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Gene: SMAD6 |
Gene summary for SMAD6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMAD6 | Gene ID | 4091 |
| Gene name | SMAD family member 6 | |
| Gene Alias | AOVD2 | |
| Cytomap | 15q22.31 | |
| Gene Type | protein-coding | GO ID | GO:0000578 | UniProtAcc | O43541 |
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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 |
| 4091 | SMAD6 | HCC2_Meng | Human | Liver | HCC | 9.68e-07 | 7.62e-02 | 0.0107 |
| 4091 | SMAD6 | HCC1 | Human | Liver | HCC | 3.89e-02 | 1.32e+00 | 0.5336 |
| 4091 | SMAD6 | S015 | Human | Liver | HCC | 4.59e-04 | 2.04e-01 | 0.2375 |
| 4091 | SMAD6 | S027 | Human | Liver | HCC | 4.89e-02 | 2.18e-01 | 0.2446 |
| 4091 | SMAD6 | S028 | Human | Liver | HCC | 5.01e-11 | 4.07e-01 | 0.2503 |
| 4091 | SMAD6 | S029 | Human | Liver | HCC | 1.41e-12 | 5.69e-01 | 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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004325422 | Liver | HCC | regulation of protein-containing complex assembly | 264/7958 | 428/18723 | 5.47e-16 | 4.39e-14 | 264 |
| GO:001056322 | Liver | HCC | negative regulation of phosphorus metabolic process | 259/7958 | 442/18723 | 4.29e-12 | 1.92e-10 | 259 |
| GO:004593622 | Liver | HCC | negative regulation of phosphate metabolic process | 258/7958 | 441/18723 | 6.00e-12 | 2.60e-10 | 258 |
| GO:004232622 | Liver | HCC | negative regulation of phosphorylation | 227/7958 | 385/18723 | 3.98e-11 | 1.52e-09 | 227 |
| GO:000193322 | Liver | HCC | negative regulation of protein phosphorylation | 196/7958 | 342/18723 | 1.95e-08 | 4.63e-07 | 196 |
| GO:003133312 | Liver | HCC | negative regulation of protein-containing complex assembly | 91/7958 | 141/18723 | 1.01e-07 | 1.98e-06 | 91 |
| GO:007155921 | Liver | HCC | response to transforming growth factor beta | 141/7958 | 256/18723 | 3.08e-05 | 3.16e-04 | 141 |
| GO:007156021 | Liver | HCC | cellular response to transforming growth factor beta stimulus | 137/7958 | 250/18723 | 5.47e-05 | 5.14e-04 | 137 |
| GO:003158922 | Liver | HCC | cell-substrate adhesion | 188/7958 | 363/18723 | 2.00e-04 | 1.55e-03 | 188 |
| GO:000717921 | Liver | HCC | transforming growth factor beta receptor signaling pathway | 106/7958 | 198/18723 | 1.09e-03 | 6.23e-03 | 106 |
| GO:003249611 | Liver | HCC | response to lipopolysaccharide | 174/7958 | 343/18723 | 1.19e-03 | 6.62e-03 | 174 |
| GO:006161422 | Liver | HCC | pri-miRNA transcription by RNA polymerase II | 35/7958 | 55/18723 | 1.26e-03 | 6.92e-03 | 35 |
| GO:00454441 | Liver | HCC | fat cell differentiation | 120/7958 | 229/18723 | 1.52e-03 | 8.05e-03 | 120 |
| GO:190289312 | Liver | HCC | regulation of pri-miRNA transcription by RNA polymerase II | 34/7958 | 54/18723 | 1.92e-03 | 9.78e-03 | 34 |
| GO:00016553 | Liver | HCC | urogenital system development | 170/7958 | 338/18723 | 2.15e-03 | 1.08e-02 | 170 |
| GO:000223711 | Liver | HCC | response to molecule of bacterial origin | 181/7958 | 363/18723 | 2.58e-03 | 1.24e-02 | 181 |
| GO:19038442 | Liver | HCC | regulation of cellular response to transforming growth factor beta stimulus | 72/7958 | 131/18723 | 2.65e-03 | 1.27e-02 | 72 |
| GO:00018222 | Liver | HCC | kidney development | 148/7958 | 293/18723 | 3.25e-03 | 1.49e-02 | 148 |
| GO:00436271 | Liver | HCC | response to estrogen | 44/7958 | 75/18723 | 3.44e-03 | 1.55e-02 | 44 |
| GO:00720012 | Liver | HCC | renal system development | 152/7958 | 302/18723 | 3.45e-03 | 1.56e-02 | 152 |
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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 |
| SMAD6 | MVA | Prostate | BPH | BTNL9,PDGFD,FCN3, etc. | 2.06e-01 |  |
| SMAD6 | MVA | Thyroid | goiters | SLCO2A1,PLVAP,HPCAL1, etc. | 6.33e-01 |  |
| ∗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 |
| SMAD6 | SNV | Missense_Mutation | rs757635348 | c.1025G>A | p.Arg342His | p.R342H | O43541 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AR-A5QN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | taxotere | SD |
| SMAD6 | SNV | Missense_Mutation | novel | c.1076A>G | p.Asp359Gly | p.D359G | O43541 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| SMAD6 | SNV | Missense_Mutation | c.1157A>G | p.Lys386Arg | p.K386R | O43541 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-3810-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| SMAD6 | SNV | Missense_Mutation | rs748124400 | c.1151N>A | p.Arg384His | p.R384H | O43541 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-5916-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| SMAD6 | SNV | Missense_Mutation | c.1213N>T | p.Arg405Cys | p.R405C | O43541 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SMAD6 | deletion | Frame_Shift_Del | c.1296delC | p.Gly433AlafsTer106 | p.G433Afs*106 | O43541 | protein_coding | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |||
| SMAD6 | SNV | Missense_Mutation | novel | c.1163N>A | p.Gly388Asp | p.G388D | O43541 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A1E1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMAD6 | SNV | Missense_Mutation | novel | c.948N>A | p.Phe316Leu | p.F316L | O43541 | protein_coding | tolerated(0.38) | benign(0.006) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| SMAD6 | SNV | Missense_Mutation | novel | c.907N>G | p.Thr303Ala | p.T303A | O43541 | protein_coding | tolerated(0.07) | benign(0.003) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| SMAD6 | SNV | Missense_Mutation | novel | c.1007A>G | p.Tyr336Cys | p.Y336C | O43541 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BG-A221-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=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 |
| Page: 1 |
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