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Gene: SYNC |
Gene summary for SYNC |
Gene summary. |
Gene information | Species | Human | Gene symbol | SYNC | Gene ID | 81493 |
Gene name | syncoilin, intermediate filament protein | |
Gene Alias | SYNC1 | |
Cytomap | 1p35.1 | |
Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | Q9H7C4 |
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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 |
81493 | SYNC | LZE4T | Human | Esophagus | ESCC | 2.17e-07 | 2.43e-01 | 0.0811 |
81493 | SYNC | LZE5T | Human | Esophagus | ESCC | 1.55e-04 | 4.48e-01 | 0.0514 |
81493 | SYNC | LZE7T | Human | Esophagus | ESCC | 1.96e-16 | 1.00e+00 | 0.0667 |
81493 | SYNC | LZE8T | Human | Esophagus | ESCC | 2.34e-05 | 2.78e-01 | 0.067 |
81493 | SYNC | LZE20T | Human | Esophagus | ESCC | 2.20e-08 | 2.94e-01 | 0.0662 |
81493 | SYNC | LZE22T | Human | Esophagus | ESCC | 1.18e-10 | 6.34e-01 | 0.068 |
81493 | SYNC | LZE24T | Human | Esophagus | ESCC | 1.06e-22 | 6.11e-01 | 0.0596 |
81493 | SYNC | LZE6T | Human | Esophagus | ESCC | 2.09e-09 | 3.93e-01 | 0.0845 |
81493 | SYNC | P2T-E | Human | Esophagus | ESCC | 1.08e-05 | 1.03e-01 | 0.1177 |
81493 | SYNC | P10T-E | Human | Esophagus | ESCC | 3.29e-13 | 2.17e-01 | 0.116 |
81493 | SYNC | P16T-E | Human | Esophagus | ESCC | 1.88e-02 | 3.11e-02 | 0.1153 |
81493 | SYNC | P21T-E | Human | Esophagus | ESCC | 1.50e-03 | 9.06e-02 | 0.1617 |
81493 | SYNC | P57T-E | Human | Esophagus | ESCC | 1.22e-05 | 4.68e-02 | 0.0926 |
81493 | SYNC | P79T-E | Human | Esophagus | ESCC | 2.86e-05 | 4.35e-02 | 0.1154 |
81493 | SYNC | P130T-E | Human | Esophagus | ESCC | 5.72e-19 | 2.99e-01 | 0.1676 |
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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 |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000838026 | Esophagus | HGIN | RNA splicing | 160/2587 | 434/18723 | 3.74e-34 | 1.12e-30 | 160 |
GO:000037520 | Esophagus | HGIN | RNA splicing, via transesterification reactions | 115/2587 | 324/18723 | 3.16e-23 | 3.80e-20 | 115 |
GO:000037720 | Esophagus | HGIN | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
GO:000039820 | Esophagus | HGIN | mRNA splicing, via spliceosome | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
GO:000641727 | Esophagus | HGIN | regulation of translation | 139/2587 | 468/18723 | 1.46e-19 | 7.98e-17 | 139 |
GO:190331120 | Esophagus | HGIN | regulation of mRNA metabolic process | 91/2587 | 288/18723 | 5.06e-15 | 9.78e-13 | 91 |
GO:000989520 | Esophagus | HGIN | negative regulation of catabolic process | 87/2587 | 320/18723 | 1.74e-10 | 1.68e-08 | 87 |
GO:003133026 | Esophagus | HGIN | negative regulation of cellular catabolic process | 74/2587 | 262/18723 | 6.27e-10 | 5.30e-08 | 74 |
GO:000640120 | Esophagus | HGIN | RNA catabolic process | 77/2587 | 278/18723 | 7.63e-10 | 6.36e-08 | 77 |
GO:000640220 | Esophagus | HGIN | mRNA catabolic process | 67/2587 | 232/18723 | 1.47e-09 | 1.13e-07 | 67 |
GO:003465519 | Esophagus | HGIN | nucleobase-containing compound catabolic process | 98/2587 | 407/18723 | 1.44e-08 | 8.94e-07 | 98 |
GO:004670017 | Esophagus | HGIN | heterocycle catabolic process | 103/2587 | 445/18723 | 5.44e-08 | 2.99e-06 | 103 |
GO:004427018 | Esophagus | HGIN | cellular nitrogen compound catabolic process | 103/2587 | 451/18723 | 1.10e-07 | 5.56e-06 | 103 |
GO:001943917 | Esophagus | HGIN | aromatic compound catabolic process | 105/2587 | 467/18723 | 1.89e-07 | 9.31e-06 | 105 |
GO:190136117 | Esophagus | HGIN | organic cyclic compound catabolic process | 106/2587 | 495/18723 | 1.94e-06 | 7.13e-05 | 106 |
GO:00342496 | Esophagus | HGIN | negative regulation of cellular amide metabolic process | 66/2587 | 273/18723 | 2.74e-06 | 9.60e-05 | 66 |
GO:190331226 | Esophagus | HGIN | negative regulation of mRNA metabolic process | 29/2587 | 92/18723 | 1.01e-05 | 2.92e-04 | 29 |
GO:00171486 | Esophagus | HGIN | negative regulation of translation | 59/2587 | 245/18723 | 1.03e-05 | 2.96e-04 | 59 |
GO:006101318 | Esophagus | HGIN | regulation of mRNA catabolic process | 43/2587 | 166/18723 | 2.48e-05 | 6.53e-04 | 43 |
GO:000164917 | Esophagus | HGIN | osteoblast differentiation | 50/2587 | 229/18723 | 5.88e-04 | 8.30e-03 | 50 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
SYNC | SNV | Missense_Mutation | rs557197732 | c.166N>A | p.Glu56Lys | p.E56K | Q9H7C4 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.468) | TCGA-E6-A1M0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
SYNC | SNV | Missense_Mutation | novel | c.1302G>T | p.Lys434Asn | p.K434N | Q9H7C4 | protein_coding | deleterious(0.01) | probably_damaging(0.99) | TCGA-EO-A22X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unspecific | Carboplatin | Complete Response |
SYNC | SNV | Missense_Mutation | novel | c.746T>C | p.Val249Ala | p.V249A | Q9H7C4 | protein_coding | tolerated(0.07) | probably_damaging(0.994) | TCGA-DD-AA3A-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | novel | c.1202N>T | p.Gln401Leu | p.Q401L | Q9H7C4 | protein_coding | tolerated(0.09) | possibly_damaging(0.596) | TCGA-L4-A4E5-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | novel | c.1181A>T | p.Asp394Val | p.D394V | Q9H7C4 | protein_coding | deleterious(0) | probably_damaging(0.93) | TCGA-34-2608-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | rs751771078 | c.1180G>A | p.Asp394Asn | p.D394N | Q9H7C4 | protein_coding | deleterious(0.03) | benign(0.066) | TCGA-34-2608-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | novel | c.1195G>C | p.Val399Leu | p.V399L | Q9H7C4 | protein_coding | tolerated(0.22) | benign(0.022) | TCGA-51-6867-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
SYNC | SNV | Missense_Mutation | novel | c.1384N>A | p.Glu462Lys | p.E462K | Q9H7C4 | protein_coding | deleterious_low_confidence(0.01) | benign(0.081) | TCGA-CQ-A4C6-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | rs201938976 | c.1355N>G | p.Tyr452Cys | p.Y452C | Q9H7C4 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CV-6954-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SYNC | SNV | Missense_Mutation | rs201938976 | c.1355N>G | p.Tyr452Cys | p.Y452C | Q9H7C4 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-HC-7078-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 7 | 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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