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Fusion Protein:NEBL-KMT2A |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: NEBL-KMT2A | FusionPDB ID: 58344 | FusionGDB2.0 ID: 58344 | Hgene | Tgene | Gene symbol | NEBL | KMT2A | Gene ID | 10529 | 4297 |
Gene name | nebulette | lysine methyltransferase 2A | |
Synonyms | C10orf113|LASP2|LNEBL|bA165O3.1 | ALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTS | |
Cytomap | 10p12.31 | 11q23.3 | |
Type of gene | protein-coding | protein-coding | |
Description | nebuletteLIM and SH3 protein 2LIM-nebuletteactin-binding Z-disk protein | histone-lysine N-methyltransferase 2ACXXC-type zinc finger protein 7lysine (K)-specific methyltransferase 2Alysine N-methyltransferase 2Amixed lineage leukemia 1myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)trithorax-like | |
Modification date | 20200313 | 20200319 | |
UniProtAcc | O76041 Main function of 5'-partner protein: FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}. | Q03164 Main function of 5'-partner protein: FUNCTION: Histone methyltransferase that plays an essential role in early development and hematopoiesis (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac) (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:24235145, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism. Part of chromatin remodeling machinery predominantly forms H3K4me1 and H3K4me2 methylation marks at active chromatin sites where transcription and DNA repair take place (PubMed:25561738, PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Has weak methyltransferase activity by itself, and requires other component of the MLL1/MLL complex to obtain full methyltransferase activity (PubMed:19187761, PubMed:26886794). Has no activity toward histone H3 phosphorylated on 'Thr-3', less activity toward H3 dimethylated on 'Arg-8' or 'Lys-9', while it has higher activity toward H3 acetylated on 'Lys-9' (PubMed:19187761). Binds to unmethylated CpG elements in the promoter of target genes and helps maintain them in the nonmethylated state (PubMed:20010842). Required for transcriptional activation of HOXA9 (PubMed:12453419, PubMed:20677832, PubMed:20010842). Promotes PPP1R15A-induced apoptosis (PubMed:10490642). Plays a critical role in the control of circadian gene expression and is essential for the transcriptional activation mediated by the CLOCK-ARNTL/BMAL1 heterodimer (By similarity). Establishes a permissive chromatin state for circadian transcription by mediating a rhythmic methylation of 'Lys-4' of histone H3 (H3K4me) and this histone modification directs the circadian acetylation at H3K9 and H3K14 allowing the recruitment of CLOCK-ARNTL/BMAL1 to chromatin (By similarity). Also has auto-methylation activity on Cys-3882 in absence of histone H3 substrate (PubMed:24235145). {ECO:0000250|UniProtKB:P55200, ECO:0000269|PubMed:10490642, ECO:0000269|PubMed:12453419, ECO:0000269|PubMed:15960975, ECO:0000269|PubMed:19187761, ECO:0000269|PubMed:19556245, ECO:0000269|PubMed:20010842, ECO:0000269|PubMed:21220120, ECO:0000269|PubMed:24235145, ECO:0000269|PubMed:26886794, ECO:0000305|PubMed:20677832}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000377159, ENST00000417816, ENST00000377119, ENST00000377122, ENST00000464278, | ENST00000420751, ENST00000354520, ENST00000389506, ENST00000534358, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 15 X 12 X 6=1080 | 31 X 72 X 3=6696 |
# samples | 16 | 79 | |
** MAII score | log2(16/1080*10)=-2.75488750216347 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(79/6696*10)=-3.08337496948588 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: NEBL [Title/Abstract] AND KMT2A [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: NEBL [Title/Abstract] AND KMT2A [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KMT2A(118353224)-NEBL(21250710), # samples:1 NEBL(21309045)-KMT2A(118354896), # samples:1 | ||
Anticipated loss of major functional domain due to fusion event. | NEBL-KMT2A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. NEBL-KMT2A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. NEBL-KMT2A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. NEBL-KMT2A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Tgene | KMT2A | GO:0044648 | histone H3-K4 dimethylation | 25561738 |
Tgene | KMT2A | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20861184 |
Tgene | KMT2A | GO:0051568 | histone H3-K4 methylation | 19556245 |
Tgene | KMT2A | GO:0065003 | protein-containing complex assembly | 15199122 |
Tgene | KMT2A | GO:0080182 | histone H3-K4 trimethylation | 20861184 |
Tgene | KMT2A | GO:0097692 | histone H3-K4 monomethylation | 25561738|26324722 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:118353224/chr11:21250710) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
ENST00000417816 | NEBL | chr10 | 21309045 | - | ENST00000534358 | KMT2A | chr11 | 118354896 | + | 13088 | 603 | 354 | 8435 | 2693 |
ENST00000417816 | NEBL | chr10 | 21309045 | - | ENST00000389506 | KMT2A | chr11 | 118354896 | + | 10172 | 603 | 354 | 8426 | 2690 |
ENST00000417816 | NEBL | chr10 | 21309045 | - | ENST00000354520 | KMT2A | chr11 | 118354896 | + | 10837 | 603 | 354 | 8312 | 2652 |
ENST00000377159 | NEBL | chr10 | 21309045 | - | ENST00000534358 | KMT2A | chr11 | 118354896 | + | 12634 | 149 | 2 | 7981 | 2659 |
ENST00000377159 | NEBL | chr10 | 21309045 | - | ENST00000389506 | KMT2A | chr11 | 118354896 | + | 9718 | 149 | 2 | 7972 | 2656 |
ENST00000377159 | NEBL | chr10 | 21309045 | - | ENST00000354520 | KMT2A | chr11 | 118354896 | + | 10383 | 149 | 2 | 7858 | 2618 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000417816 | ENST00000534358 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000368709 | 0.9996313 |
ENST00000417816 | ENST00000389506 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000655885 | 0.99934405 |
ENST00000417816 | ENST00000354520 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000760757 | 0.9992392 |
ENST00000377159 | ENST00000534358 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000236956 | 0.9997631 |
ENST00000377159 | ENST00000389506 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000422122 | 0.9995778 |
ENST00000377159 | ENST00000354520 | NEBL | chr10 | 21309045 | - | KMT2A | chr11 | 118354896 | + | 0.000485639 | 0.99951434 |
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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for NEBL-KMT2A |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
NEBL | chr10 | 21309045 | KMT2A | chr11 | 118354896 | 149 | 49 | NLRLKQQSELQSQEKPPPVNKQENAG |
NEBL | chr10 | 21309045 | KMT2A | chr11 | 118354896 | 603 | 83 | NLRLKQQSELQSQEKPPPVNKQENAG |
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Potential FusionNeoAntigen Information of NEBL-KMT2A in HLA I |
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NEBL-KMT2A_21309045_118354896.msa |
![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B45:01 | SELQSQEKP | 0.9953 | 0.9556 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B50:02 | SELQSQEKP | 0.9917 | 0.7423 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B47:01 | QEKPPPVNK | 0.7606 | 0.545 | 12 | 21 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B41:01 | SELQSQEKP | 0.7403 | 0.9527 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B50:01 | SELQSQEKP | 0.6577 | 0.7989 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B45:01 | SELQSQEKPP | 0.9897 | 0.9759 | 7 | 17 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-A30:08 | SQEKPPPVNK | 0.8744 | 0.6721 | 11 | 21 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-A30:08 | QSQEKPPPVNK | 0.9958 | 0.6761 | 10 | 21 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B40:06 | SELQSQEKP | 0.9924 | 0.7075 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B50:04 | SELQSQEKP | 0.6577 | 0.7989 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-B50:05 | SELQSQEKP | 0.6577 | 0.7989 | 7 | 16 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-A30:01 | SQEKPPPVNK | 0.8715 | 0.7705 | 11 | 21 |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 | HLA-A30:01 | QSQEKPPPVNK | 0.9953 | 0.831 | 10 | 21 |
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Potential FusionNeoAntigen Information of NEBL-KMT2A in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of NEBL-KMT2A |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
7577 | QSELQSQEKPPPVN | NEBL | KMT2A | chr10 | 21309045 | chr11 | 118354896 | 149 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NEBL-KMT2A |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
HLA-B14:02 | 3BVN | 7577 | QSELQSQEKPPPVN | -7.9962 | -8.1096 |
HLA-B14:02 | 3BVN | 7577 | QSELQSQEKPPPVN | -5.70842 | -6.74372 |
HLA-B52:01 | 3W39 | 7577 | QSELQSQEKPPPVN | -6.83737 | -6.95077 |
HLA-B52:01 | 3W39 | 7577 | QSELQSQEKPPPVN | -4.4836 | -5.5189 |
HLA-A11:01 | 4UQ2 | 7577 | QSELQSQEKPPPVN | -10.0067 | -10.1201 |
HLA-A11:01 | 4UQ2 | 7577 | QSELQSQEKPPPVN | -9.03915 | -10.0745 |
HLA-A24:02 | 5HGA | 7577 | QSELQSQEKPPPVN | -6.56204 | -6.67544 |
HLA-A24:02 | 5HGA | 7577 | QSELQSQEKPPPVN | -5.42271 | -6.45801 |
HLA-B44:05 | 3DX8 | 7577 | QSELQSQEKPPPVN | -7.85648 | -8.89178 |
HLA-B44:05 | 3DX8 | 7577 | QSELQSQEKPPPVN | -5.3978 | -5.5112 |
HLA-A02:01 | 6TDR | 7577 | QSELQSQEKPPPVN | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of NEBL-KMT2A |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 10 | 21 | QSQEKPPPVNK | CAGAGTCAGGAAAAACCACCTCCGGTCAATAAG |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 11 | 21 | SQEKPPPVNK | AGTCAGGAAAAACCACCTCCGGTCAATAAG |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 12 | 21 | QEKPPPVNK | CAGGAAAAACCACCTCCGGTCAATAAG |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 7 | 16 | SELQSQEKP | AGTGAATTGCAGAGTCAGGAAAAACCA |
NEBL-KMT2A | chr10 | 21309045 | chr11 | 118354896 | 7 | 17 | SELQSQEKPP | AGTGAATTGCAGAGTCAGGAAAAACCACCT |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of NEBL-KMT2A |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
N/A | NEBL-KMT2A | chr10 | 21309045 | ENST00000377159 | chr11 | 118354896 | ENST00000354520 | MH319862 |
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Potential target of CAR-T therapy development for NEBL-KMT2A |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to NEBL-KMT2A |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to NEBL-KMT2A |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Tgene | KMT2A | C2826025 | Mixed phenotype acute leukemia | 3 | ORPHANET |
Tgene | KMT2A | C0023418 | leukemia | 2 | CTD_human |
Tgene | KMT2A | C0023452 | Childhood Acute Lymphoblastic Leukemia | 2 | CTD_human |
Tgene | KMT2A | C0023453 | L2 Acute Lymphoblastic Leukemia | 2 | CTD_human |
Tgene | KMT2A | C0023466 | Leukemia, Monocytic, Chronic | 2 | CTD_human |
Tgene | KMT2A | C0023467 | Leukemia, Myelocytic, Acute | 2 | CTD_human |
Tgene | KMT2A | C0023470 | Myeloid Leukemia | 2 | CTD_human |
Tgene | KMT2A | C0026998 | Acute Myeloid Leukemia, M1 | 2 | CTD_human |
Tgene | KMT2A | C1854630 | Growth Deficiency and Mental Retardation with Facial Dysmorphism | 2 | CTD_human;GENOMICS_ENGLAND;ORPHANET |
Tgene | KMT2A | C1879321 | Acute Myeloid Leukemia (AML-M2) | 2 | CTD_human |
Tgene | KMT2A | C1961102 | Precursor Cell Lymphoblastic Leukemia Lymphoma | 2 | CTD_human |
Tgene | KMT2A | C0001418 | Adenocarcinoma | 1 | CTD_human |
Tgene | KMT2A | C0004403 | Autosome Abnormalities | 1 | CTD_human |
Tgene | KMT2A | C0005684 | Malignant neoplasm of urinary bladder | 1 | CTD_human |
Tgene | KMT2A | C0005695 | Bladder Neoplasm | 1 | CTD_human |
Tgene | KMT2A | C0007138 | Carcinoma, Transitional Cell | 1 | CTD_human |
Tgene | KMT2A | C0008625 | Chromosome Aberrations | 1 | CTD_human |
Tgene | KMT2A | C0023448 | Lymphoid leukemia | 1 | CTD_human |
Tgene | KMT2A | C0023465 | Acute monocytic leukemia | 1 | CTD_human |
Tgene | KMT2A | C0023479 | Acute myelomonocytic leukemia | 1 | CTD_human |
Tgene | KMT2A | C0024623 | Malignant neoplasm of stomach | 1 | CTD_human |
Tgene | KMT2A | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
Tgene | KMT2A | C0036341 | Schizophrenia | 1 | PSYGENET |
Tgene | KMT2A | C0038356 | Stomach Neoplasms | 1 | CTD_human |
Tgene | KMT2A | C0149925 | Small cell carcinoma of lung | 1 | CTD_human |
Tgene | KMT2A | C0205641 | Adenocarcinoma, Basal Cell | 1 | CTD_human |
Tgene | KMT2A | C0205642 | Adenocarcinoma, Oxyphilic | 1 | CTD_human |
Tgene | KMT2A | C0205643 | Carcinoma, Cribriform | 1 | CTD_human |
Tgene | KMT2A | C0205644 | Carcinoma, Granular Cell | 1 | CTD_human |
Tgene | KMT2A | C0205645 | Adenocarcinoma, Tubular | 1 | CTD_human |
Tgene | KMT2A | C0270972 | Cornelia De Lange Syndrome | 1 | ORPHANET |
Tgene | KMT2A | C0280141 | Acute Undifferentiated Leukemia | 1 | ORPHANET |
Tgene | KMT2A | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
Tgene | KMT2A | C0856823 | Undifferentiated type acute leukemia | 1 | ORPHANET |
Tgene | KMT2A | C1535926 | Neurodevelopmental Disorders | 1 | CTD_human |
Tgene | KMT2A | C1708349 | Hereditary Diffuse Gastric Cancer | 1 | CTD_human |
Tgene | KMT2A | C2239176 | Liver carcinoma | 1 | CTD_human |
Tgene | KMT2A | C2930974 | Acute erythroleukemia | 1 | CTD_human |
Tgene | KMT2A | C2930975 | Acute erythroleukemia - M6a subtype | 1 | CTD_human |
Tgene | KMT2A | C2930976 | Acute myeloid leukemia FAB-M6 | 1 | CTD_human |
Tgene | KMT2A | C2930977 | Acute erythroleukemia - M6b subtype | 1 | CTD_human |