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Gene: SMAD7 |
Gene summary for SMAD7 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMAD7 | Gene ID | 4092 |
| Gene name | SMAD family member 7 | |
| Gene Alias | CRCS3 | |
| Cytomap | 18q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | O15105 |
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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 |
| 4092 | SMAD7 | C04 | Human | Oral cavity | OSCC | 6.23e-03 | 2.93e-01 | 0.2633 |
| 4092 | SMAD7 | C30 | Human | Oral cavity | OSCC | 3.22e-15 | 6.80e-01 | 0.3055 |
| 4092 | SMAD7 | C38 | Human | Oral cavity | OSCC | 1.26e-08 | 7.53e-01 | 0.172 |
| 4092 | SMAD7 | C51 | Human | Oral cavity | OSCC | 5.63e-04 | 2.40e-01 | 0.2674 |
| 4092 | SMAD7 | C06 | Human | Oral cavity | OSCC | 3.64e-03 | 4.15e-01 | 0.2699 |
| 4092 | SMAD7 | C09 | Human | Oral cavity | OSCC | 7.08e-04 | 1.93e-01 | 0.1431 |
| 4092 | SMAD7 | EOLP-1 | Human | Oral cavity | EOLP | 4.36e-03 | 1.79e-01 | -0.0202 |
| 4092 | SMAD7 | NEOLP-1 | Human | Oral cavity | NEOLP | 6.06e-09 | 3.61e-01 | -0.0194 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:004316120 | Oral cavity | OSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 285/7305 | 412/18723 | 5.68e-36 | 5.99e-33 | 285 |
| GO:000989620 | Oral cavity | OSCC | positive regulation of catabolic process | 307/7305 | 492/18723 | 2.29e-26 | 7.64e-24 | 307 |
| GO:003133120 | Oral cavity | OSCC | positive regulation of cellular catabolic process | 273/7305 | 427/18723 | 6.39e-26 | 2.02e-23 | 273 |
| GO:004217620 | Oral cavity | OSCC | regulation of protein catabolic process | 254/7305 | 391/18723 | 1.07e-25 | 3.22e-23 | 254 |
| GO:004586220 | Oral cavity | OSCC | positive regulation of proteolysis | 236/7305 | 372/18723 | 6.53e-22 | 1.38e-19 | 236 |
| GO:190336220 | Oral cavity | OSCC | regulation of cellular protein catabolic process | 174/7305 | 255/18723 | 2.04e-21 | 3.70e-19 | 174 |
| GO:190332020 | Oral cavity | OSCC | regulation of protein modification by small protein conjugation or removal | 165/7305 | 242/18723 | 2.52e-20 | 3.99e-18 | 165 |
| GO:003164720 | Oral cavity | OSCC | regulation of protein stability | 193/7305 | 298/18723 | 1.30e-19 | 1.95e-17 | 193 |
| GO:190305020 | Oral cavity | OSCC | regulation of proteolysis involved in cellular protein catabolic process | 152/7305 | 221/18723 | 2.16e-19 | 3.15e-17 | 152 |
| GO:006113620 | Oral cavity | OSCC | regulation of proteasomal protein catabolic process | 132/7305 | 187/18723 | 1.57e-18 | 1.81e-16 | 132 |
| GO:200005820 | Oral cavity | OSCC | regulation of ubiquitin-dependent protein catabolic process | 118/7305 | 164/18723 | 9.37e-18 | 9.27e-16 | 118 |
| GO:003139620 | Oral cavity | OSCC | regulation of protein ubiquitination | 143/7305 | 210/18723 | 1.01e-17 | 9.80e-16 | 143 |
| GO:003243420 | Oral cavity | OSCC | regulation of proteasomal ubiquitin-dependent protein catabolic process | 100/7305 | 134/18723 | 4.72e-17 | 4.04e-15 | 100 |
| GO:004573220 | Oral cavity | OSCC | positive regulation of protein catabolic process | 150/7305 | 231/18723 | 1.06e-15 | 7.64e-14 | 150 |
| GO:005134820 | Oral cavity | OSCC | negative regulation of transferase activity | 165/7305 | 268/18723 | 5.02e-14 | 2.74e-12 | 165 |
| GO:001604917 | Oral cavity | OSCC | cell growth | 268/7305 | 482/18723 | 6.55e-14 | 3.51e-12 | 268 |
| GO:190336420 | Oral cavity | OSCC | positive regulation of cellular protein catabolic process | 106/7305 | 155/18723 | 1.07e-13 | 5.53e-12 | 106 |
| GO:001056320 | Oral cavity | OSCC | negative regulation of phosphorus metabolic process | 246/7305 | 442/18723 | 6.12e-13 | 2.89e-11 | 246 |
| GO:004593620 | Oral cavity | OSCC | negative regulation of phosphate metabolic process | 245/7305 | 441/18723 | 8.85e-13 | 4.09e-11 | 245 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0439016 | Oral cavity | OSCC | Hippo signaling pathway | 86/3704 | 157/8465 | 3.30e-03 | 8.24e-03 | 4.20e-03 | 86 |
| hsa043506 | Oral cavity | OSCC | TGF-beta signaling pathway | 60/3704 | 108/8465 | 8.66e-03 | 1.97e-02 | 1.00e-02 | 60 |
| hsa0439017 | Oral cavity | OSCC | Hippo signaling pathway | 86/3704 | 157/8465 | 3.30e-03 | 8.24e-03 | 4.20e-03 | 86 |
| hsa0435013 | Oral cavity | OSCC | TGF-beta signaling pathway | 60/3704 | 108/8465 | 8.66e-03 | 1.97e-02 | 1.00e-02 | 60 |
| hsa0435022 | Oral cavity | EOLP | TGF-beta signaling pathway | 29/1218 | 108/8465 | 4.81e-04 | 1.92e-03 | 1.13e-03 | 29 |
| hsa0435032 | Oral cavity | EOLP | TGF-beta signaling pathway | 29/1218 | 108/8465 | 4.81e-04 | 1.92e-03 | 1.13e-03 | 29 |
| hsa0435041 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
| hsa0439025 | Oral cavity | NEOLP | Hippo signaling pathway | 35/1112 | 157/8465 | 9.91e-04 | 4.85e-03 | 3.05e-03 | 35 |
| hsa0435051 | Oral cavity | NEOLP | TGF-beta signaling pathway | 28/1112 | 108/8465 | 2.46e-04 | 1.62e-03 | 1.02e-03 | 28 |
| hsa0439035 | Oral cavity | NEOLP | Hippo signaling pathway | 35/1112 | 157/8465 | 9.91e-04 | 4.85e-03 | 3.05e-03 | 35 |
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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 |
| SMAD7 | A.X | Stomach | ADJ | AL627171.2,CPSF1,CTSB, etc. | 1.19e-02 |  |
| SMAD7 | D | Stomach | ADJ | AL627171.2,CPSF1,CTSB, etc. | 2.40e-03 | |
| SMAD7 | GOB | Stomach | ADJ | AL627171.2,CPSF1,CTSB, etc. | 0.00e+00 | |
| SMAD7 | MESC | Stomach | CSG | AL627171.2,CPSF1,CTSB, etc. | 4.29e-03 |  |
| SMAD7 | D | Stomach | CSG | AL627171.2,CPSF1,CTSB, etc. | 1.95e-02 | |
| SMAD7 | PARI | Stomach | CSG | AL627171.2,CPSF1,CTSB, etc. | 5.26e-03 | |
| SMAD7 | D | Stomach | GC | AL627171.2,CPSF1,CTSB, etc. | 0.00e+00 |  |
| SMAD7 | PARI | Stomach | GC | AL627171.2,CPSF1,CTSB, etc. | 3.00e-03 | |
| SMAD7 | GOB | Stomach | GC | AL627171.2,CPSF1,CTSB, etc. | 0.00e+00 | |
| SMAD7 | PARI | Stomach | WIM | AL627171.2,CPSF1,CTSB, etc. | 0.00e+00 |  |
| ∗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 |
| SMAD7 | SNV | Missense_Mutation | novel | c.854N>T | p.Asp285Val | p.D285V | O15105 | protein_coding | deleterious(0.02) | benign(0.222) | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
| SMAD7 | SNV | Missense_Mutation | c.484N>C | p.Val162Leu | p.V162L | O15105 | protein_coding | tolerated(1) | benign(0.02) | TCGA-AO-A124-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SMAD7 | insertion | Nonsense_Mutation | novel | c.617_618insCATTTAACAAGTAACTCCATTTCCTGCCTGCCTCTATTG | p.Ser206_Pro207insIleTerGlnValThrProPheProAlaCysLeuTyrCys | p.S206_P207insI*QVTPFPACLYC | O15105 | protein_coding | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |||
| SMAD7 | insertion | In_Frame_Ins | novel | c.854_855insCGTTTTTTTTTTGTTTGTTGG | p.Asp285_Ile286insValPhePheLeuPheValGly | p.D285_I286insVFFLFVG | O15105 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| SMAD7 | SNV | Missense_Mutation | c.850N>A | p.Leu284Met | p.L284M | O15105 | protein_coding | deleterious(0.01) | probably_damaging(0.979) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| SMAD7 | SNV | Missense_Mutation | c.920N>T | p.Ser307Ile | p.S307I | O15105 | protein_coding | deleterious(0) | possibly_damaging(0.886) | TCGA-DY-A1DD-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SMAD7 | deletion | Frame_Shift_Del | c.626delN | p.Pro209LeufsTer115 | p.P209Lfs*115 | O15105 | protein_coding | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
| SMAD7 | deletion | Frame_Shift_Del | c.626delC | p.Pro209LeufsTer115 | p.P209Lfs*115 | O15105 | protein_coding | TCGA-EI-6507-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |||
| SMAD7 | SNV | Missense_Mutation | novel | c.688N>T | p.Pro230Ser | p.P230S | O15105 | protein_coding | tolerated(0.74) | benign(0.017) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| SMAD7 | SNV | Missense_Mutation | c.1150G>A | p.Glu384Lys | p.E384K | O15105 | protein_coding | deleterious(0.01) | possibly_damaging(0.65) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | 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 |
| 4092 | SMAD7 | KINASE | GED-0301 | MONGERSEN SODIUM | ||
| 4092 | SMAD7 | KINASE | TPA | ALTEPLASE | 15033458 |
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