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Gene: SMYD4 |
Gene summary for SMYD4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SMYD4 | Gene ID | 114826 |
Gene name | SET and MYND domain containing 4 | |
Gene Alias | ZMYND21 | |
Cytomap | 17p13.3 | |
Gene Type | protein-coding | GO ID | GO:0007275 | UniProtAcc | Q8IYR2 |
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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 |
114826 | SMYD4 | ATC12 | Human | Thyroid | ATC | 5.83e-12 | 2.35e-01 | 0.34 |
114826 | SMYD4 | ATC13 | Human | Thyroid | ATC | 1.28e-29 | 5.13e-01 | 0.34 |
114826 | SMYD4 | ATC1 | Human | Thyroid | ATC | 4.95e-05 | 2.34e-01 | 0.2878 |
114826 | SMYD4 | ATC2 | Human | Thyroid | ATC | 9.94e-09 | 7.57e-01 | 0.34 |
114826 | SMYD4 | ATC3 | Human | Thyroid | ATC | 6.53e-05 | 3.05e-01 | 0.338 |
114826 | SMYD4 | ATC4 | Human | Thyroid | ATC | 1.06e-14 | 2.91e-01 | 0.34 |
114826 | SMYD4 | ATC5 | Human | Thyroid | ATC | 7.53e-34 | 5.65e-01 | 0.34 |
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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:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
GO:00322594 | Thyroid | PTC | methylation | 146/5968 | 364/18723 | 4.99e-04 | 3.26e-03 | 146 |
GO:003225911 | Thyroid | ATC | methylation | 148/6293 | 364/18723 | 2.69e-03 | 1.23e-02 | 148 |
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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 |
SMYD4 | SNV | Missense_Mutation | c.2347N>A | p.Gln783Lys | p.Q783K | Q8IYR2 | protein_coding | deleterious(0.01) | benign(0.355) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
SMYD4 | SNV | Missense_Mutation | c.117N>G | p.His39Gln | p.H39Q | Q8IYR2 | protein_coding | tolerated(0.27) | benign(0.003) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SMYD4 | SNV | Missense_Mutation | c.832N>G | p.His278Asp | p.H278D | Q8IYR2 | protein_coding | tolerated(0.25) | benign(0.288) | TCGA-BH-A0C0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
SMYD4 | SNV | Missense_Mutation | c.359N>A | p.Gly120Asp | p.G120D | Q8IYR2 | protein_coding | tolerated(0.07) | benign(0.28) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
SMYD4 | insertion | Frame_Shift_Ins | novel | c.1097_1098insTTTGAGACGGAGTCTCACTCTGTCACCCCCAGGCTGGGGTG | p.Ile367LeufsTer15 | p.I367Lfs*15 | Q8IYR2 | protein_coding | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
SMYD4 | insertion | Nonsense_Mutation | novel | c.1970_1971insGATTTCAGCTGTTGTTTTCTTCTGCATCTGATTGCTAAGTTG | p.Leu657_Gln658insIleSerAlaValValPhePheCysIleTerLeuLeuSerTer | p.L657_Q658insISAVVFFCI*LLS* | Q8IYR2 | protein_coding | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
SMYD4 | insertion | Frame_Shift_Ins | novel | c.1041_1042insCCAATTGAGAGATATTTCCC | p.Cys348ProfsTer12 | p.C348Pfs*12 | Q8IYR2 | protein_coding | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR | ||
SMYD4 | deletion | Frame_Shift_Del | c.1919delN | p.Cys640LeufsTer34 | p.C640Lfs*34 | Q8IYR2 | protein_coding | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
SMYD4 | insertion | Frame_Shift_Ins | novel | c.1228_1229insGAGATCGTGCCACTGCACTCCAGCCTGGCGA | p.Pro410ArgfsTer16 | p.P410Rfs*16 | Q8IYR2 | protein_coding | TCGA-BH-A0HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
SMYD4 | deletion | Frame_Shift_Del | novel | c.2188delN | p.Glu730ArgfsTer32 | p.E730Rfs*32 | Q8IYR2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | 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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