|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 18501 |
FusionGeneSummary for KDM5C_PPP4R1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: KDM5C_PPP4R1 | Fusion gene ID: 18501 | Hgene | Tgene | Gene symbol | KDM5C | PPP4R1 | Gene ID | 8242 | 9989 |
| Gene name | lysine demethylase 5C | protein phosphatase 4 regulatory subunit 1 | |
| Synonyms | DXS1272E|JARID1C|MRX13|MRXJ|MRXSCJ|MRXSJ|SMCX|XE169 | MEG1|PP4(Rmeg)|PP4R1 | |
| Cytomap | Xp11.22 | 18p11.22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | lysine-specific demethylase 5CJmjC domain-containing protein SMCXJumonji, AT rich interactive domain 1C (RBP2-like)Jumonji/ARID domain-containing protein 1CSmcx homolog, X chromosomeSmcy homolog, X-linkedhistone demethylase JARID1Clysine (K)-specif | serine/threonine-protein phosphatase 4 regulatory subunit 1serine/threonine phosphatase 4 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P41229 | Q8TF05 | |
| Ensembl transtripts involved in fusion gene | ENST00000452825, ENST00000375401, ENST00000404049, ENST00000375379, ENST00000375383, ENST00000465402, | ENST00000400556, ENST00000400555, ENST00000580583, | |
| Fusion gene scores | * DoF score | 12 X 12 X 5=720 | 8 X 7 X 5=280 |
| # samples | 12 | 8 | |
| ** MAII score | log2(12/720*10)=-2.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/280*10)=-1.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: KDM5C [Title/Abstract] AND PPP4R1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift. | ||
| * 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 | KDM5C | GO:0034720 | histone H3-K4 demethylation | 17320160 |
| 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 |
| TCGA | RV | LUAD | TCGA-05-4398-01A | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| * 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 |
| Frame-shift | ENST00000452825 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000452825 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| 5CDS-intron | ENST00000452825 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375401 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375401 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| 5CDS-intron | ENST00000375401 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000404049 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000404049 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| 5CDS-intron | ENST00000404049 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375379 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375379 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| 5CDS-intron | ENST00000375379 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375383 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| Frame-shift | ENST00000375383 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| 5CDS-intron | ENST00000375383 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| intron-3CDS | ENST00000465402 | ENST00000400556 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| intron-3CDS | ENST00000465402 | ENST00000400555 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
| intron-intron | ENST00000465402 | ENST00000580583 | KDM5C | chrX | 53240679 | - | PPP4R1 | chr18 | 9550396 | - |
Top |
FusionProtFeatures for KDM5C_PPP4R1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| KDM5C | PPP4R1 |
| Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code(PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylatestrimethylated and dimethylated but not monomethylated H3 'Lys-4'.Participates in transcriptional repression of neuronal genes byrecruiting histone deacetylases and REST at neuron-restrictivesilencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock componentPER2 (By similarity). {ECO:0000250|UniProtKB:P41230,ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161,ECO:0000269|PubMed:17468742, ECO:0000269|PubMed:26645689,ECO:0000269|PubMed:28262558}. | Regulatory subunit of serine/threonine-proteinphosphatase 4. May play a role in regulation of cell division inrenal glomeruli. The PPP4C-PPP4R1 PP4 complex may play a role indephosphorylation and regulation of HDAC3.{ECO:0000269|PubMed:15805470}. |
| 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 |
Top |
FusionGeneSequence for KDM5C_PPP4R1 |
| 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). |
Top |
FusionGenePPI for KDM5C_PPP4R1 |
| 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 |
| KDM5C | HIST2H3A, NCOR1, REST, HDAC1, HDAC2, RING1, E2F6, MAX, CBX3, RNF2, KDM5C, SMAD3, CALM1, CNOT4, PCNA, THTPA, SPTBN2, USP5, NXF1, SCML4, HLA-F, LHX6, ARHGAP25, IER2, ACTN1, LSM2, PITHD1, CSNK2A1, CSNK2B, SET, XPO1, MBD2, ZNF592, TOX4, MGA, ZMYND8, VPS41, ZNF532, ZNF687, TSPYL2, CENPK, SLC25A22, FOXJ2, MAP3K1, BRCA2, HDAC6, TSC1, BRD4, MTOR, WEE1, VHL, KIAA1683, SPATA1, SSH3, TRIM35, DEF8, OLFM2, SKP2, TKT | PPP4R1 | PPP4C, DISC1, CEP63, MAP4, EHBP1L1, GPHN, HNRNPR, MTA2, POLR2A, POLR2C, SPTAN1, TRAF2, TRAF6, PPP2CB, PMPCB, AQR, NTRK1, XPO1, CTNND1, LDHB, NDUFB4, PPP2CA, PPP2R1A, PPP2R1B, CCDC6, MAP7, MED24, SEC61A1, FASTKD5, RALBP1, C1S, KIF1B, TRIM25 |
| - 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 |
Top |
RelatedDrugs for KDM5C_PPP4R1 |
| 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 |
Top |
RelatedDiseases for KDM5C_PPP4R1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | KDM5C | C1845243 | MENTAL RETARDATION, X-LINKED, SYNDROMIC, CLAES-JENSEN TYPE | 4 | CTD_human;ORPHANET;UNIPROT |
| Hgene | KDM5C | C0004352 | Autistic Disorder | 1 | CTD_human |
| Hgene | KDM5C | C0007134 | Renal Cell Carcinoma | 1 | CTD_human |
| Hgene | KDM5C | C3714756 | Intellectual Disability | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|