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Gene: SMAD2 |
Gene summary for SMAD2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SMAD2 | Gene ID | 4087 |
Gene name | SMAD family member 2 | |
Gene Alias | JV18 | |
Cytomap | 18q21.1 | |
Gene Type | protein-coding | GO ID | GO:0000578 | UniProtAcc | Q15796 |
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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 |
4087 | SMAD2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.22e-27 | -7.62e-01 | 0.0155 |
4087 | SMAD2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.69e-06 | -5.35e-01 | -0.1808 |
4087 | SMAD2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.15e-04 | -8.75e-01 | 0.0216 |
4087 | SMAD2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.30e-12 | -7.62e-01 | -0.1207 |
4087 | SMAD2 | HTA11_83_2000001011 | Human | Colorectum | SER | 5.00e-05 | -5.68e-01 | -0.1526 |
4087 | SMAD2 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.33e-20 | -5.97e-01 | -0.1464 |
4087 | SMAD2 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.22e-16 | -5.56e-01 | -0.1001 |
4087 | SMAD2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.33e-07 | -5.07e-01 | -0.059 |
4087 | SMAD2 | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.07e-03 | -7.82e-01 | -0.1462 |
4087 | SMAD2 | HTA11_7862_2000001011 | Human | Colorectum | AD | 3.35e-02 | -4.18e-01 | -0.0179 |
4087 | SMAD2 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.09e-08 | -5.55e-01 | 0.096 |
4087 | SMAD2 | HTA11_4255_2000001011 | Human | Colorectum | SER | 2.11e-03 | -7.23e-01 | 0.0446 |
4087 | SMAD2 | HTA11_9408_2000001011 | Human | Colorectum | AD | 7.57e-03 | -8.53e-01 | 0.0451 |
4087 | SMAD2 | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.80e-07 | -8.35e-01 | 0.0528 |
4087 | SMAD2 | HTA11_10623_2000001011 | Human | Colorectum | AD | 2.54e-02 | -6.05e-01 | -0.0177 |
4087 | SMAD2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.55e-12 | -7.17e-01 | 0.0338 |
4087 | SMAD2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.41e-28 | -7.10e-01 | 0.0674 |
4087 | SMAD2 | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.31e-02 | -6.32e-01 | 0.0112 |
4087 | SMAD2 | HTA11_11156_2000001011 | Human | Colorectum | AD | 3.40e-02 | -8.79e-01 | 0.0397 |
4087 | SMAD2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.25e-03 | -5.26e-01 | 0.0588 |
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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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
GO:0051098 | Colorectum | AD | regulation of binding | 126/3918 | 363/18723 | 6.01e-10 | 4.88e-08 | 126 |
GO:0009743 | Colorectum | AD | response to carbohydrate | 86/3918 | 253/18723 | 8.43e-07 | 2.90e-05 | 86 |
GO:0042060 | Colorectum | AD | wound healing | 128/3918 | 422/18723 | 2.73e-06 | 7.89e-05 | 128 |
GO:0034284 | Colorectum | AD | response to monosaccharide | 76/3918 | 225/18723 | 4.64e-06 | 1.23e-04 | 76 |
GO:0009746 | Colorectum | AD | response to hexose | 73/3918 | 219/18723 | 1.20e-05 | 2.65e-04 | 73 |
GO:0009749 | Colorectum | AD | response to glucose | 71/3918 | 212/18723 | 1.31e-05 | 2.85e-04 | 71 |
GO:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
GO:0009306 | Colorectum | AD | protein secretion | 105/3918 | 359/18723 | 1.05e-04 | 1.57e-03 | 105 |
GO:0035592 | Colorectum | AD | establishment of protein localization to extracellular region | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
GO:0071692 | Colorectum | AD | protein localization to extracellular region | 106/3918 | 368/18723 | 1.86e-04 | 2.49e-03 | 106 |
GO:0030073 | Colorectum | AD | insulin secretion | 61/3918 | 195/18723 | 4.28e-04 | 4.81e-03 | 61 |
GO:0015833 | Colorectum | AD | peptide transport | 77/3918 | 264/18723 | 8.90e-04 | 8.60e-03 | 77 |
GO:0007178 | Colorectum | AD | transmembrane receptor protein serine/threonine kinase signaling pathway | 99/3918 | 355/18723 | 9.92e-04 | 9.28e-03 | 99 |
GO:0009791 | Colorectum | AD | post-embryonic development | 29/3918 | 80/18723 | 1.13e-03 | 1.03e-02 | 29 |
GO:0071559 | Colorectum | AD | response to transforming growth factor beta | 74/3918 | 256/18723 | 1.45e-03 | 1.23e-02 | 74 |
GO:0071560 | Colorectum | AD | cellular response to transforming growth factor beta stimulus | 72/3918 | 250/18723 | 1.85e-03 | 1.52e-02 | 72 |
GO:0007179 | Colorectum | AD | transforming growth factor beta receptor signaling pathway | 59/3918 | 198/18723 | 1.94e-03 | 1.58e-02 | 59 |
GO:0030072 | Colorectum | AD | peptide hormone secretion | 68/3918 | 236/18723 | 2.39e-03 | 1.85e-02 | 68 |
GO:0035196 | Colorectum | AD | production of miRNAs involved in gene silencing by miRNA | 20/3918 | 52/18723 | 2.87e-03 | 2.14e-02 | 20 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa05210 | Colorectum | AD | Colorectal cancer | 35/2092 | 86/8465 | 7.54e-04 | 5.49e-03 | 3.50e-03 | 35 |
hsa05205 | Colorectum | AD | Proteoglycans in cancer | 70/2092 | 205/8465 | 1.37e-03 | 8.46e-03 | 5.39e-03 | 70 |
hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa05166 | Colorectum | AD | Human T-cell leukemia virus 1 infection | 72/2092 | 222/8465 | 5.24e-03 | 2.44e-02 | 1.55e-02 | 72 |
hsa04218 | Colorectum | AD | Cellular senescence | 53/2092 | 156/8465 | 5.55e-03 | 2.48e-02 | 1.58e-02 | 53 |
hsa05212 | Colorectum | AD | Pancreatic cancer | 29/2092 | 76/8465 | 6.25e-03 | 2.68e-02 | 1.71e-02 | 29 |
hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa041441 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa052101 | Colorectum | AD | Colorectal cancer | 35/2092 | 86/8465 | 7.54e-04 | 5.49e-03 | 3.50e-03 | 35 |
hsa052051 | Colorectum | AD | Proteoglycans in cancer | 70/2092 | 205/8465 | 1.37e-03 | 8.46e-03 | 5.39e-03 | 70 |
hsa052251 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa051661 | Colorectum | AD | Human T-cell leukemia virus 1 infection | 72/2092 | 222/8465 | 5.24e-03 | 2.44e-02 | 1.55e-02 | 72 |
hsa042181 | Colorectum | AD | Cellular senescence | 53/2092 | 156/8465 | 5.55e-03 | 2.48e-02 | 1.58e-02 | 53 |
hsa052121 | Colorectum | AD | Pancreatic cancer | 29/2092 | 76/8465 | 6.25e-03 | 2.68e-02 | 1.71e-02 | 29 |
hsa054152 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
hsa041442 | Colorectum | SER | Endocytosis | 81/1580 | 251/8465 | 1.14e-07 | 2.36e-06 | 1.71e-06 | 81 |
hsa052052 | Colorectum | SER | Proteoglycans in cancer | 58/1580 | 205/8465 | 4.37e-04 | 3.82e-03 | 2.77e-03 | 58 |
hsa04350 | Colorectum | SER | TGF-beta signaling pathway | 31/1580 | 108/8465 | 7.00e-03 | 3.77e-02 | 2.74e-02 | 31 |
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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 |
∗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 |
SMAD2 | SNV | Missense_Mutation | novel | c.1370G>C | p.Gly457Ala | p.G457A | Q15796 | protein_coding | deleterious(0) | possibly_damaging(0.62) | TCGA-96-A4JK-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | gemcitabine | CR |
SMAD2 | insertion | In_Frame_Ins | novel | c.1159_1160insTAGGCTGTAATCTGAAGATCTTCAACA | p.Asn386_Asn387insIleGlyCysAsnLeuLysIlePheAsn | p.N386_N387insIGCNLKIFN | Q15796 | protein_coding | TCGA-75-6214-01 | Lung | lung adenocarcinoma | Female | Unknown | III/IV | Unknown | Unknown | PD | ||
SMAD2 | SNV | Missense_Mutation | novel | c.1193N>C | p.Val398Ala | p.V398A | Q15796 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-BA-6872-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unspecific | PD | |
SMAD2 | SNV | Missense_Mutation | novel | c.981G>C | p.Met327Ile | p.M327I | Q15796 | protein_coding | tolerated(0.19) | benign(0) | TCGA-CR-6484-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
SMAD2 | SNV | Missense_Mutation | c.1297N>G | p.Ser433Gly | p.S433G | Q15796 | protein_coding | deleterious(0.01) | probably_damaging(0.926) | TCGA-HC-7078-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 7 | Unknown | Unknown | SD | |
SMAD2 | SNV | Missense_Mutation | c.446N>A | p.Cys149Tyr | p.C149Y | Q15796 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-A4QL-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | CR | |
SMAD2 | SNV | Missense_Mutation | c.962G>A | p.Arg321Gln | p.R321Q | Q15796 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-CG-4444-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
SMAD2 | SNV | Missense_Mutation | c.407A>T | p.Asp136Val | p.D136V | Q15796 | protein_coding | deleterious(0.01) | benign(0.33) | TCGA-HU-A4H3-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Chemotherapy | ts-1 | PD | |
SMAD2 | insertion | Frame_Shift_Ins | novel | c.1216_1217insTATTTTACATAAAG | p.Tyr406LeufsTer8 | p.Y406Lfs*8 | Q15796 | protein_coding | TCGA-EL-A3ZG-01 | Thyroid | thyroid carcinoma | Male | <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 |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | GERANIIN | GERANIIN | 26169124 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | DEMETHOXYCURCUMIN | DEMETHOXYCURCUMIN | 23145932 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | ATRA | TRETINOIN | 15799023 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | BLEOMYCIN | BLEOMYCIN | 17274978 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | BISDEMETHOXYCURCUMIN | BISDEMETHOXYCURCUMIN | 23145932 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | HYDROCORTISONE | HYDROCORTISONE | 16644034 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | BLM | BLEOMYCIN | 17274978 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | AMIFOSTINE | AMIFOSTINE | 12410567 | |
4087 | SMAD2 | KINASE, CLINICALLY ACTIONABLE, TRANSCRIPTION FACTOR COMPLEX | CURCUMIN | CURCUMIN | 23145932 |
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