
| 5764 | PTN | LP16 | Human | Oral cavity | LP | 2.99e-15 | 4.12e-01 | 0.1055 |
| 5764 | PTN | LP17 | Human | Oral cavity | LP | 6.43e-09 | 1.78e+00 | 0.2349 |
| 5764 | PTN | SYSMH1 | Human | Oral cavity | OSCC | 3.66e-03 | 6.31e-01 | 0.1127 |
| 5764 | PTN | SYSMH2 | Human | Oral cavity | OSCC | 4.75e-08 | 8.35e-01 | 0.2326 |
| 5764 | PTN | SYSMH4 | Human | Oral cavity | OSCC | 4.01e-30 | 1.12e+00 | 0.1226 |
| 5764 | PTN | SYSMH5 | Human | Oral cavity | OSCC | 9.39e-03 | -2.33e-01 | 0.0647 |
| 5764 | PTN | ATC09 | Human | Thyroid | ATC | 2.55e-05 | 3.48e-01 | 0.2871 |
| 5764 | PTN | ATC12 | Human | Thyroid | ATC | 1.70e-83 | 2.55e+00 | 0.34 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| 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:004854514 | Breast | IDC | response to steroid hormone | 70/1434 | 339/18723 | 1.34e-14 | 4.23e-12 | 70 |
| GO:007048214 | Breast | IDC | response to oxygen levels | 64/1434 | 347/18723 | 3.45e-11 | 5.57e-09 | 64 |
| GO:003629314 | Breast | IDC | response to decreased oxygen levels | 60/1434 | 322/18723 | 9.26e-11 | 1.25e-08 | 60 |
| GO:000166614 | Breast | IDC | response to hypoxia | 58/1434 | 307/18723 | 1.09e-10 | 1.38e-08 | 58 |
| GO:000756511 | Breast | IDC | female pregnancy | 39/1434 | 193/18723 | 1.81e-08 | 1.27e-06 | 39 |
| GO:003629413 | Breast | IDC | cellular response to decreased oxygen levels | 34/1434 | 161/18723 | 4.73e-08 | 3.02e-06 | 34 |
| GO:00447061 | Breast | IDC | multi-multicellular organism process | 41/1434 | 220/18723 | 8.58e-08 | 5.19e-06 | 41 |
| GO:007145613 | Breast | IDC | cellular response to hypoxia | 32/1434 | 151/18723 | 1.07e-07 | 6.26e-06 | 32 |
| GO:007145313 | Breast | IDC | cellular response to oxygen levels | 35/1434 | 177/18723 | 1.68e-07 | 9.10e-06 | 35 |
| GO:004873214 | Breast | IDC | gland development | 64/1434 | 436/18723 | 3.47e-07 | 1.74e-05 | 64 |
| GO:004578514 | Breast | IDC | positive regulation of cell adhesion | 62/1434 | 437/18723 | 1.70e-06 | 7.16e-05 | 62 |
| GO:004860812 | Breast | IDC | reproductive structure development | 60/1434 | 424/18723 | 2.71e-06 | 1.03e-04 | 60 |
| GO:005090011 | Breast | IDC | leukocyte migration | 54/1434 | 369/18723 | 3.10e-06 | 1.15e-04 | 54 |
| GO:006145813 | Breast | IDC | reproductive system development | 60/1434 | 427/18723 | 3.41e-06 | 1.24e-04 | 60 |
| GO:003059511 | Breast | IDC | leukocyte chemotaxis | 38/1434 | 230/18723 | 5.36e-06 | 1.76e-04 | 38 |
| GO:000166714 | Breast | IDC | ameboidal-type cell migration | 64/1434 | 475/18723 | 6.65e-06 | 2.05e-04 | 64 |
| GO:000931412 | Breast | IDC | response to radiation | 62/1434 | 456/18723 | 6.91e-06 | 2.10e-04 | 62 |
| GO:005067313 | Breast | IDC | epithelial cell proliferation | 60/1434 | 437/18723 | 7.13e-06 | 2.15e-04 | 60 |
| GO:003235512 | Breast | IDC | response to estradiol | 27/1434 | 141/18723 | 7.87e-06 | 2.35e-04 | 27 |
| GO:005067812 | Breast | IDC | regulation of epithelial cell proliferation | 54/1434 | 381/18723 | 8.07e-06 | 2.39e-04 | 54 |
| 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 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| 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 |
| Page: 1 2 3 4 5 |
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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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