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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: 7059

FusionGeneSummary for CHGB_LIMCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: CHGB_LIMCH1
Fusion gene ID: 7059
HgeneTgene
Gene symbol

CHGB

LIMCH1

Gene ID

1114

22998

Gene namechromogranin BLIM and calponin homology domains 1
SynonymsSCG1LIMCH1A|LMO7B
Cytomap

20p12.3

4p13

Type of geneprotein-codingprotein-coding
Descriptionsecretogranin-1cgBsecretogranin Bsecretogranin IsgILIM and calponin homology domains-containing protein 1
Modification date2018052320180519
UniProtAcc

P05060

Q9UPQ0

Ensembl transtripts involved in fusion geneENST00000378961, ENST00000488832, 
ENST00000513024, ENST00000509638, 
ENST00000508501, ENST00000512946, 
ENST00000313860, ENST00000512632, 
ENST00000512820, ENST00000503057, 
ENST00000511496, ENST00000514096, 
ENST00000509277, ENST00000396595, 
ENST00000381753, ENST00000509454, 
ENST00000515785, 
Fusion gene scores* DoF score4 X 2 X 2=1610 X 10 X 6=600
# samples 610
** MAII scorelog2(6/16*10)=1.90689059560852
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(10/600*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CHGB [Title/Abstract] AND LIMCH1 [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)

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

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
TCGARVPCPGTCGA-P8-A6RY-01ACHGBchr20

5903719

+LIMCH1chr4

41648502

+
* 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-shiftENST00000378961ENST00000513024CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000509638CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000508501CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000512946CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000313860CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000512632CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000512820CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000503057CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000511496CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000514096CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000509277CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000396595CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000381753CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000509454CHGBchr20

5903719

+LIMCH1chr4

41648502

+
5CDS-intronENST00000378961ENST00000515785CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-3CDSENST00000488832ENST00000513024CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000509638CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000508501CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000512946CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000313860CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000512632CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000512820CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000503057CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000511496CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000514096CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000509277CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000396595CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000381753CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000509454CHGBchr20

5903719

+LIMCH1chr4

41648502

+
intron-intronENST00000488832ENST00000515785CHGBchr20

5903719

+LIMCH1chr4

41648502

+

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FusionProtFeatures for CHGB_LIMCH1


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

P05060

LIMCH1

Q9UPQ0

Secretogranin-1 is a neuroendocrine secretory granuleprotein, which may be the precursor for other biologically activepeptides.

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 CHGB_LIMCH1


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 CHGB_LIMCH1


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
CHGBACACA, CBFB, SGK223, CCDC92, MOGS, MARK3, MGLL, OGG1, TWF2, SAFB2, ATXN2, TAZ, FGFR3, POLD1, PTEN, S100A8, SLC25A6, YLPM1, TUBB2A, RAC2, RAP1B, TK1, CDKN1A, RCC1, PKN2, ANXA7, UBQLN1, APP, PARK2LIMCH1ELAVL1, SH3KBP1, APP, HUWE1, CUTC, DIABLO, GABPA, KPNA1, NPM1, TRMT61A, RPA3, RPA2, RPA1, OTUD6B, KLHL15, RFC2, YES1, NAGK, GNB4, UNK, NTRK1, CEP120, ODF2, XPO1, CAPZA2, CDK2, MYH9, PPP1CB, IQGAP1, ANLN, MYO19, MYO18A, CDH1, 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 CHGB_LIMCH1


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 CHGB_LIMCH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCHGBC0036341Schizophrenia3PSYGENET
HgeneCHGBC0221765Chronic schizophrenia1PSYGENET
TgeneLIMCH1C0236969Substance-Related Disorders1CTD_human
TgeneLIMCH1C0345967Malignant mesothelioma1CTD_human