HCSGD entry for HMGB1
1. General information
| Official gene symbol | HMGB1 |
|---|---|
| Entrez ID | 3146 |
| Gene full name | high mobility group box 1 |
| Other gene symbols | HMG1 HMG3 SBP-1 |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IMP | biological_process |
| GO:0000793 | Condensed chromosome | IDA | cellular_component |
| GO:0001773 | Myeloid dendritic cell activation | ISS | biological_process |
| GO:0002407 | Dendritic cell chemotaxis | ISS | biological_process |
| GO:0002437 | Inflammatory response to antigenic stimulus | IEP | biological_process |
| GO:0003677 | DNA binding | IEA | molecular_function |
| GO:0003684 | Damaged DNA binding | ISS | molecular_function |
| GO:0003690 | Double-stranded DNA binding | ISS | molecular_function |
| GO:0003697 | Single-stranded DNA binding | ISS | molecular_function |
| GO:0003700 | Sequence-specific DNA binding transcription factor activity | IDA | molecular_function |
| GO:0005125 | Cytokine activity | ISS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005576 | Extracellular region | TAS | cellular_component |
| GO:0005615 | Extracellular space | IDA | cellular_component |
| GO:0005634 | Nucleus | IDA IEA | cellular_component |
| GO:0005654 | Nucleoplasm | TAS | cellular_component |
| GO:0006265 | DNA topological change | ISS | biological_process |
| GO:0006288 | Base-excision repair, DNA ligation | IDA | biological_process |
| GO:0006309 | Apoptotic DNA fragmentation | TAS | biological_process |
| GO:0006310 | DNA recombination | ISS | biological_process |
| GO:0006357 | Regulation of transcription from RNA polymerase II promoter | IDA | biological_process |
| GO:0006915 | Apoptotic process | TAS | biological_process |
| GO:0006921 | Cellular component disassembly involved in execution phase of apoptosis | TAS | biological_process |
| GO:0008134 | Transcription factor binding | IPI | molecular_function |
| GO:0008301 | DNA binding, bending | IMP ISS | molecular_function |
| GO:0009986 | Cell surface | IDA | cellular_component |
| GO:0017053 | Transcriptional repressor complex | IDA | cellular_component |
| GO:0017055 | Negative regulation of RNA polymerase II transcriptional preinitiation complex assembly | IDA | biological_process |
| GO:0031175 | Neuron projection development | ISS | biological_process |
| GO:0033151 | V(D)J recombination | IDA | biological_process |
| GO:0042056 | Chemoattractant activity | ISS | molecular_function |
| GO:0043065 | Positive regulation of apoptotic process | IDA | biological_process |
| GO:0043280 | Positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | IDA | biological_process |
| GO:0043388 | Positive regulation of DNA binding | IDA | biological_process |
| GO:0045087 | Innate immune response | TAS | biological_process |
| GO:0045944 | Positive regulation of transcription from RNA polymerase II promoter | IDA | biological_process |
| GO:0050786 | RAGE receptor binding | ISS | molecular_function |
| GO:0050918 | Positive chemotaxis | ISS | biological_process |
| GO:0051103 | DNA ligation involved in DNA repair | ISS | biological_process |
| GO:0070491 | Repressing transcription factor binding | IPI | molecular_function |
| GO:2000426 | Negative regulation of apoptotic cell clearance | 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 |
|---|---|---|---|
| 0.9932101706 | 0.0053394742 | 0.9999902473 | 0.1480930453 |
- 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 | -0.3420586649 |
| GSE13712_SHEAR | Up | 0.0183675352 |
| GSE13712_STATIC | Down | -0.3313173106 |
| GSE19018 | Down | -0.5920106288 |
| GSE19899_A1 | Down | -1.0201462737 |
| GSE19899_A2 | Down | -1.1400710989 |
| PubMed_21979375_A1 | Down | -0.8126962808 |
| PubMed_21979375_A2 | Down | -1.1999921735 |
| GSE35957 | Down | -0.5471255953 |
| GSE36640 | Down | -1.2876339671 |
| GSE54402 | Down | -0.1822976538 |
| GSE9593 | Down | -0.7648697745 |
| GSE43922 | Up | 0.0275441049 |
| GSE24585 | Down | -0.1163683707 |
| GSE37065 | Up | 0.3081184465 |
| GSE28863_A1 | Down | -0.0491465012 |
| GSE28863_A2 | Down | -0.0905486770 |
| GSE28863_A3 | Up | 0.1740594262 |
| GSE28863_A4 | Down | -0.0350100716 |
| GSE48662 | Down | -0.2675824185 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Name | Drug | Accession number |
|---|---|---|
| CTI-01 | DB05869 | - |
- MicroRNAs
- mirTarBase
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-22-3p | MIMAT0000077 | MIRT007157 | Luciferase reporter assay//qRT-PCR//Western blot | Functional MTI | 23303785 |
| hsa-miR-193b-3p | MIMAT0002819 | MIRT016305 | Microarray | Functional MTI (Weak) | 20304954 |
| hsa-miR-877-3p | MIMAT0004950 | MIRT037020 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-652-3p | MIMAT0003322 | MIRT039473 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-18a-3p | MIMAT0002891 | MIRT040864 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-181d-5p | MIMAT0002821 | MIRT041163 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-148b-3p | MIMAT0000759 | MIRT043587 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-328-3p | MIMAT0000752 | MIRT043798 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-let-7g-5p | MIMAT0000414 | MIRT046564 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-148a-3p | MIMAT0000243 | MIRT048039 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-100-5p | MIMAT0000098 | MIRT048569 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-92a-3p | MIMAT0000092 | MIRT049759 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-26b-5p | MIMAT0000083 | MIRT050047 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-let-7e-5p | MIMAT0000066 | MIRT051522 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-let-7b-5p | MIMAT0000063 | MIRT052166 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
No target information from mirRecord
- mirRecord
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 |
|---|---|
| 26851389 | Placental membrane aging and HMGB1 signaling associated with human parturition |
| 26851389 | Bioinformatics analysis of differentially expressed SASP genes revealed HMGB1 signaling among the top pathways involved in labor |
| 26851389 | Further, we show that recombinant HMGB1 upregulates the expression of genes associated with parturition in myometrial cells |
| 26522327 | Inflammatory signal-mediated release of high-mobility group box 1 (HMGB1) is a damage-associated molecular pattern or alarmin |
| 26522327 | The inflammatory functions of HMGB1 have been extensively investigated; however, less is known about the mechanisms controlling HMGB1 release |
| 26522327 | We show that SIRT1, the human homolog of the Saccharomyces cerevisiae protein silent information regulator 2, which is involved in cellular senescence and possibly the response to inflammation, forms a stable complex with HMGB1 in murine macrophage RAW264 |
| 26522327 | SIRT1 directly interacted with HMGB1 via its N-terminal lysine residues (28-30), and thereby inhibited HMGB1 release to improve survival in an experimental model of sepsis |
| 26522327 | By contrast, inflammatory stimuli such as lipopolysaccharide (LPS) and tumor necrosis factor-alpha promoted HMGB1 release by provoking its dissociation from SIRT1 dependent on acetylation, thereby increasing the association between HMGB1 and chromosome region maintenance 1, leading to HMGB1 translocation |
| 26522327 | 7%) during endotoxemia more than infection with wild-type SIRT1 and HMGB1-expressing adenovirus, indicating that the acetylation-dependent interaction between HMGB1 and SIRT1 is critical for LPS-induced lethality |
| 26522327 | Taken together, we propose that SIRT1 forms an anti-inflammatory complex with HMGB1, allowing cells to bypass the response to inflammation |
| 25572145 | Another observation in the present study is the significant up-regulation of key senescence messaging factors regulated by NF-kappaB namely interleukin (IL)-6, IL-8, high-mobility group protein A (HMGA)1 and B (HMGB)1 in E2-transfected cells treated with TNF-alpha |
| 23649808 | HMGB1 (high mobility group box 1) modulates gene expression in the nucleus, but certain immune cells secrete HMGB1 as an extracellular Alarmin to signal tissue damage |
| 23649808 | We show that nuclear HMGB1 relocalized to the extracellular milieu in senescent human and mouse cells in culture and in vivo |
| 23649808 | In contrast to cytokine secretion, HMGB1 redistribution required the p53 tumor suppressor, but not its activator ATM |
| 23649808 | Moreover, altered HMGB1 expression induced a p53-dependent senescent growth arrest |
| 23649808 | Senescent fibroblasts secreted oxidized HMGB1, which stimulated cytokine secretion through TLR-4 signaling |
| 23649808 | HMGB1 depletion, HMGB1 blocking antibody, or TLR-4 inhibition attenuated senescence-associated IL-6 secretion, and exogenous HMGB1 stimulated NF-kappaB activity and restored IL-6 secretion to HMGB1-depleted cells |
| 23649808 | Our findings identify senescence as a novel biological setting in which HMGB1 functions and link HMGB1 redistribution to p53 activity and senescence-associated inflammation |
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