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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 19763

FusionGeneSummary for LIN9_KDM5B

check button Fusion gene summary
Fusion gene informationFusion gene name: LIN9_KDM5B
Fusion gene ID: 19763
HgeneTgene
Gene symbol

LIN9

KDM5B

Gene ID

286826

10765

Gene namelin-9 DREAM MuvB core complex componentlysine demethylase 5B
SynonymsBARA|BARPsv|Lin-9|TGS|TGS1|TGS2CT31|JARID1B|PLU-1|PLU1|PPP1R98|PUT1|RBBP2H1A|RBP2-H1
Cytomap

1q42.12

1q32.1

Type of geneprotein-codingprotein-coding
Descriptionprotein lin-9 homologTUDOR gene similar proteinbeta subunit-associated regulator of apoptosislin-9 homologpRB-associated proteinrb related pathway actortype I interferon receptor beta chain-associated proteinlysine-specific demethylase 5Bcancer/testis antigen 31histone demethylase JARID1Bjumonji, AT rich interactive domain 1Bjumonji/ARID domain-containing protein 1Blysine (K)-specific demethylase 5Bprotein phosphatase 1, regulatory subunit 98putative D
Modification date2018052320180523
UniProtAcc

Q5TKA1

Q9UGL1

Ensembl transtripts involved in fusion geneENST00000328205, ENST00000366801, 
ENST00000481685, 
ENST00000367265, 
ENST00000367264, ENST00000456180, 
Fusion gene scores* DoF score2 X 2 X 2=85 X 5 X 3=75
# samples 25
** MAII scorelog2(2/8*10)=1.32192809488736log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LIN9 [Title/Abstract] AND KDM5B [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneKDM5B

GO:0034720

histone H3-K4 demethylation

20228790


check button 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 typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLGGTCGA-CS-5395-01ALIN9chr1

226465476

-KDM5Bchr1

202746222

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000328205ENST00000367265LIN9chr1

226465476

-KDM5Bchr1

202746222

-
Frame-shiftENST00000328205ENST00000367264LIN9chr1

226465476

-KDM5Bchr1

202746222

-
5CDS-intronENST00000328205ENST00000456180LIN9chr1

226465476

-KDM5Bchr1

202746222

-
Frame-shiftENST00000366801ENST00000367265LIN9chr1

226465476

-KDM5Bchr1

202746222

-
Frame-shiftENST00000366801ENST00000367264LIN9chr1

226465476

-KDM5Bchr1

202746222

-
5CDS-intronENST00000366801ENST00000456180LIN9chr1

226465476

-KDM5Bchr1

202746222

-
Frame-shiftENST00000481685ENST00000367265LIN9chr1

226465476

-KDM5Bchr1

202746222

-
Frame-shiftENST00000481685ENST00000367264LIN9chr1

226465476

-KDM5Bchr1

202746222

-
5CDS-intronENST00000481685ENST00000456180LIN9chr1

226465476

-KDM5Bchr1

202746222

-

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FusionProtFeatures for LIN9_KDM5B


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LIN9

Q5TKA1

KDM5B

Q9UGL1

Acts as a tumor suppressor. Inhibits DNA synthesis. Itsability to inhibit oncogenic transformation is mediated throughits association with RB1. Plays a role in the expression of genesrequired for the G1/S transition. {ECO:0000269|PubMed:15538385,ECO:0000269|PubMed:16730350}. Histone demethylase that demethylates 'Lys-4' of histoneH3, thereby playing a central role in histone code(PubMed:24952722, PubMed:27214403, PubMed:28262558). Does notdemethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylatestrimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts asa transcriptional corepressor for FOXG1B and PAX9. Favors theproliferation of breast cancer cells by repressing tumorsuppressor genes such as BRCA1 and HOXA5 (PubMed:24952722). Incontrast, may act as a tumor suppressor for melanoma. Repressesthe CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptionalactivation of the core clock component PER2 (By similarity).{ECO:0000250|UniProtKB:Q80Y84, ECO:0000269|PubMed:12657635,ECO:0000269|PubMed:16645588, ECO:0000269|PubMed:17320161,ECO:0000269|PubMed:17363312, ECO:0000269|PubMed:24952722,ECO:0000269|PubMed:26645689, ECO:0000269|PubMed:26741168,ECO:0000269|PubMed:27214403, ECO:0000269|PubMed:28262558}.

check buttonRetention 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

download page

.

* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for LIN9_KDM5B


check button 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 LIN9_KDM5B


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
LIN9RB1, LIN54, LIN37, LIN52, MYBL2, E2F4, RBL2, TFDP1, TFDP2, LIN9, MYBL1, RBBP4, RBL1, SHMT2, MOV10, NXF1, PHF20L1, RBBP7, HIST1H2BG, XPO1, TEAD2, FOXM1, DIS3L, FAM167A, RGS13, SLMAP, RPN2, COL1A1, TCF19, HBS1L, MOCS3KDM5BFOXG1, PAX9, PRPF4, CACNA1H, CDC20, PCNX, SMARCC2, DGKQ, CACNA1A, NR4A3, BMP2K, VGLL3, CDX2, CBX4, SLITRK3, AXIN2, FOXC2, ONECUT2, MAF, ELF4, SLC39A6, BRD4, RNF43, RBM15B, PRDM13, GTF2A1, DBNL, CECR6, RHOBTB2, TAF2, SHOX2, ARID1B, HOXA1, GRIN2B, MEOX2, ZNF217, RCOR1, RB1, AR, LMO2, KLF10, HDAC1, CHD3, KDM1A, MTA2, MTA3, HDAC2, RBBP7, RBBP4, MBD2, MBD3, HDAC4, HDAC5, HDAC7, NCOR1, ELAVL1, TFAP2C, MYC, FBXW11, FAM90A1, KRAS, TSPYL6, TRIM25


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for LIN9_KDM5B


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for LIN9_KDM5B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKDM5BC0009375Colonic Neoplasms1CTD_human