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Fusion gene ID: 16462 |
FusionGeneSummary for HMGB2_PTMA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: HMGB2_PTMA | Fusion gene ID: 16462 | Hgene | Tgene | Gene symbol | HMGB2 | PTMA | Gene ID | 3148 | 5757 |
| Gene name | high mobility group box 2 | prothymosin alpha | |
| Synonyms | HMG2 | TMSA | |
| Cytomap | 4q34.1 | 2q37.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | high mobility group protein B2HMG-2high mobility group protein 2high-mobility group (nonhistone chromosomal) protein 2 | prothymosin alphagene sequence 28prothymosin alpha proteinprothymosin-I+/- | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | P26583 | P06454 | |
| Ensembl transtripts involved in fusion gene | ENST00000296503, ENST00000438704, ENST00000446922, | ENST00000466801, ENST00000409321, ENST00000409115, ENST00000341369, ENST00000409683, ENST00000410064, | |
| Fusion gene scores | * DoF score | 4 X 4 X 1=16 | 17 X 17 X 2=578 |
| # samples | 4 | 18 | |
| ** MAII score | log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(18/578*10)=-1.683072586171 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: HMGB2 [Title/Abstract] AND PTMA [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | HMGB2 | GO:0001938 | positive regulation of endothelial cell proliferation | 19811285 |
| Hgene | HMGB2 | GO:0006357 | regulation of transcription by RNA polymerase II | 7797075 |
| Hgene | HMGB2 | GO:0032075 | positive regulation of nuclease activity | 978439 |
| Hgene | HMGB2 | GO:0043388 | positive regulation of DNA binding | 19965638 |
| Hgene | HMGB2 | GO:0045892 | negative regulation of transcription, DNA-templated | 9636147 |
| Hgene | HMGB2 | GO:0045893 | positive regulation of transcription, DNA-templated | 19965638 |
| Hgene | HMGB2 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19223331|19965638 |
| Hgene | HMGB2 | GO:0050829 | defense response to Gram-negative bacterium | 23877675 |
| Hgene | HMGB2 | GO:0050830 | defense response to Gram-positive bacterium | 23877675 |
| Hgene | HMGB2 | GO:0060326 | cell chemotaxis | 19811285 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | BM836871 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| intron-3UTR | ENST00000296503 | ENST00000466801 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000296503 | ENST00000409321 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000296503 | ENST00000409115 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000296503 | ENST00000341369 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000296503 | ENST00000409683 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000296503 | ENST00000410064 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000466801 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000409321 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000409115 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000341369 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000409683 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000438704 | ENST00000410064 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000466801 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000409321 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000409115 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000341369 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000409683 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
| intron-3UTR | ENST00000446922 | ENST00000410064 | HMGB2 | chr4 | 174254250 | - | PTMA | chr2 | 232576643 | + |
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FusionProtFeatures for HMGB2_PTMA |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| HMGB2 | PTMA |
| Multifunctional protein with various roles in differentcellular compartments. May act in a redox sensitive manner. In thenucleus is an abundant chromatin-associated non-histone proteininvolved in transcription, chromatin remodeling and V(D)Jrecombination and probably other processes. Binds DNA with apreference to non-canonical DNA structures such as single-strandedDNA. Can bent DNA and enhance DNA flexibility by looping thusproviding a mechanism to promote activities on various genepromoters by enhancing transcription factor binding and/orbringing distant regulatory sequences into close proximity(PubMed:7797075, PubMed:11909973, PubMed:19522541,PubMed:18413230, PubMed:19965638, PubMed:20123072). Involved inV(D)J recombination by acting as a cofactor of the RAG complex:acts by stimulating cleavage and RAG protein binding at the 23 bpspacer of conserved recombination signal sequences (RSS) (Bysimilarity). Proposed to be involved in the innate immune responseto nucleic acids by acting as a promiscuous immunogenic DNA/RNAsensor which cooperates with subsequent discriminative sensing byspecific pattern recognition receptors (By similarity). In theextracellular compartment acts as a chemokine. Promotesproliferation and migration of endothelial cells implicatingAGER/RAGE (PubMed:19811285). Has antimicrobial activity ingastrointestinal epithelial tissues (PubMed:23877675). Involved ininflammatory response to antigenic stimulus coupled withproinflammatory activity (By similarity). Involved in modulationof neurogenesis probably by regulation of neural stemproliferation (By similarity). Involved in articular cartilagesurface maintenance implicating LEF1 and the Wnt/beta-cateninpathway (By similarity). {ECO:0000250|UniProtKB:P09429,ECO:0000250|UniProtKB:P30681, ECO:0000269|PubMed:11909973,ECO:0000269|PubMed:18413230, ECO:0000269|PubMed:19522541,ECO:0000269|PubMed:19811285, ECO:0000269|PubMed:19965638,ECO:0000269|PubMed:23877675, ECO:0000269|PubMed:7797075,ECO:0000305|PubMed:20123072}. | Prothymosin alpha may mediate immune function byconferring resistance to certain opportunistic infections. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for HMGB2_PTMA |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for HMGB2_PTMA |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for HMGB2_PTMA |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for HMGB2_PTMA |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | HMGB2 | C0028754 | Obesity | 1 | CTD_human |
| Hgene | HMGB2 | C0152013 | Adenocarcinoma of lung (disorder) | 1 | CTD_human |
| Hgene | HMGB2 | C2239176 | Liver carcinoma | 1 | CTD_human |
| Tgene | PTMA | C0001430 | Adenoma | 1 | CTD_human |
| Tgene | PTMA | C0015695 | Fatty Liver | 1 | CTD_human |
| Tgene | PTMA | C0024121 | Lung Neoplasms | 1 | CTD_human |
| Tgene | PTMA | C0035412 | Rhabdomyosarcoma | 1 | CTD_human |
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