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Gene: SYS1 |
Gene summary for SYS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYS1 | Gene ID | 90196 |
| Gene name | SYS1 golgi trafficking protein | |
| Gene Alias | C20orf169 | |
| Cytomap | 20q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q8N2H4 |
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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 |
| 90196 | SYS1 | LZE4T | Human | Esophagus | ESCC | 7.94e-22 | 3.88e-01 | 0.0811 |
| 90196 | SYS1 | LZE7T | Human | Esophagus | ESCC | 1.37e-04 | 1.91e-01 | 0.0667 |
| 90196 | SYS1 | LZE8T | Human | Esophagus | ESCC | 3.43e-07 | 2.11e-01 | 0.067 |
| 90196 | SYS1 | LZE20T | Human | Esophagus | ESCC | 5.87e-04 | 3.19e-01 | 0.0662 |
| 90196 | SYS1 | LZE24T | Human | Esophagus | ESCC | 1.96e-15 | 4.67e-01 | 0.0596 |
| 90196 | SYS1 | LZE6T | Human | Esophagus | ESCC | 2.19e-03 | 1.85e-01 | 0.0845 |
| 90196 | SYS1 | P1T-E | Human | Esophagus | ESCC | 1.64e-05 | 4.29e-01 | 0.0875 |
| 90196 | SYS1 | P2T-E | Human | Esophagus | ESCC | 1.33e-26 | 4.79e-01 | 0.1177 |
| 90196 | SYS1 | P4T-E | Human | Esophagus | ESCC | 2.32e-17 | 4.44e-01 | 0.1323 |
| 90196 | SYS1 | P5T-E | Human | Esophagus | ESCC | 9.13e-15 | 1.76e-01 | 0.1327 |
| 90196 | SYS1 | P8T-E | Human | Esophagus | ESCC | 1.05e-24 | 4.88e-01 | 0.0889 |
| 90196 | SYS1 | P9T-E | Human | Esophagus | ESCC | 3.23e-10 | 2.53e-01 | 0.1131 |
| 90196 | SYS1 | P10T-E | Human | Esophagus | ESCC | 8.01e-18 | 4.28e-01 | 0.116 |
| 90196 | SYS1 | P11T-E | Human | Esophagus | ESCC | 7.10e-14 | 6.11e-01 | 0.1426 |
| 90196 | SYS1 | P12T-E | Human | Esophagus | ESCC | 7.81e-27 | 4.17e-01 | 0.1122 |
| 90196 | SYS1 | P15T-E | Human | Esophagus | ESCC | 2.45e-23 | 5.52e-01 | 0.1149 |
| 90196 | SYS1 | P16T-E | Human | Esophagus | ESCC | 5.85e-35 | 6.88e-01 | 0.1153 |
| 90196 | SYS1 | P17T-E | Human | Esophagus | ESCC | 1.80e-08 | 2.03e-01 | 0.1278 |
| 90196 | SYS1 | P19T-E | Human | Esophagus | ESCC | 5.50e-07 | 5.95e-01 | 0.1662 |
| 90196 | SYS1 | P20T-E | Human | Esophagus | ESCC | 1.13e-15 | 4.21e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
| GO:0072659110 | Esophagus | ESCC | protein localization to plasma membrane | 193/8552 | 284/18723 | 1.95e-14 | 1.03e-12 | 193 |
| GO:001648210 | Esophagus | ESCC | cytosolic transport | 124/8552 | 168/18723 | 9.69e-14 | 4.69e-12 | 124 |
| GO:199077819 | Esophagus | ESCC | protein localization to cell periphery | 217/8552 | 333/18723 | 4.08e-13 | 1.88e-11 | 217 |
| GO:000689215 | Esophagus | ESCC | post-Golgi vesicle-mediated transport | 82/8552 | 104/18723 | 4.00e-12 | 1.55e-10 | 82 |
| GO:009887615 | Esophagus | ESCC | vesicle-mediated transport to the plasma membrane | 99/8552 | 136/18723 | 1.13e-10 | 3.39e-09 | 99 |
| GO:000689315 | Esophagus | ESCC | Golgi to plasma membrane transport | 48/8552 | 60/18723 | 5.11e-08 | 9.16e-07 | 48 |
| GO:004300114 | Esophagus | ESCC | Golgi to plasma membrane protein transport | 34/8552 | 40/18723 | 3.00e-07 | 4.27e-06 | 34 |
| GO:006195114 | Esophagus | ESCC | establishment of protein localization to plasma membrane | 44/8552 | 60/18723 | 1.25e-05 | 1.15e-04 | 44 |
| GO:00340676 | Esophagus | ESCC | protein localization to Golgi apparatus | 23/8552 | 29/18723 | 2.25e-04 | 1.40e-03 | 23 |
| GO:00068953 | Esophagus | ESCC | Golgi to endosome transport | 13/8552 | 17/18723 | 1.00e-02 | 3.42e-02 | 13 |
| GO:004819311 | Liver | Cirrhotic | Golgi vesicle transport | 153/4634 | 296/18723 | 1.02e-23 | 6.43e-21 | 153 |
| GO:00901507 | Liver | Cirrhotic | establishment of protein localization to membrane | 123/4634 | 260/18723 | 1.85e-15 | 2.15e-13 | 123 |
| GO:199077811 | Liver | Cirrhotic | protein localization to cell periphery | 135/4634 | 333/18723 | 1.18e-10 | 6.21e-09 | 135 |
| GO:007265911 | Liver | Cirrhotic | protein localization to plasma membrane | 119/4634 | 284/18723 | 1.30e-10 | 6.80e-09 | 119 |
| GO:004300111 | Liver | Cirrhotic | Golgi to plasma membrane protein transport | 27/4634 | 40/18723 | 1.43e-08 | 5.36e-07 | 27 |
| GO:001648211 | Liver | Cirrhotic | cytosolic transport | 74/4634 | 168/18723 | 3.34e-08 | 1.12e-06 | 74 |
| GO:000689211 | Liver | Cirrhotic | post-Golgi vesicle-mediated transport | 51/4634 | 104/18723 | 7.12e-08 | 2.15e-06 | 51 |
| GO:00619515 | Liver | Cirrhotic | establishment of protein localization to plasma membrane | 33/4634 | 60/18723 | 5.09e-07 | 1.14e-05 | 33 |
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| 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 |
| 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 |
| SYS1 | SNV | Missense_Mutation | c.188G>T | p.Gly63Val | p.G63V | Q8N2H4 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | |
| SYS1 | SNV | Missense_Mutation | c.69G>C | p.Gln23His | p.Q23H | Q8N2H4 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD | |
| SYS1 | SNV | Missense_Mutation | rs776461956 | c.419N>A | p.Arg140Gln | p.R140Q | Q8N2H4 | protein_coding | deleterious(0.03) | benign(0.417) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SYS1 | SNV | Missense_Mutation | c.187N>A | p.Gly63Ser | p.G63S | Q8N2H4 | protein_coding | deleterious(0) | possibly_damaging(0.876) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYS1 | SNV | Missense_Mutation | c.340N>A | p.Pro114Thr | p.P114T | Q8N2H4 | protein_coding | deleterious(0) | probably_damaging(0.964) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYS1 | SNV | Missense_Mutation | c.277G>T | p.Asp93Tyr | p.D93Y | Q8N2H4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AG-A011-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SYS1 | SNV | Missense_Mutation | novel | c.157N>A | p.Ala53Thr | p.A53T | Q8N2H4 | protein_coding | tolerated(0.05) | benign(0.001) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYS1 | SNV | Missense_Mutation | rs199934485 | c.344N>T | p.Ser115Leu | p.S115L | Q8N2H4 | protein_coding | tolerated(0.27) | benign(0.01) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| SYS1 | SNV | Missense_Mutation | novel | c.346N>A | p.Ala116Thr | p.A116T | Q8N2H4 | protein_coding | tolerated(1) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SYS1 | SNV | Missense_Mutation | novel | c.466N>A | p.Val156Ile | p.V156I | Q8N2H4 | protein_coding | deleterious(0.04) | benign(0.138) | TCGA-5R-AA1C-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | 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 |
| Page: 1 |
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