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Gene: SYNGR2 |
Gene summary for SYNGR2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYNGR2 | Gene ID | 9144 |
| Gene name | synaptogyrin 2 | |
| Gene Alias | SYNGR2 | |
| Cytomap | 17q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | O43760 |
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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 |
| 9144 | SYNGR2 | GSM4909281 | Human | Breast | IDC | 9.03e-05 | 2.50e-01 | 0.21 |
| 9144 | SYNGR2 | GSM4909282 | Human | Breast | IDC | 1.04e-08 | 3.45e-01 | -0.0288 |
| 9144 | SYNGR2 | GSM4909290 | Human | Breast | IDC | 4.66e-14 | 5.61e-01 | 0.2096 |
| 9144 | SYNGR2 | GSM4909291 | Human | Breast | IDC | 2.21e-13 | 5.49e-01 | 0.1753 |
| 9144 | SYNGR2 | GSM4909293 | Human | Breast | IDC | 3.06e-44 | 6.83e-01 | 0.1581 |
| 9144 | SYNGR2 | GSM4909296 | Human | Breast | IDC | 3.04e-06 | -5.70e-02 | 0.1524 |
| 9144 | SYNGR2 | GSM4909297 | Human | Breast | IDC | 1.97e-05 | -9.17e-02 | 0.1517 |
| 9144 | SYNGR2 | GSM4909298 | Human | Breast | IDC | 7.21e-09 | 2.90e-01 | 0.1551 |
| 9144 | SYNGR2 | GSM4909301 | Human | Breast | IDC | 7.72e-06 | 2.65e-01 | 0.1577 |
| 9144 | SYNGR2 | GSM4909305 | Human | Breast | IDC | 3.03e-02 | 3.12e-01 | 0.0436 |
| 9144 | SYNGR2 | GSM4909306 | Human | Breast | IDC | 6.40e-04 | 2.05e-01 | 0.1564 |
| 9144 | SYNGR2 | GSM4909311 | Human | Breast | IDC | 2.32e-24 | 2.93e-02 | 0.1534 |
| 9144 | SYNGR2 | GSM4909312 | Human | Breast | IDC | 1.96e-24 | 4.38e-01 | 0.1552 |
| 9144 | SYNGR2 | GSM4909317 | Human | Breast | IDC | 8.35e-12 | 4.97e-01 | 0.1355 |
| 9144 | SYNGR2 | GSM4909319 | Human | Breast | IDC | 8.33e-47 | 3.25e-01 | 0.1563 |
| 9144 | SYNGR2 | GSM4909320 | Human | Breast | IDC | 2.23e-12 | 4.72e-01 | 0.1575 |
| 9144 | SYNGR2 | GSM4909321 | Human | Breast | IDC | 1.71e-23 | 3.93e-01 | 0.1559 |
| 9144 | SYNGR2 | brca1 | Human | Breast | Precancer | 2.49e-04 | 2.38e-01 | -0.0338 |
| 9144 | SYNGR2 | brca2 | Human | Breast | Precancer | 8.75e-13 | 3.34e-01 | -0.024 |
| 9144 | SYNGR2 | brca3 | Human | Breast | Precancer | 1.17e-09 | 3.17e-01 | -0.0263 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0006887 | Colorectum | AD | exocytosis | 96/3918 | 352/18723 | 2.48e-03 | 1.90e-02 | 96 |
| GO:00068871 | Colorectum | SER | exocytosis | 75/2897 | 352/18723 | 2.05e-03 | 2.03e-02 | 75 |
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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 |
| SYNGR2 | SNV | Missense_Mutation | novel | c.183N>G | p.Phe61Leu | p.F61L | O43760 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| SYNGR2 | SNV | Missense_Mutation | c.161N>G | p.Ser54Cys | p.S54C | O43760 | protein_coding | deleterious(0) | possibly_damaging(0.87) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYNGR2 | SNV | Missense_Mutation | rs78947498 | c.178N>A | p.Val60Met | p.V60M | O43760 | protein_coding | tolerated(0.14) | possibly_damaging(0.787) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SYNGR2 | SNV | Missense_Mutation | novel | c.397N>C | p.Thr133Pro | p.T133P | O43760 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYNGR2 | SNV | Missense_Mutation | c.247N>A | p.Ala83Thr | p.A83T | O43760 | protein_coding | tolerated(0.23) | benign(0.197) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNGR2 | SNV | Missense_Mutation | c.125N>A | p.Cys42Tyr | p.C42Y | O43760 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AP-A0LP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Hormone Therapy | megace | SD | |
| SYNGR2 | SNV | Missense_Mutation | rs544604839 | c.404C>T | p.Pro135Leu | p.P135L | O43760 | protein_coding | tolerated(0.16) | benign(0.017) | TCGA-D1-A1O8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| SYNGR2 | SNV | Missense_Mutation | rs9889851 | c.646N>A | p.Glu216Lys | p.E216K | O43760 | protein_coding | tolerated(0.68) | possibly_damaging(0.603) | TCGA-EC-A24G-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SYNGR2 | SNV | Missense_Mutation | rs533720150 | c.635N>T | p.Ala212Val | p.A212V | O43760 | protein_coding | tolerated(0.34) | benign(0) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
| SYNGR2 | SNV | Missense_Mutation | c.305N>T | p.Lys102Met | p.K102M | O43760 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-BR-8373-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
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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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