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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:0007163 | Colorectum | AD | establishment or maintenance of cell polarity | 77/3918 | 218/18723 | 5.72e-07 | 2.08e-05 | 77 |
| GO:0042060 | Colorectum | AD | wound healing | 128/3918 | 422/18723 | 2.73e-06 | 7.89e-05 | 128 |
| GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
| GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
| GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
| GO:0031532 | Colorectum | AD | actin cytoskeleton reorganization | 41/3918 | 107/18723 | 2.81e-05 | 5.28e-04 | 41 |
| GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
| GO:0030010 | Colorectum | AD | establishment of cell polarity | 50/3918 | 143/18723 | 6.90e-05 | 1.11e-03 | 50 |
| GO:0031346 | Colorectum | AD | positive regulation of cell projection organization | 104/3918 | 353/18723 | 8.26e-05 | 1.30e-03 | 104 |
| GO:0060070 | Colorectum | AD | canonical Wnt signaling pathway | 90/3918 | 303/18723 | 1.76e-04 | 2.38e-03 | 90 |
| GO:0060828 | Colorectum | AD | regulation of canonical Wnt signaling pathway | 77/3918 | 253/18723 | 2.19e-04 | 2.87e-03 | 77 |
| GO:0045197 | Colorectum | AD | establishment or maintenance of epithelial cell apical/basal polarity | 20/3918 | 44/18723 | 2.26e-04 | 2.94e-03 | 20 |
| GO:0035088 | Colorectum | AD | establishment or maintenance of apical/basal cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0061245 | Colorectum | AD | establishment or maintenance of bipolar cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0060562 | Colorectum | AD | epithelial tube morphogenesis | 93/3918 | 325/18723 | 5.65e-04 | 6.00e-03 | 93 |
| GO:0014020 | Colorectum | AD | primary neural tube formation | 33/3918 | 94/18723 | 1.02e-03 | 9.50e-03 | 33 |
| GO:0001841 | Colorectum | AD | neural tube formation | 35/3918 | 102/18723 | 1.16e-03 | 1.05e-02 | 35 |
| GO:0030177 | Colorectum | AD | positive regulation of Wnt signaling pathway | 45/3918 | 140/18723 | 1.23e-03 | 1.09e-02 | 45 |
| GO:0001843 | Colorectum | AD | neural tube closure | 30/3918 | 88/18723 | 2.83e-03 | 2.12e-02 | 30 |
| GO:0060606 | Colorectum | AD | tube closure | 30/3918 | 89/18723 | 3.42e-03 | 2.49e-02 | 30 |
| 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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