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Gene: PTK7 |
Gene summary for PTK7 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTK7 | Gene ID | 5754 |
| Gene name | protein tyrosine kinase 7 (inactive) | |
| Gene Alias | CCK-4 | |
| Cytomap | 6p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0001568 | UniProtAcc | Q13308 |
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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 |
| 5754 | PTK7 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.95e-12 | 5.01e-01 | 0.096 |
| 5754 | PTK7 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.46e-10 | 6.96e-01 | 0.0338 |
| 5754 | PTK7 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.70e-08 | 4.01e-01 | 0.0674 |
| 5754 | PTK7 | HTA11_6818_2000001011 | Human | Colorectum | AD | 9.87e-03 | 3.85e-01 | 0.0112 |
| 5754 | PTK7 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.30e-19 | 5.07e-01 | 0.294 |
| 5754 | PTK7 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.24e-05 | 4.49e-01 | 0.281 |
| 5754 | PTK7 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 6.66e-14 | 6.28e-01 | 0.3859 |
| 5754 | PTK7 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.77e-13 | 8.53e-01 | 0.2585 |
| 5754 | PTK7 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.98e-42 | 1.06e+00 | 0.3005 |
| 5754 | PTK7 | A001-C-119 | Human | Colorectum | FAP | 1.22e-04 | 5.10e-01 | -0.1557 |
| 5754 | PTK7 | A002-C-021 | Human | Colorectum | FAP | 1.89e-08 | 4.21e-01 | 0.1171 |
| 5754 | PTK7 | CRC-1-8810 | Human | Colorectum | CRC | 1.98e-18 | 7.38e-01 | 0.6257 |
| 5754 | PTK7 | CRC-3-11773 | Human | Colorectum | CRC | 2.12e-06 | 4.57e-01 | 0.2564 |
| 5754 | PTK7 | LZE2T | Human | Esophagus | ESCC | 1.19e-09 | 1.22e+00 | 0.082 |
| 5754 | PTK7 | LZE4T | Human | Esophagus | ESCC | 7.51e-05 | 1.34e-01 | 0.0811 |
| 5754 | PTK7 | LZE24T | Human | Esophagus | ESCC | 1.24e-07 | 1.29e-01 | 0.0596 |
| 5754 | PTK7 | P2T-E | Human | Esophagus | ESCC | 4.73e-56 | 9.05e-01 | 0.1177 |
| 5754 | PTK7 | P4T-E | Human | Esophagus | ESCC | 6.75e-32 | 6.55e-01 | 0.1323 |
| 5754 | PTK7 | P5T-E | Human | Esophagus | ESCC | 6.87e-25 | 5.13e-01 | 0.1327 |
| 5754 | PTK7 | P8T-E | Human | Esophagus | ESCC | 2.65e-13 | 2.29e-01 | 0.0889 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:006124511 | Lung | AIS | establishment or maintenance of bipolar cell polarity | 13/1849 | 49/18723 | 7.13e-04 | 1.04e-02 | 13 |
| GO:00901751 | Lung | AIS | regulation of establishment of planar polarity | 14/1849 | 56/18723 | 8.61e-04 | 1.17e-02 | 14 |
| GO:002191511 | Lung | AIS | neural tube development | 28/1849 | 152/18723 | 8.81e-04 | 1.19e-02 | 28 |
| GO:20000271 | Lung | AIS | regulation of animal organ morphogenesis | 24/1849 | 125/18723 | 1.10e-03 | 1.42e-02 | 24 |
| GO:00163311 | Lung | AIS | morphogenesis of embryonic epithelium | 27/1849 | 147/18723 | 1.13e-03 | 1.45e-02 | 27 |
| GO:003514811 | Lung | AIS | tube formation | 27/1849 | 148/18723 | 1.25e-03 | 1.58e-02 | 27 |
| GO:0035567 | Lung | AIS | non-canonical Wnt signaling pathway | 16/1849 | 72/18723 | 1.50e-03 | 1.81e-02 | 16 |
| GO:00611621 | Lung | AIS | establishment of monopolar cell polarity | 8/1849 | 24/18723 | 1.54e-03 | 1.82e-02 | 8 |
| GO:00613391 | Lung | AIS | establishment or maintenance of monopolar cell polarity | 8/1849 | 25/18723 | 2.07e-03 | 2.27e-02 | 8 |
| GO:007217511 | Lung | AIS | epithelial tube formation | 24/1849 | 132/18723 | 2.37e-03 | 2.48e-02 | 24 |
| GO:004519711 | Lung | AIS | establishment or maintenance of epithelial cell apical/basal polarity | 11/1849 | 44/18723 | 3.01e-03 | 2.97e-02 | 11 |
| GO:00032812 | Lung | AIS | ventricular septum development | 15/1849 | 71/18723 | 3.49e-03 | 3.31e-02 | 15 |
| GO:0035089 | Lung | AIS | establishment of apical/basal cell polarity | 7/1849 | 22/18723 | 4.07e-03 | 3.65e-02 | 7 |
| GO:003032412 | Lung | AIS | lung development | 29/1849 | 177/18723 | 4.48e-03 | 3.97e-02 | 29 |
| GO:003032312 | Lung | AIS | respiratory tube development | 29/1849 | 181/18723 | 6.16e-03 | 4.98e-02 | 29 |
| GO:004206020 | Oral cavity | OSCC | wound healing | 237/7305 | 422/18723 | 4.51e-13 | 2.18e-11 | 237 |
| GO:000716318 | Oral cavity | OSCC | establishment or maintenance of cell polarity | 129/7305 | 218/18723 | 1.16e-09 | 2.86e-08 | 129 |
| GO:001605510 | Oral cavity | OSCC | Wnt signaling pathway | 227/7305 | 444/18723 | 1.10e-07 | 1.87e-06 | 227 |
| GO:019873810 | Oral cavity | OSCC | cell-cell signaling by wnt | 227/7305 | 446/18723 | 1.75e-07 | 2.86e-06 | 227 |
| GO:003153216 | Oral cavity | OSCC | actin cytoskeleton reorganization | 65/7305 | 107/18723 | 4.25e-06 | 4.93e-05 | 65 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| PTK7 | SNV | Missense_Mutation | c.1028C>A | p.Ala343Asp | p.A343D | Q13308 | protein_coding | deleterious(0.01) | possibly_damaging(0.471) | TCGA-A2-A0D2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PTK7 | SNV | Missense_Mutation | novel | c.2262N>A | p.Met754Ile | p.M754I | Q13308 | protein_coding | deleterious(0.04) | benign(0.067) | TCGA-A7-A6VX-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| PTK7 | SNV | Missense_Mutation | c.2124G>T | p.Lys708Asn | p.K708N | Q13308 | protein_coding | deleterious(0.04) | benign(0.082) | TCGA-A8-A0A9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| PTK7 | SNV | Missense_Mutation | rs374956441 | c.493C>T | p.Arg165Trp | p.R165W | Q13308 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PTK7 | SNV | Missense_Mutation | novel | c.2578N>C | p.Lys860Gln | p.K860Q | Q13308 | protein_coding | deleterious(0) | possibly_damaging(0.734) | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| PTK7 | SNV | Missense_Mutation | c.2317G>A | p.Glu773Lys | p.E773K | Q13308 | protein_coding | deleterious(0.03) | benign(0.119) | TCGA-D8-A1JN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozolum | SD | |
| PTK7 | SNV | Missense_Mutation | novel | c.1769N>T | p.Ala590Val | p.A590V | Q13308 | protein_coding | deleterious(0.01) | possibly_damaging(0.475) | TCGA-E9-A228-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| PTK7 | SNV | Missense_Mutation | rs767634504 | c.581N>T | p.Thr194Met | p.T194M | Q13308 | protein_coding | deleterious(0.03) | benign(0.104) | TCGA-S3-AA14-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| PTK7 | insertion | In_Frame_Ins | novel | c.2208_2209insGATCTGGGCCCAAACAGAGTCCGGTTTGGCAGACGTGGAATGTCA | p.Lys736_Arg737insAspLeuGlyProAsnArgValArgPheGlyArgArgGlyMetSer | p.K736_R737insDLGPNRVRFGRRGMS | Q13308 | protein_coding | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | ||
| PTK7 | insertion | Frame_Shift_Ins | novel | c.2577_2578insCTTCC | p.Lys860LeufsTer4 | p.K860Lfs*4 | Q13308 | protein_coding | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| 5754 | PTK7 | DRUGGABLE GENOME, KINASE, TYROSINE KINASE, CLINICALLY ACTIONABLE | PF-06647020 | COFETUZUMAB PELIDOTIN |
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