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Gene: SYNE1 |
Gene summary for SYNE1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SYNE1 | Gene ID | 23345 |
Gene name | spectrin repeat containing nuclear envelope protein 1 | |
Gene Alias | 8B | |
Cytomap | 6q25.2 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | B4E3R1 |
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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 |
23345 | SYNE1 | TD9 | Human | Lung | IAC | 4.73e-07 | 9.61e-01 | 0.088 |
23345 | SYNE1 | RNA-P10T1-P10T1-4 | Human | Lung | AIS | 1.40e-02 | 1.39e+00 | -0.1173 |
23345 | SYNE1 | RNA-P10T2-P10T2-1 | Human | Lung | AAH | 9.97e-07 | 1.15e+00 | -0.1271 |
23345 | SYNE1 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 9.61e-04 | 9.08e-01 | -0.1406 |
23345 | SYNE1 | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 3.19e-04 | 1.02e+00 | -0.1408 |
23345 | SYNE1 | RNA-P17T-P17T-2 | Human | Lung | IAC | 9.10e-05 | 4.19e-01 | 0.3371 |
23345 | SYNE1 | RNA-P17T-P17T-4 | Human | Lung | IAC | 2.89e-04 | 3.21e-01 | 0.343 |
23345 | SYNE1 | RNA-P17T-P17T-6 | Human | Lung | IAC | 5.10e-07 | 3.63e-01 | 0.3385 |
23345 | SYNE1 | RNA-P17T-P17T-8 | Human | Lung | IAC | 4.35e-03 | 1.32e-01 | 0.3329 |
23345 | SYNE1 | RNA-P23T2-P23T2-1 | Human | Lung | MIAC | 1.94e-04 | 1.13e+00 | -0.037 |
23345 | SYNE1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 5.47e-22 | 1.01e+00 | -0.2116 |
23345 | SYNE1 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 5.12e-12 | 1.10e+00 | -0.1941 |
23345 | SYNE1 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 9.83e-10 | 9.36e-01 | -0.2107 |
23345 | SYNE1 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 7.67e-23 | 9.81e-01 | -0.2119 |
23345 | SYNE1 | RNA-P6T1-P6T1-1 | Human | Lung | MIAC | 1.20e-02 | 8.71e-01 | -0.0238 |
23345 | SYNE1 | RNA-P6T1-P6T1-2 | Human | Lung | MIAC | 2.46e-07 | 9.90e-01 | -0.0186 |
23345 | SYNE1 | RNA-P6T1-P6T1-3 | Human | Lung | MIAC | 1.30e-05 | 1.13e+00 | -0.0296 |
23345 | SYNE1 | RNA-P6T1-P6T1-4 | Human | Lung | MIAC | 1.09e-06 | 9.18e-01 | -0.0263 |
23345 | SYNE1 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 1.54e-25 | 6.72e-01 | -0.0166 |
23345 | SYNE1 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 5.21e-26 | 6.75e-01 | -0.0132 |
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Transcriptomic changes along malignancy continuum. |
∗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:00512357 | Lung | IAC | maintenance of location | 58/2061 | 327/18723 | 1.66e-04 | 2.96e-03 | 58 |
GO:0042692 | Lung | IAC | muscle cell differentiation | 65/2061 | 384/18723 | 2.75e-04 | 4.54e-03 | 65 |
GO:00070303 | Lung | IAC | Golgi organization | 32/2061 | 157/18723 | 4.13e-04 | 6.22e-03 | 32 |
GO:00345047 | Lung | IAC | protein localization to nucleus | 50/2061 | 290/18723 | 8.71e-04 | 1.11e-02 | 50 |
GO:00516518 | Lung | IAC | maintenance of location in cell | 39/2061 | 214/18723 | 1.07e-03 | 1.26e-02 | 39 |
GO:00325075 | Lung | IAC | maintenance of protein location in cell | 15/2061 | 65/18723 | 4.02e-03 | 3.30e-02 | 15 |
GO:00451858 | Lung | IAC | maintenance of protein location | 19/2061 | 94/18723 | 6.26e-03 | 4.48e-02 | 19 |
GO:005123512 | Lung | AIS | maintenance of location | 55/1849 | 327/18723 | 5.93e-05 | 1.65e-03 | 55 |
GO:005165113 | Lung | AIS | maintenance of location in cell | 39/1849 | 214/18723 | 1.23e-04 | 2.81e-03 | 39 |
GO:000703011 | Lung | AIS | Golgi organization | 30/1849 | 157/18723 | 3.09e-04 | 5.63e-03 | 30 |
GO:00426921 | Lung | AIS | muscle cell differentiation | 58/1849 | 384/18723 | 7.00e-04 | 1.03e-02 | 58 |
GO:003250713 | Lung | AIS | maintenance of protein location in cell | 15/1849 | 65/18723 | 1.39e-03 | 1.70e-02 | 15 |
GO:004518513 | Lung | AIS | maintenance of protein location | 19/1849 | 94/18723 | 1.88e-03 | 2.08e-02 | 19 |
GO:005165122 | Lung | AAH | maintenance of location in cell | 17/613 | 214/18723 | 7.07e-04 | 2.55e-02 | 17 |
GO:005123522 | Lung | AAH | maintenance of location | 22/613 | 327/18723 | 1.20e-03 | 3.33e-02 | 22 |
GO:00426922 | Lung | MIAC | muscle cell differentiation | 39/967 | 384/18723 | 4.51e-05 | 2.36e-03 | 39 |
GO:000703021 | Lung | MIAC | Golgi organization | 18/967 | 157/18723 | 1.27e-03 | 2.37e-02 | 18 |
GO:003450410 | Prostate | BPH | protein localization to nucleus | 98/3107 | 290/18723 | 4.78e-13 | 4.35e-11 | 98 |
GO:004518518 | Prostate | BPH | maintenance of protein location | 35/3107 | 94/18723 | 1.16e-06 | 2.07e-05 | 35 |
GO:00325079 | Prostate | BPH | maintenance of protein location in cell | 27/3107 | 65/18723 | 1.65e-06 | 2.78e-05 | 27 |
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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 |
SYNE1 | SNV | Missense_Mutation | novel | c.24418T>A | p.Cys8140Ser | p.C8140S | Q8NF91 | protein_coding | probably_damaging(1) | TCGA-34-2605-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Chemotherapy | cisplatin | PD | |
SYNE1 | SNV | Missense_Mutation | c.8553N>C | p.Glu2851Asp | p.E2851D | Q8NF91 | protein_coding | benign(0.108) | TCGA-34-5231-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
SYNE1 | SNV | Missense_Mutation | c.21845N>T | p.Trp7282Leu | p.W7282L | Q8NF91 | protein_coding | probably_damaging(0.999) | TCGA-34-5236-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | ||
SYNE1 | SNV | Missense_Mutation | novel | c.15255N>C | p.Met5085Ile | p.M5085I | Q8NF91 | protein_coding | benign(0) | TCGA-34-8454-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
SYNE1 | SNV | Missense_Mutation | novel | c.12964N>C | p.Glu4322Gln | p.E4322Q | Q8NF91 | protein_coding | probably_damaging(0.998) | TCGA-34-8454-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
SYNE1 | SNV | Missense_Mutation | novel | c.21682N>C | p.Ala7228Pro | p.A7228P | Q8NF91 | protein_coding | possibly_damaging(0.88) | TCGA-37-A5EL-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | temodal | PD | |
SYNE1 | SNV | Missense_Mutation | novel | c.1709N>T | p.Tyr570Phe | p.Y570F | Q8NF91 | protein_coding | benign(0.406) | TCGA-37-A5EN-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
SYNE1 | SNV | Missense_Mutation | c.19189N>A | p.Val6397Ile | p.V6397I | Q8NF91 | protein_coding | probably_damaging(0.921) | TCGA-39-5019-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
SYNE1 | SNV | Missense_Mutation | c.14950N>G | p.Arg4984Gly | p.R4984G | Q8NF91 | protein_coding | benign(0.291) | TCGA-39-5027-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
SYNE1 | SNV | Missense_Mutation | rs199673397 | c.13922N>A | p.Leu4641His | p.L4641H | Q8NF91 | protein_coding | probably_damaging(0.999) | TCGA-39-5027-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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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