HCSGD entry for MMP13
1. General information
| Official gene symbol | MMP13 |
|---|---|
| Entrez ID | 4322 |
| Gene full name | matrix metallopeptidase 13 (collagenase 3) |
| Other gene symbols | CLG3 MANDP1 |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
This gene isn't in PPI subnetwork.
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0004222 | Metalloendopeptidase activity | IEA | molecular_function |
| GO:0005509 | Calcium ion binding | IEA | molecular_function |
| GO:0005576 | Extracellular region | TAS | cellular_component |
| GO:0005578 | Proteinaceous extracellular matrix | IEA | cellular_component |
| GO:0005615 | Extracellular space | TAS | cellular_component |
| GO:0006508 | Proteolysis | IEA | biological_process |
| GO:0008270 | Zinc ion binding | IEA | molecular_function |
| GO:0022617 | Extracellular matrix disassembly | TAS | biological_process |
| GO:0030198 | Extracellular matrix organization | TAS | biological_process |
| GO:0030282 | Bone mineralization | IEA | biological_process |
| GO:0030574 | Collagen catabolic process | TAS | biological_process |
| GO:0031012 | Extracellular matrix | IEA | cellular_component |
| GO:0044267 | Cellular protein metabolic process | IEA | biological_process |
| GO:0051216 | Cartilage development | IEA | biological_process |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.4005042134 | 0.5428409711 | 0.9999902473 | 1.0000000000 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | 0.0000000000 |
| GSE13712_SHEAR | Up | 0.1313129769 |
| GSE13712_STATIC | Down | -0.1896030130 |
| GSE19018 | Down | -0.0351709788 |
| GSE19899_A1 | Up | 0.0464759094 |
| GSE19899_A2 | Up | 0.0841249450 |
| PubMed_21979375_A1 | Up | 0.4897512516 |
| PubMed_21979375_A2 | Up | 0.2690455590 |
| GSE35957 | Down | -0.1768769282 |
| GSE36640 | Down | -0.1145207977 |
| GSE54402 | Up | 0.2832442650 |
| GSE9593 | Down | -0.3360780860 |
| GSE43922 | Up | 0.0132665551 |
| GSE24585 | Up | 0.3330550727 |
| GSE37065 | Down | -0.3229782540 |
| GSE28863_A1 | Down | -0.0091180144 |
| GSE28863_A2 | Up | 0.0521168071 |
| GSE28863_A3 | Up | 0.1239614030 |
| GSE28863_A4 | Down | -0.0654584289 |
| GSE48662 | Up | 0.0511372035 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
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- Drugs
Name | Drug | Accession number |
|---|---|---|
| Marimastat | DB00786 | APRD00559 |
| 3-Methylpyridine | DB01996 | EXPT00181 |
| 2-{4-[4-(4-Chloro-Phenoxy)-Benzenesulfonyl]-Tetrahydro-Pyran-4-Yl}-N-Hydroxy-Acetamide | DB02049 | EXPT00849 |
| WAY-151693 | DB02071 | EXPT03240 |
| Hydroxyaminovaline | DB02697 | EXPT01693 |
| 1-Methyloxy-4-Sulfone-Benzene | DB03033 | EXPT02236 |
| PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-(3-METHYL-BENZYLAMIDE) | DB04759 | - |
| PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-(4-FLUORO-3-METHYL-BENZYLAMIDE) | DB04760 | - |
| PYRIMIDINE-4,6-DICARBOXYLIC ACID BIS-[(PYRIDIN-3-YLMETHYL)-AMIDE] | DB04761 | - |
| TERT-BUTYL 4-({[4-(BUT-2-YN-1-YLAMINO)PHENYL]SULFONYL}METHYL)-4-[(HYDROXYAMINO)CARBONYL]PIPERIDINE-1-CARBOXYLATE | DB07013 | - |
| 4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID | DB07827 | - |
| 5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE | DB08388 | - |
| 4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE | DB08490 | - |
| BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE | DB08561 | - |
- MicroRNAs
- mirTarBase
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-9-5p | MIMAT0000441 | MIRT000025 | Luciferase reporter assay | Functional MTI | 19008124 |
| hsa-miR-27a-3p | MIMAT0000084 | MIRT006557 | qRT-PCR | Functional MTI (Weak) | 19948051 |
| hsa-miR-100-5p | MIMAT0000098 | MIRT003420 | Microarray//qRT-PCR//Western blot | Functional MTI | 19396866 |
| hsa-miR-27b-3p | MIMAT0000419 | MIRT003427 | ELISA//Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 20131257 |
| hsa-miR-140-5p | MIMAT0000431 | MIRT003961 | Microarray | Functional MTI (Weak) | 17875710 |
| hsa-miR-140-5p | MIMAT0000431 | MIRT003961 | qRT-PCR | Functional MTI (Weak) | 19948051 |
| hsa-miR-125b-5p | MIMAT0000423 | MIRT006990 | Luciferase reporter assay | Functional MTI | 22782903 |
| hsa-miR-143-3p | MIMAT0000435 | MIRT021540 | Western blot;Microarray | Functional MTI | 21427707 |
| hsa-miR-132-3p | MIMAT0000426 | MIRT021796 | Microarray | Functional MTI (Weak) | 17612493 |
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- mirRecord
- mirRecord
MicroRNA name | mirBase ID | Target site number | MiRNA mature ID | Test method inter | MiRNA regulation site | Reporter target site | Pubmed ID |
|---|---|---|---|---|---|---|---|
| hsa-miR-27b-3p | MIMAT0000419 | 1 | hsa-miR-27b | {ELISA} | {overexpression by miRNA precursor transfection} | 20131257 |
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6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 4 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 25819580 | Real-time PCR analysis showed that matrix metalloproteinase 1 (MMP-1) and MMP-13 mRNA were significantly increased by SIRT6 inhibition |
| 24964749 | The inhibition of ERCC1 by siRNA increased the expression of matrix metallopeptidase 13 and decreased collagen type II |
| 22454193 | RESULTS: Chondrocytes stimulated by IL-1beta showed increased MMP-1, MMP-3, and MMP-13 levels, whereas the expression of COL2A1 and ACAN decreased |
| 22454193 | However, in cells co-treated with IL-1beta and Rg3, the levels of MMP-1 and MMP-13 were lower than in cells treated with IL-1beta alone, and COL2A1 and ACAN expression levels recovered from the low values seen when cultured only in the presence of IL-1beta |
| 17498290 | RNA from tissue and cultured cells was used for real-time polymerase chain reaction analysis for matrix metalloproteinase-13, ADAMTS 5 (a disintegrin and metalloprotease with thrombospondin motifs 5), and P16INK4A |
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