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Gene: SYNCRIP |
Gene summary for SYNCRIP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYNCRIP | Gene ID | 10492 |
| Gene name | synaptotagmin binding cytoplasmic RNA interacting protein | |
| Gene Alias | GRY-RBP | |
| Cytomap | 6q14.3 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | B7Z645 |
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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 |
| 10492 | SYNCRIP | LZE2T | Human | Esophagus | ESCC | 3.07e-03 | 1.08e+00 | 0.082 |
| 10492 | SYNCRIP | LZE4T | Human | Esophagus | ESCC | 6.94e-05 | 5.91e-01 | 0.0811 |
| 10492 | SYNCRIP | LZE7T | Human | Esophagus | ESCC | 7.01e-04 | 7.96e-01 | 0.0667 |
| 10492 | SYNCRIP | LZE20T | Human | Esophagus | ESCC | 1.99e-03 | -1.44e-01 | 0.0662 |
| 10492 | SYNCRIP | LZE22D1 | Human | Esophagus | HGIN | 1.63e-02 | -3.33e-01 | 0.0595 |
| 10492 | SYNCRIP | LZE24T | Human | Esophagus | ESCC | 6.49e-07 | 4.37e-01 | 0.0596 |
| 10492 | SYNCRIP | P1T-E | Human | Esophagus | ESCC | 5.18e-05 | 6.13e-01 | 0.0875 |
| 10492 | SYNCRIP | P2T-E | Human | Esophagus | ESCC | 7.64e-48 | 1.27e+00 | 0.1177 |
| 10492 | SYNCRIP | P4T-E | Human | Esophagus | ESCC | 7.90e-45 | 1.68e+00 | 0.1323 |
| 10492 | SYNCRIP | P5T-E | Human | Esophagus | ESCC | 7.33e-34 | 1.05e+00 | 0.1327 |
| 10492 | SYNCRIP | P8T-E | Human | Esophagus | ESCC | 7.73e-24 | 7.89e-01 | 0.0889 |
| 10492 | SYNCRIP | P9T-E | Human | Esophagus | ESCC | 1.16e-14 | 5.88e-01 | 0.1131 |
| 10492 | SYNCRIP | P10T-E | Human | Esophagus | ESCC | 8.72e-37 | 1.02e+00 | 0.116 |
| 10492 | SYNCRIP | P11T-E | Human | Esophagus | ESCC | 1.57e-06 | 6.66e-01 | 0.1426 |
| 10492 | SYNCRIP | P12T-E | Human | Esophagus | ESCC | 1.54e-34 | 1.01e+00 | 0.1122 |
| 10492 | SYNCRIP | P15T-E | Human | Esophagus | ESCC | 9.81e-22 | 9.81e-01 | 0.1149 |
| 10492 | SYNCRIP | P16T-E | Human | Esophagus | ESCC | 2.38e-46 | 1.38e+00 | 0.1153 |
| 10492 | SYNCRIP | P17T-E | Human | Esophagus | ESCC | 1.26e-04 | 5.53e-01 | 0.1278 |
| 10492 | SYNCRIP | P19T-E | Human | Esophagus | ESCC | 6.83e-03 | 1.05e+00 | 0.1662 |
| 10492 | SYNCRIP | P20T-E | Human | Esophagus | ESCC | 1.17e-21 | 7.87e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| 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:0044270110 | Skin | cSCC | cellular nitrogen compound catabolic process | 179/4864 | 451/18723 | 8.34e-11 | 3.79e-09 | 179 |
| GO:0019439110 | Skin | cSCC | aromatic compound catabolic process | 183/4864 | 467/18723 | 1.76e-10 | 7.68e-09 | 183 |
| GO:003133028 | Skin | cSCC | negative regulation of cellular catabolic process | 115/4864 | 262/18723 | 2.03e-10 | 8.72e-09 | 115 |
| GO:000989527 | Skin | cSCC | negative regulation of catabolic process | 133/4864 | 320/18723 | 6.99e-10 | 2.77e-08 | 133 |
| GO:0061013110 | Skin | cSCC | regulation of mRNA catabolic process | 79/4864 | 166/18723 | 1.57e-09 | 5.92e-08 | 79 |
| GO:1901361110 | Skin | cSCC | organic cyclic compound catabolic process | 188/4864 | 495/18723 | 1.92e-09 | 7.01e-08 | 188 |
| GO:0043487110 | Skin | cSCC | regulation of RNA stability | 80/4864 | 170/18723 | 2.39e-09 | 8.52e-08 | 80 |
| GO:004348824 | Skin | cSCC | regulation of mRNA stability | 75/4864 | 158/18723 | 4.64e-09 | 1.55e-07 | 75 |
| GO:190331228 | Skin | cSCC | negative regulation of mRNA metabolic process | 47/4864 | 92/18723 | 2.24e-07 | 4.77e-06 | 47 |
| GO:003424915 | Skin | cSCC | negative regulation of cellular amide metabolic process | 104/4864 | 273/18723 | 6.44e-06 | 9.00e-05 | 104 |
| GO:000164923 | Skin | cSCC | osteoblast differentiation | 89/4864 | 229/18723 | 1.18e-05 | 1.51e-04 | 89 |
| GO:001714814 | Skin | cSCC | negative regulation of translation | 93/4864 | 245/18723 | 2.28e-05 | 2.63e-04 | 93 |
| GO:003434115 | Skin | cSCC | response to interferon-gamma | 57/4864 | 141/18723 | 1.20e-04 | 1.11e-03 | 57 |
| GO:000150323 | Skin | cSCC | ossification | 137/4864 | 408/18723 | 3.39e-04 | 2.68e-03 | 137 |
| GO:190236918 | Skin | cSCC | negative regulation of RNA catabolic process | 33/4864 | 75/18723 | 5.35e-04 | 3.97e-03 | 33 |
| GO:007134613 | Skin | cSCC | cellular response to interferon-gamma | 47/4864 | 118/18723 | 6.71e-04 | 4.79e-03 | 47 |
| GO:004348915 | Skin | cSCC | RNA stabilization | 27/4864 | 65/18723 | 4.45e-03 | 2.29e-02 | 27 |
| GO:000838028 | Thyroid | HT | RNA splicing | 84/1272 | 434/18723 | 1.23e-18 | 1.14e-15 | 84 |
| GO:000037527 | Thyroid | HT | RNA splicing, via transesterification reactions | 66/1272 | 324/18723 | 4.86e-16 | 2.08e-13 | 66 |
| GO:000037727 | Thyroid | HT | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 65/1272 | 320/18723 | 9.43e-16 | 3.50e-13 | 65 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| 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 |
| SYNCRIP | SNV | Missense_Mutation | c.1324C>T | p.Pro442Ser | p.P442S | O60506 | protein_coding | tolerated(0.17) | probably_damaging(0.968) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYNCRIP | SNV | Missense_Mutation | rs750883103 | c.1555N>A | p.Gly519Ser | p.G519S | O60506 | protein_coding | tolerated(0.14) | probably_damaging(0.987) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SYNCRIP | SNV | Missense_Mutation | novel | c.857N>A | p.Arg286Lys | p.R286K | O60506 | protein_coding | deleterious(0.01) | probably_damaging(0.945) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SYNCRIP | SNV | Missense_Mutation | c.575G>A | p.Arg192His | p.R192H | O60506 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-D8-A142-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamid | SD | |
| SYNCRIP | SNV | Missense_Mutation | c.48N>A | p.Asp16Glu | p.D16E | O60506 | protein_coding | tolerated(0.55) | benign(0.007) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| SYNCRIP | SNV | Missense_Mutation | novel | c.617C>T | p.Ala206Val | p.A206V | O60506 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SYNCRIP | SNV | Missense_Mutation | rs370683161 | c.1564G>A | p.Gly522Ser | p.G522S | O60506 | protein_coding | tolerated(0.12) | benign(0.272) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SYNCRIP | SNV | Missense_Mutation | c.1598G>C | p.Arg533Thr | p.R533T | O60506 | protein_coding | tolerated(0.48) | benign(0) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNCRIP | SNV | Missense_Mutation | c.316N>A | p.Glu106Lys | p.E106K | O60506 | protein_coding | tolerated(0.72) | benign(0.031) | TCGA-MY-A5BD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| SYNCRIP | SNV | Missense_Mutation | novel | c.508N>T | p.Pro170Ser | p.P170S | O60506 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-ZJ-AAXD-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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