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Gene: SYNGR1 |
Gene summary for SYNGR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYNGR1 | Gene ID | 9145 |
| Gene name | synaptogyrin 1 | |
| Gene Alias | SYNGR1 | |
| Cytomap | 22q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | O43759 |
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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 |
| 9145 | SYNGR1 | GSM4909281 | Human | Breast | IDC | 7.40e-22 | 5.25e-01 | 0.21 |
| 9145 | SYNGR1 | GSM4909282 | Human | Breast | IDC | 7.59e-24 | 5.37e-01 | -0.0288 |
| 9145 | SYNGR1 | GSM4909286 | Human | Breast | IDC | 1.62e-13 | 3.78e-01 | 0.1081 |
| 9145 | SYNGR1 | GSM4909293 | Human | Breast | IDC | 1.64e-04 | -1.60e-01 | 0.1581 |
| 9145 | SYNGR1 | GSM4909297 | Human | Breast | IDC | 2.78e-02 | -9.87e-02 | 0.1517 |
| 9145 | SYNGR1 | GSM4909308 | Human | Breast | IDC | 8.77e-04 | -1.69e-01 | 0.158 |
| 9145 | SYNGR1 | GSM4909311 | Human | Breast | IDC | 3.24e-05 | -1.14e-01 | 0.1534 |
| 9145 | SYNGR1 | GSM4909312 | Human | Breast | IDC | 4.48e-02 | -6.89e-02 | 0.1552 |
| 9145 | SYNGR1 | GSM4909319 | Human | Breast | IDC | 5.58e-12 | -6.14e-02 | 0.1563 |
| 9145 | SYNGR1 | GSM4909320 | Human | Breast | IDC | 1.80e-04 | 1.38e-01 | 0.1575 |
| 9145 | SYNGR1 | NCCBC14 | Human | Breast | DCIS | 9.14e-03 | -2.22e-02 | 0.2021 |
| 9145 | SYNGR1 | NCCBC5 | Human | Breast | DCIS | 5.77e-04 | -1.28e-01 | 0.2046 |
| 9145 | SYNGR1 | P1 | Human | Breast | IDC | 1.83e-05 | -9.29e-02 | 0.1527 |
| 9145 | SYNGR1 | DCIS2 | Human | Breast | DCIS | 2.07e-39 | 1.53e-01 | 0.0085 |
| 9145 | SYNGR1 | LZE2T | Human | Esophagus | ESCC | 1.50e-03 | 2.96e-01 | 0.082 |
| 9145 | SYNGR1 | LZE4T | Human | Esophagus | ESCC | 2.38e-02 | 5.38e-02 | 0.0811 |
| 9145 | SYNGR1 | LZE24T | Human | Esophagus | ESCC | 6.75e-13 | 3.08e-01 | 0.0596 |
| 9145 | SYNGR1 | LZE21T | Human | Esophagus | ESCC | 5.52e-04 | 2.47e-01 | 0.0655 |
| 9145 | SYNGR1 | P1T-E | Human | Esophagus | ESCC | 6.50e-04 | 2.80e-01 | 0.0875 |
| 9145 | SYNGR1 | P2T-E | Human | Esophagus | ESCC | 4.27e-33 | 5.70e-01 | 0.1177 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 |
| ∗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:000660514 | Breast | IDC | protein targeting | 43/1434 | 314/18723 | 1.44e-04 | 2.53e-03 | 43 |
| GO:19908301 | Breast | IDC | cellular response to leukemia inhibitory factor | 15/1434 | 94/18723 | 5.06e-03 | 3.79e-02 | 15 |
| GO:199082311 | Breast | IDC | response to leukemia inhibitory factor | 15/1434 | 95/18723 | 5.59e-03 | 4.07e-02 | 15 |
| GO:000660523 | Breast | DCIS | protein targeting | 43/1390 | 314/18723 | 7.17e-05 | 1.41e-03 | 43 |
| GO:19908302 | Breast | DCIS | cellular response to leukemia inhibitory factor | 15/1390 | 94/18723 | 3.79e-03 | 3.03e-02 | 15 |
| GO:19908232 | Breast | DCIS | response to leukemia inhibitory factor | 15/1390 | 95/18723 | 4.20e-03 | 3.31e-02 | 15 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:199082316 | Esophagus | ESCC | response to leukemia inhibitory factor | 60/8552 | 95/18723 | 4.41e-04 | 2.48e-03 | 60 |
| GO:199083015 | Esophagus | ESCC | cellular response to leukemia inhibitory factor | 59/8552 | 94/18723 | 6.19e-04 | 3.32e-03 | 59 |
| GO:00066057 | Liver | Cirrhotic | protein targeting | 148/4634 | 314/18723 | 3.86e-18 | 6.20e-16 | 148 |
| GO:000660512 | Liver | HCC | protein targeting | 219/7958 | 314/18723 | 7.74e-23 | 1.49e-20 | 219 |
| GO:000660520 | Oral cavity | OSCC | protein targeting | 204/7305 | 314/18723 | 6.78e-21 | 1.13e-18 | 204 |
| GO:19908237 | Oral cavity | OSCC | response to leukemia inhibitory factor | 58/7305 | 95/18723 | 1.10e-05 | 1.14e-04 | 58 |
| GO:19908307 | Oral cavity | OSCC | cellular response to leukemia inhibitory factor | 57/7305 | 94/18723 | 1.75e-05 | 1.71e-04 | 57 |
| GO:0006605110 | Oral cavity | LP | protein targeting | 156/4623 | 314/18723 | 5.43e-22 | 1.62e-19 | 156 |
| GO:000660527 | Skin | cSCC | protein targeting | 153/4864 | 314/18723 | 2.62e-18 | 3.36e-16 | 153 |
| GO:199082317 | Skin | cSCC | response to leukemia inhibitory factor | 42/4864 | 95/18723 | 8.79e-05 | 8.27e-04 | 42 |
| GO:199083016 | Skin | cSCC | cellular response to leukemia inhibitory factor | 41/4864 | 94/18723 | 1.53e-04 | 1.35e-03 | 41 |
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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 |
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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 |
| SYNGR1 | SNV | Missense_Mutation | c.285N>G | p.Ile95Met | p.I95M | O43759 | protein_coding | tolerated(0.07) | possibly_damaging(0.81) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| SYNGR1 | SNV | Missense_Mutation | rs774993653 | c.188G>A | p.Arg63His | p.R63H | O43759 | protein_coding | tolerated(0.32) | benign(0.042) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SYNGR1 | SNV | Missense_Mutation | novel | c.689N>G | p.Ser230Trp | p.S230W | O43759 | protein_coding | deleterious(0.03) | possibly_damaging(0.487) | TCGA-AJ-A3EM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYNGR1 | SNV | Missense_Mutation | c.311C>T | p.Ala104Val | p.A104V | O43759 | protein_coding | tolerated(0.54) | benign(0.174) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNGR1 | SNV | Missense_Mutation | novel | c.611G>T | p.Gly204Val | p.G204V | O43759 | protein_coding | tolerated(0.44) | benign(0.127) | TCGA-AP-A0LP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Hormone Therapy | megace | SD |
| SYNGR1 | SNV | Missense_Mutation | rs774993653 | c.188N>A | p.Arg63His | p.R63H | O43759 | protein_coding | tolerated(0.32) | benign(0.042) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| SYNGR1 | SNV | Missense_Mutation | rs541640344 | c.454G>A | p.Ala152Thr | p.A152T | O43759 | protein_coding | tolerated(0.83) | benign(0.003) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| SYNGR1 | SNV | Missense_Mutation | novel | c.347N>A | p.Ala116Asp | p.A116D | O43759 | protein_coding | deleterious(0) | probably_damaging(0.945) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYNGR1 | SNV | Missense_Mutation | c.302N>A | p.Arg101His | p.R101H | O43759 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNGR1 | SNV | Missense_Mutation | novel | c.196N>G | p.Asn66Asp | p.N66D | O43759 | protein_coding | tolerated(1) | benign(0.017) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | 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 |
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