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Gene: YKT6 |
Gene summary for YKT6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YKT6 | Gene ID | 10652 |
| Gene name | YKT6 v-SNARE homolog | |
| Gene Alias | YKT6 | |
| Cytomap | 7p13 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | A4D2J0 |
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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 |
| 10652 | YKT6 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.36e-02 | 1.69e-01 | 0.0155 |
| 10652 | YKT6 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.38e-12 | 5.48e-01 | -0.1808 |
| 10652 | YKT6 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.16e-02 | 2.87e-01 | -0.0811 |
| 10652 | YKT6 | HTA11_78_2000001011 | Human | Colorectum | AD | 9.08e-07 | 3.57e-01 | -0.1088 |
| 10652 | YKT6 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.08e-13 | 3.73e-01 | -0.1954 |
| 10652 | YKT6 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.75e-08 | 8.75e-01 | -0.2602 |
| 10652 | YKT6 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.17e-02 | 5.56e-01 | -0.2196 |
| 10652 | YKT6 | HTA11_3361_2000001011 | Human | Colorectum | AD | 9.34e-07 | 3.65e-01 | -0.1207 |
| 10652 | YKT6 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.78e-05 | 3.77e-01 | -0.1526 |
| 10652 | YKT6 | HTA11_696_2000001011 | Human | Colorectum | AD | 6.58e-23 | 6.10e-01 | -0.1464 |
| 10652 | YKT6 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.49e-06 | 2.32e-01 | -0.1001 |
| 10652 | YKT6 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.68e-13 | 4.95e-01 | -0.059 |
| 10652 | YKT6 | HTA11_2992_2000001011 | Human | Colorectum | SER | 4.03e-06 | 5.12e-01 | -0.1706 |
| 10652 | YKT6 | HTA11_5212_2000001011 | Human | Colorectum | AD | 5.05e-06 | 4.79e-01 | -0.2061 |
| 10652 | YKT6 | HTA11_5216_2000001011 | Human | Colorectum | SER | 6.62e-04 | 4.61e-01 | -0.1462 |
| 10652 | YKT6 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.47e-04 | 4.01e-01 | -0.0842 |
| 10652 | YKT6 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.04e-07 | 2.86e-01 | 0.096 |
| 10652 | YKT6 | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.42e-03 | 3.67e-01 | 0.0528 |
| 10652 | YKT6 | HTA11_6801_2000001011 | Human | Colorectum | SER | 9.91e-04 | 3.61e-01 | 0.0171 |
| 10652 | YKT6 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.59e-12 | 3.32e-01 | 0.0674 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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 | ||
| 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:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
| GO:0016482 | Colorectum | AD | cytosolic transport | 68/3918 | 168/18723 | 6.00e-09 | 3.72e-07 | 68 |
| GO:0042147 | Colorectum | AD | retrograde transport, endosome to Golgi | 37/3918 | 91/18723 | 1.46e-05 | 3.14e-04 | 37 |
| GO:0051650 | Colorectum | AD | establishment of vesicle localization | 57/3918 | 161/18723 | 1.47e-05 | 3.15e-04 | 57 |
| GO:0051648 | Colorectum | AD | vesicle localization | 59/3918 | 177/18723 | 7.83e-05 | 1.25e-03 | 59 |
| GO:0006888 | Colorectum | AD | endoplasmic reticulum to Golgi vesicle-mediated transport | 44/3918 | 130/18723 | 4.13e-04 | 4.68e-03 | 44 |
| GO:0022406 | Colorectum | AD | membrane docking | 31/3918 | 86/18723 | 8.67e-04 | 8.45e-03 | 31 |
| GO:0006903 | Colorectum | AD | vesicle targeting | 19/3918 | 45/18723 | 9.94e-04 | 9.28e-03 | 19 |
| GO:0140056 | Colorectum | AD | organelle localization by membrane tethering | 28/3918 | 77/18723 | 1.29e-03 | 1.14e-02 | 28 |
| GO:0006887 | Colorectum | AD | exocytosis | 96/3918 | 352/18723 | 2.48e-03 | 1.90e-02 | 96 |
| GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
| GO:00481931 | Colorectum | SER | Golgi vesicle transport | 79/2897 | 296/18723 | 4.20e-07 | 2.15e-05 | 79 |
| GO:00161971 | Colorectum | SER | endosomal transport | 61/2897 | 230/18723 | 1.03e-05 | 3.35e-04 | 61 |
| GO:00164821 | Colorectum | SER | cytosolic transport | 46/2897 | 168/18723 | 5.20e-05 | 1.25e-03 | 46 |
| GO:00516501 | Colorectum | SER | establishment of vesicle localization | 42/2897 | 161/18723 | 3.38e-04 | 5.35e-03 | 42 |
| GO:00224061 | Colorectum | SER | membrane docking | 25/2897 | 86/18723 | 9.88e-04 | 1.17e-02 | 25 |
| GO:00068881 | Colorectum | SER | endoplasmic reticulum to Golgi vesicle-mediated transport | 34/2897 | 130/18723 | 1.13e-03 | 1.29e-02 | 34 |
| GO:00516481 | Colorectum | SER | vesicle localization | 43/2897 | 177/18723 | 1.41e-03 | 1.53e-02 | 43 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041305 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
| hsa0413012 | Esophagus | ESCC | SNARE interactions in vesicular transport | 28/4205 | 33/8465 | 2.75e-05 | 1.32e-04 | 6.75e-05 | 28 |
| hsa041302 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
| hsa041303 | Liver | HCC | SNARE interactions in vesicular transport | 25/4020 | 33/8465 | 8.78e-04 | 3.38e-03 | 1.88e-03 | 25 |
| hsa041304 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
| hsa0413011 | Oral cavity | OSCC | SNARE interactions in vesicular transport | 28/3704 | 33/8465 | 1.31e-06 | 7.18e-06 | 3.66e-06 | 28 |
| hsa0413021 | Oral cavity | LP | SNARE interactions in vesicular transport | 22/2418 | 33/8465 | 6.00e-06 | 4.76e-05 | 3.07e-05 | 22 |
| hsa0413031 | Oral cavity | LP | SNARE interactions in vesicular transport | 22/2418 | 33/8465 | 6.00e-06 | 4.76e-05 | 3.07e-05 | 22 |
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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 |
| Page: 1 |
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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 |
| YKT6 | SNV | Missense_Mutation | novel | c.491G>A | p.Gly164Asp | p.G164D | O15498 | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| YKT6 | insertion | Nonsense_Mutation | novel | c.148_149insCCTTTGTATGA | p.Arg50ProfsTer4 | p.R50Pfs*4 | O15498 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| YKT6 | insertion | Nonsense_Mutation | novel | c.150_151insCATTTCCCACTTCTTTGTCTTGGATGAGCAGT | p.Ser51HisfsTer9 | p.S51Hfs*9 | O15498 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| YKT6 | SNV | Missense_Mutation | novel | c.457N>G | p.Leu153Val | p.L153V | O15498 | protein_coding | deleterious(0.02) | benign(0.029) | TCGA-MA-AA3Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| YKT6 | SNV | Missense_Mutation | rs780133803 | c.433G>A | p.Glu145Lys | p.E145K | O15498 | protein_coding | deleterious(0) | possibly_damaging(0.906) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| YKT6 | SNV | Missense_Mutation | novel | c.316N>A | p.Asp106Asn | p.D106N | O15498 | protein_coding | tolerated(0.08) | benign(0.001) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| YKT6 | SNV | Missense_Mutation | c.557A>C | p.Lys186Thr | p.K186T | O15498 | protein_coding | tolerated(0.32) | benign(0.158) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| YKT6 | SNV | Missense_Mutation | c.331N>T | p.Pro111Ser | p.P111S | O15498 | protein_coding | tolerated(0.21) | benign(0.104) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| YKT6 | SNV | Missense_Mutation | novel | c.511G>A | p.Val171Met | p.V171M | O15498 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-B5-A5OC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | SD |
| YKT6 | SNV | Missense_Mutation | novel | c.512N>C | p.Val171Ala | p.V171A | O15498 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
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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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