Gene description for HMGB1
Gene name high mobility group box 1
Gene symbol HMGB1
Other names/aliases HMG1
HMG3
SBP-1
Species Homo sapiens
 Database cross references - HMGB1
ExoCarta ExoCarta_3146
Entrez Gene 3146
HGNC 4983
MIM 163905
UniProt P09429  
 HMGB1 identified in exosomes derived from the following tissue/cell type
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Neuroblastoma cells 25944692    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Squamous carcinoma cells 20124223    
 Gene ontology annotations for HMGB1
Molecular Function
    single-stranded DNA binding GO:0003697 ISS
    cytokine activity GO:0005125 ISS
    protein binding GO:0005515 IPI
    double-stranded DNA binding GO:0003690 ISS
    repressing transcription factor binding GO:0070491 IPI
    poly(A) RNA binding GO:0044822 IDA
    damaged DNA binding GO:0003684 ISS
    sequence-specific DNA binding transcription factor activity GO:0003700 IDA
    chemoattractant activity GO:0042056 ISS
    RAGE receptor binding GO:0050786 ISS
    chromatin binding GO:0003682 IBA
    DNA binding, bending GO:0008301 ISS
    transcription factor binding GO:0008134 IPI
Biological Process
    chromatin remodeling GO:0006338 IBA
    positive regulation of transcription from RNA polymerase II promoter GO:0045944 IDA
    DNA topological change GO:0006265 ISS
    apoptotic DNA fragmentation GO:0006309 TAS
    apoptotic process GO:0006915 TAS
    base-excision repair, DNA ligation GO:0006288 IDA
    inflammatory response GO:0006954 IDA
    cellular component disassembly involved in execution phase of apoptosis GO:0006921 TAS
    myeloid dendritic cell activation GO:0001773 ISS
    inflammatory response to antigenic stimulus GO:0002437 IEP
    positive regulation of cysteine-type endopeptidase activity involved in apoptotic process GO:0043280 IDA
    regulation of transcription from RNA polymerase II promoter GO:0006357 IDA
    programmed cell death GO:0012501 TAS
    negative regulation of blood vessel endothelial cell migration GO:0043537 IDA
    positive regulation of apoptotic process GO:0043065 IDA
    DNA recombination GO:0006310 ISS
    positive chemotaxis GO:0050918 ISS
    V(D)J recombination GO:0033151 IDA
    negative regulation of RNA polymerase II transcriptional preinitiation complex assembly GO:0017055 IDA
    positive regulation of DNA binding GO:0043388 IDA
    dendritic cell chemotaxis GO:0002407 ISS
    innate immune response GO:0045087 TAS
    DNA ligation involved in DNA repair GO:0051103 ISS
    negative regulation of apoptotic cell clearance GO:2000426 IEA
    negative regulation of transcription from RNA polymerase II promoter GO:0000122 IMP
    neuron projection development GO:0031175 ISS
Subcellular Localization
    transcriptional repressor complex GO:0017053 IDA
    nucleus GO:0005634 IDA
    nucleoplasm GO:0005654 TAS
    cell surface GO:0009986 IDA
    extracellular space GO:0005615 IDA
    condensed chromosome GO:0000793 IDA
    extracellular region GO:0005576 TAS
 Experiment description of studies that identified HMGB1 in exosomes
1
Experiment ID 282
ISEV standards
CEM
EV Biophysical techniques
Alix|TSG101
EV Cytosolic markers
CD63|CD81|EpCAM
EV Membrane markers
EV Negative markers
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
2
Experiment ID 283
ISEV standards
CEM
EV Biophysical techniques
Alix|TSG101
EV Cytosolic markers
CD63|CD81|EpCAM
EV Membrane markers
EV Negative markers
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
3
Experiment ID 285
ISEV standards
CEM
EV Biophysical techniques
Alix|TSG101
EV Cytosolic markers
CD63|CD81|EpCAM
EV Membrane markers
EV Negative markers
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
4
Experiment ID 286
ISEV standards
CEM
EV Biophysical techniques
Alix|TSG101
EV Cytosolic markers
CD63|CD81|EpCAM
EV Membrane markers
EV Negative markers
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
5
Experiment ID 224
ISEV standards
EM|AFM
EV Biophysical techniques
Alix|TSG101
EV Cytosolic markers
CD63|CD81
EV Membrane markers
GOLGA2
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25944692    
Organism Homo sapiens
Experiment description Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes
Authors Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S
Journal name Oncotarget
Publication year 2015
Sample Neuroblastoma cells
Sample name SH-SY5Y
Isolation/purification methods Differential centrifugation
Ultracentrifugation
OptiPrep density gradient
Flotation density 1.10 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
6
Experiment ID 211
ISEV standards
EM
EV Biophysical techniques
TSG101|Alix
EV Cytosolic markers
EpCAM|TFRC
EV Membrane markers
cytochrome c|GOLGA2
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name IGROV1
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
7
Experiment ID 212
ISEV standards
CEM
EV Biophysical techniques
TSG101|Alix
EV Cytosolic markers
EpCAM|TFRC
EV Membrane markers
Cytochrome C|GOLGA2
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name OVCAR-3
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
8
Experiment ID 191
ISEV standards
EV Biophysical techniques
Alix
EV Cytosolic markers
CD81|CD9
EV Membrane markers
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 20124223    
Organism Homo sapiens
Experiment description Hypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes.
Authors Park JE, Tan HS, Datta A, Lai RC, Zhang H, Meng W, Lim SK, Sze SK.
Journal name Mol Cell Proteomics
Publication year 2010
Sample Squamous carcinoma cells
Sample name Squamous carcinoma cell (A431)
Isolation/purification methods Differential centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for HMGB1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 PLAT 5327
Invitro Homo sapiens
Affinity Capture-MS Homo sapiens
2 HOXB3 3213
Reconstituted Complex Homo sapiens
3 TLE1  
Invitro Homo sapiens
Affinity Capture-MS Homo sapiens
4 C14orf1 11161
Two-hybrid Homo sapiens
5 RIF1  
Two-hybrid Homo sapiens
6 AES 166
Invitro Homo sapiens
7 RB1 5925
Invitro Homo sapiens
Affinity Capture-MS Homo sapiens
8 CSNK1A1 1452
Co-purification Homo sapiens
9 HOXD9  
Reconstituted Complex Homo sapiens
10 HOXD11  
Reconstituted Complex Homo sapiens
11 RELA  
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
12 POU5F1  
Affinity Capture-Western Homo sapiens
13 UNC119  
Two-hybrid Homo sapiens
14 HOXC6  
Reconstituted Complex Homo sapiens
15 CSPG3  
Reconstituted Complex Homo sapiens
16 PLG 5340
Reconstituted Complex Homo sapiens
17 TP73  
Invitro Homo sapiens
18 PRKDC 5591
Invitro Homo sapiens
19 HNRNPK 3190
Invitro Homo sapiens
Affinity Capture-MS Homo sapiens
20 HOXD10  
Reconstituted Complex Homo sapiens
21 HOXD8  
Reconstituted Complex Homo sapiens
22 TBP  
Invitro Homo sapiens
23 HOXB1  
Reconstituted Complex Homo sapiens
24 RAG1  
Invitro Homo sapiens
Invivo Homo sapiens
25 TP53  
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
26 PTPRZ1  
Reconstituted Complex Homo sapiens
27 HOXD3  
Reconstituted Complex Homo sapiens
28 NFKB1 4790
Reconstituted Complex Homo sapiens
29 TAF1  
Invitro Homo sapiens
30 AR 367
Invivo Homo sapiens
Invitro Homo sapiens
31 CRMP1 1400
Two-hybrid Homo sapiens
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