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Gene: SYT13 |
Gene summary for SYT13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYT13 | Gene ID | 57586 |
| Gene name | synaptotagmin 13 | |
| Gene Alias | SYT13 | |
| Cytomap | 11p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q7L8C5 |
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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 |
| 57586 | SYT13 | HCC2_Meng | Human | Liver | HCC | 3.51e-55 | 4.62e-01 | 0.0107 |
| 57586 | SYT13 | cirrhotic2 | Human | Liver | Cirrhotic | 4.12e-03 | 7.00e-02 | 0.0201 |
| 57586 | SYT13 | S027 | Human | Liver | HCC | 4.21e-08 | 8.08e-01 | 0.2446 |
| 57586 | SYT13 | S028 | Human | Liver | HCC | 4.86e-22 | 8.17e-01 | 0.2503 |
| 57586 | SYT13 | S029 | Human | Liver | HCC | 1.38e-31 | 1.05e+00 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:001605011 | Liver | Cirrhotic | vesicle organization | 133/4634 | 300/18723 | 7.35e-14 | 6.41e-12 | 133 |
| GO:001003812 | Liver | Cirrhotic | response to metal ion | 150/4634 | 373/18723 | 2.27e-11 | 1.37e-09 | 150 |
| GO:005159211 | Liver | Cirrhotic | response to calcium ion | 61/4634 | 149/18723 | 9.47e-06 | 1.38e-04 | 61 |
| GO:00712487 | Liver | Cirrhotic | cellular response to metal ion | 73/4634 | 197/18723 | 7.73e-05 | 8.54e-04 | 73 |
| GO:00712417 | Liver | Cirrhotic | cellular response to inorganic substance | 81/4634 | 226/18723 | 1.21e-04 | 1.20e-03 | 81 |
| GO:00482842 | Liver | Cirrhotic | organelle fusion | 52/4634 | 141/18723 | 8.77e-04 | 6.31e-03 | 52 |
| GO:0006906 | Liver | Cirrhotic | vesicle fusion | 40/4634 | 106/18723 | 2.01e-03 | 1.24e-02 | 40 |
| GO:0090174 | Liver | Cirrhotic | organelle membrane fusion | 40/4634 | 110/18723 | 4.32e-03 | 2.29e-02 | 40 |
| GO:001605021 | Liver | HCC | vesicle organization | 194/7958 | 300/18723 | 5.58e-15 | 3.97e-13 | 194 |
| GO:001003822 | Liver | HCC | response to metal ion | 208/7958 | 373/18723 | 1.35e-07 | 2.56e-06 | 208 |
| GO:004828411 | Liver | HCC | organelle fusion | 84/7958 | 141/18723 | 3.13e-05 | 3.20e-04 | 84 |
| GO:00901741 | Liver | HCC | organelle membrane fusion | 63/7958 | 110/18723 | 1.24e-03 | 6.85e-03 | 63 |
| GO:00069061 | Liver | HCC | vesicle fusion | 61/7958 | 106/18723 | 1.25e-03 | 6.90e-03 | 61 |
| GO:007124112 | Liver | HCC | cellular response to inorganic substance | 119/7958 | 226/18723 | 1.26e-03 | 6.92e-03 | 119 |
| GO:0061025 | Liver | HCC | membrane fusion | 88/7958 | 163/18723 | 1.98e-03 | 1.00e-02 | 88 |
| GO:005159221 | Liver | HCC | response to calcium ion | 81/7958 | 149/18723 | 2.26e-03 | 1.13e-02 | 81 |
| GO:007124812 | Liver | HCC | cellular response to metal ion | 101/7958 | 197/18723 | 7.82e-03 | 3.10e-02 | 101 |
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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 |
| SYT13 | SNV | Missense_Mutation | c.551N>T | p.Thr184Ile | p.T184I | Q7L8C5 | protein_coding | tolerated(0.11) | benign(0.409) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYT13 | insertion | Frame_Shift_Ins | novel | c.530_531insAAGCAGTCCCTTGAAGTTCAGTGGAAAG | p.Thr178SerfsTer24 | p.T178Sfs*24 | Q7L8C5 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| SYT13 | insertion | Frame_Shift_Ins | novel | c.266_267insTGTTTCCCCCAGAGTGAGCTCCACCCTTGCTCTA | p.Thr90ValfsTer41 | p.T90Vfs*41 | Q7L8C5 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SYT13 | deletion | Frame_Shift_Del | novel | c.248delN | p.Tyr83LeufsTer7 | p.Y83Lfs*7 | Q7L8C5 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| SYT13 | SNV | Missense_Mutation | rs377635830 | c.1013N>A | p.Arg338Gln | p.R338Q | Q7L8C5 | protein_coding | tolerated(0.53) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SYT13 | SNV | Missense_Mutation | rs141892837 | c.752N>A | p.Arg251His | p.R251H | Q7L8C5 | protein_coding | tolerated(0.09) | benign(0.406) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYT13 | SNV | Missense_Mutation | novel | c.331N>T | p.Pro111Ser | p.P111S | Q7L8C5 | protein_coding | tolerated(0.52) | benign(0.005) | TCGA-EX-A8YF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| SYT13 | SNV | Missense_Mutation | c.415G>C | p.Val139Leu | p.V139L | Q7L8C5 | protein_coding | tolerated(0.25) | benign(0.197) | TCGA-R2-A69V-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| SYT13 | SNV | Missense_Mutation | c.850N>T | p.Pro284Ser | p.P284S | Q7L8C5 | protein_coding | tolerated(0.5) | benign(0) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| SYT13 | SNV | Missense_Mutation | rs142224925 | c.1244G>A | p.Arg415His | p.R415H | Q7L8C5 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | 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 |
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