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Gene: RYK |
Gene summary for RYK |
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Gene information | Species | Human | Gene symbol | RYK | Gene ID | 6259 |
Gene name | receptor like tyrosine kinase | |
Gene Alias | D3S3195 | |
Cytomap | 3q22.2 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A087WUK1 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
6259 | RYK | CA_HPV_1 | Human | Cervix | CC | 5.02e-07 | -2.22e-01 | 0.0264 |
6259 | RYK | CA_HPV_3 | Human | Cervix | CC | 3.09e-03 | 2.18e-01 | 0.0414 |
6259 | RYK | CCI_2 | Human | Cervix | CC | 1.38e-09 | 1.27e+00 | 0.5249 |
6259 | RYK | CCI_3 | Human | Cervix | CC | 1.06e-14 | 1.16e+00 | 0.516 |
6259 | RYK | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.48e-09 | -4.32e-01 | 0.0155 |
6259 | RYK | HTA11_696_2000001011 | Human | Colorectum | AD | 5.79e-08 | -3.92e-01 | -0.1464 |
6259 | RYK | HTA11_866_2000001011 | Human | Colorectum | AD | 3.09e-05 | -3.02e-01 | -0.1001 |
6259 | RYK | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.95e-04 | -2.81e-01 | 0.0674 |
6259 | RYK | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.92e-05 | -3.21e-01 | 0.3005 |
6259 | RYK | A001-C-207 | Human | Colorectum | FAP | 5.74e-08 | -2.87e-01 | 0.1278 |
6259 | RYK | A015-C-203 | Human | Colorectum | FAP | 6.65e-30 | -3.76e-01 | -0.1294 |
6259 | RYK | A015-C-204 | Human | Colorectum | FAP | 1.56e-05 | -1.59e-01 | -0.0228 |
6259 | RYK | A014-C-040 | Human | Colorectum | FAP | 2.36e-05 | -4.34e-01 | -0.1184 |
6259 | RYK | A002-C-201 | Human | Colorectum | FAP | 3.65e-16 | -2.89e-01 | 0.0324 |
6259 | RYK | A002-C-203 | Human | Colorectum | FAP | 2.32e-04 | -1.67e-01 | 0.2786 |
6259 | RYK | A001-C-119 | Human | Colorectum | FAP | 1.15e-15 | -5.43e-01 | -0.1557 |
6259 | RYK | A001-C-108 | Human | Colorectum | FAP | 4.77e-22 | -3.72e-01 | -0.0272 |
6259 | RYK | A002-C-205 | Human | Colorectum | FAP | 6.70e-24 | -4.52e-01 | -0.1236 |
6259 | RYK | A001-C-104 | Human | Colorectum | FAP | 1.43e-07 | -3.01e-01 | 0.0184 |
6259 | RYK | A015-C-005 | Human | Colorectum | FAP | 9.23e-07 | -2.93e-01 | -0.0336 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004858819 | Thyroid | PTC | developmental cell growth | 106/5968 | 234/18723 | 1.07e-05 | 1.19e-04 | 106 |
GO:006056018 | Thyroid | PTC | developmental growth involved in morphogenesis | 105/5968 | 234/18723 | 1.94e-05 | 1.98e-04 | 105 |
GO:0030901111 | Thyroid | PTC | midbrain development | 48/5968 | 90/18723 | 1.95e-05 | 1.99e-04 | 48 |
GO:00507708 | Thyroid | PTC | regulation of axonogenesis | 74/5968 | 154/18723 | 1.96e-05 | 2.00e-04 | 74 |
GO:199013817 | Thyroid | PTC | neuron projection extension | 81/5968 | 172/18723 | 2.07e-05 | 2.08e-04 | 81 |
GO:000836115 | Thyroid | PTC | regulation of cell size | 83/5968 | 181/18723 | 5.45e-05 | 4.84e-04 | 83 |
GO:00313459 | Thyroid | PTC | negative regulation of cell projection organization | 83/5968 | 186/18723 | 1.72e-04 | 1.32e-03 | 83 |
GO:00519608 | Thyroid | PTC | regulation of nervous system development | 177/5968 | 443/18723 | 1.72e-04 | 1.32e-03 | 177 |
GO:00305167 | Thyroid | PTC | regulation of axon extension | 47/5968 | 95/18723 | 2.60e-04 | 1.86e-03 | 47 |
GO:00109778 | Thyroid | PTC | negative regulation of neuron projection development | 63/5968 | 137/18723 | 3.70e-04 | 2.50e-03 | 63 |
GO:004592614 | Thyroid | PTC | negative regulation of growth | 105/5968 | 249/18723 | 3.76e-04 | 2.54e-03 | 105 |
GO:00613873 | Thyroid | PTC | regulation of extent of cell growth | 52/5968 | 110/18723 | 5.20e-04 | 3.37e-03 | 52 |
GO:00303087 | Thyroid | PTC | negative regulation of cell growth | 80/5968 | 188/18723 | 1.28e-03 | 7.31e-03 | 80 |
GO:00220382 | Thyroid | PTC | corpus callosum development | 10/5968 | 14/18723 | 2.77e-03 | 1.38e-02 | 10 |
GO:00215373 | Thyroid | PTC | telencephalon development | 100/5968 | 248/18723 | 2.90e-03 | 1.44e-02 | 100 |
GO:00508089 | Thyroid | PTC | synapse organization | 161/5968 | 426/18723 | 5.11e-03 | 2.36e-02 | 161 |
GO:004863810 | Thyroid | PTC | regulation of developmental growth | 127/5968 | 330/18723 | 6.09e-03 | 2.71e-02 | 127 |
GO:0071679 | Thyroid | PTC | commissural neuron axon guidance | 8/5968 | 11/18723 | 6.50e-03 | 2.83e-02 | 8 |
GO:00309007 | Thyroid | PTC | forebrain development | 143/5968 | 379/18723 | 8.47e-03 | 3.56e-02 | 143 |
GO:00017389 | Thyroid | PTC | morphogenesis of a polarized epithelium | 41/5968 | 94/18723 | 1.10e-02 | 4.38e-02 | 41 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa043609 | Cervix | CC | Axon guidance | 47/1267 | 182/8465 | 8.13e-05 | 5.38e-04 | 3.18e-04 | 47 |
hsa043109 | Cervix | CC | Wnt signaling pathway | 43/1267 | 171/8465 | 3.03e-04 | 1.64e-03 | 9.68e-04 | 43 |
hsa0436012 | Cervix | CC | Axon guidance | 47/1267 | 182/8465 | 8.13e-05 | 5.38e-04 | 3.18e-04 | 47 |
hsa0431012 | Cervix | CC | Wnt signaling pathway | 43/1267 | 171/8465 | 3.03e-04 | 1.64e-03 | 9.68e-04 | 43 |
hsa04360 | Colorectum | AD | Axon guidance | 61/2092 | 182/8465 | 4.36e-03 | 2.17e-02 | 1.38e-02 | 61 |
hsa04310 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
hsa043601 | Colorectum | AD | Axon guidance | 61/2092 | 182/8465 | 4.36e-03 | 2.17e-02 | 1.38e-02 | 61 |
hsa043101 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
hsa043104 | Colorectum | FAP | Wnt signaling pathway | 46/1404 | 171/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 46 |
hsa043604 | Colorectum | FAP | Axon guidance | 47/1404 | 182/8465 | 9.09e-04 | 5.20e-03 | 3.16e-03 | 47 |
hsa043105 | Colorectum | FAP | Wnt signaling pathway | 46/1404 | 171/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 46 |
hsa043605 | Colorectum | FAP | Axon guidance | 47/1404 | 182/8465 | 9.09e-04 | 5.20e-03 | 3.16e-03 | 47 |
hsa043606 | Colorectum | CRC | Axon guidance | 43/1091 | 182/8465 | 4.38e-05 | 8.70e-04 | 5.90e-04 | 43 |
hsa043106 | Colorectum | CRC | Wnt signaling pathway | 40/1091 | 171/8465 | 1.01e-04 | 1.57e-03 | 1.07e-03 | 40 |
hsa043607 | Colorectum | CRC | Axon guidance | 43/1091 | 182/8465 | 4.38e-05 | 8.70e-04 | 5.90e-04 | 43 |
hsa043107 | Colorectum | CRC | Wnt signaling pathway | 40/1091 | 171/8465 | 1.01e-04 | 1.57e-03 | 1.07e-03 | 40 |
hsa0436016 | Esophagus | ESCC | Axon guidance | 108/4205 | 182/8465 | 5.13e-03 | 1.30e-02 | 6.67e-03 | 108 |
hsa0436017 | Esophagus | ESCC | Axon guidance | 108/4205 | 182/8465 | 5.13e-03 | 1.30e-02 | 6.67e-03 | 108 |
hsa0436014 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
hsa0436015 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
RYK | SNV | Missense_Mutation | novel | c.677N>T | p.Thr226Met | p.T226M | protein_coding | deleterious(0.02) | probably_damaging(0.975) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RYK | insertion | Frame_Shift_Ins | novel | c.1524dupA | p.Val509SerfsTer7 | p.V509Sfs*7 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |||
RYK | insertion | Frame_Shift_Ins | novel | c.1522_1523insATTTCCCCTGCTCACACTCACTCCATCCTGC | p.Pro508HisfsTer18 | p.P508Hfs*18 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | |||
RYK | SNV | Missense_Mutation | novel | c.246A>C | p.Glu82Asp | p.E82D | protein_coding | deleterious(0.03) | probably_damaging(0.919) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
RYK | SNV | Missense_Mutation | novel | c.1698N>T | p.Gln566His | p.Q566H | protein_coding | deleterious(0.03) | probably_damaging(0.924) | TCGA-AA-3821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RYK | SNV | Missense_Mutation | novel | c.1031T>A | p.Phe344Tyr | p.F344Y | protein_coding | deleterious(0.04) | benign(0.433) | TCGA-AA-3870-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folinic | CR | |
RYK | SNV | Missense_Mutation | novel | c.1378N>A | p.Ala460Thr | p.A460T | protein_coding | tolerated(0.14) | benign(0.098) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
RYK | SNV | Missense_Mutation | novel | c.1083N>C | p.Glu361Asp | p.E361D | protein_coding | tolerated(0.22) | benign(0.137) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
RYK | SNV | Missense_Mutation | novel | c.1064N>G | p.Glu355Gly | p.E355G | protein_coding | deleterious(0.04) | benign(0.007) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
RYK | SNV | Missense_Mutation | novel | c.394N>A | p.Ala132Thr | p.A132T | protein_coding | deleterious(0.03) | benign(0.331) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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