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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: 1018

FusionGeneSummary for AFF3_NPAS2

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF3_NPAS2
Fusion gene ID: 1018
HgeneTgene
Gene symbol

AFF3

NPAS2

Gene ID

3899

4862

Gene nameAF4/FMR2 family member 3neuronal PAS domain protein 2
SynonymsLAF4|MLLT2-likeMOP4|PASD4|bHLHe9
Cytomap

2q11.2

2q11.2

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 3MLLT2-related proteinlymphoid nuclear protein 4lymphoid nuclear protein related to AF4protein LAF-4neuronal PAS domain-containing protein 2PAS domain-containing protein 4basic-helix-loop-helix-PAS protein MOP4class E basic helix-loop-helix protein 9member of PAS protein 4member of PAS superfamily 4neuronal PAS2
Modification date2018052320180519
UniProtAcc

P51826

Q99743

Ensembl transtripts involved in fusion geneENST00000409236, ENST00000356421, 
ENST00000317233, ENST00000409579, 
ENST00000483600, 
ENST00000335681, 
ENST00000542504, ENST00000486017, 
Fusion gene scores* DoF score12 X 9 X 5=5403 X 3 X 2=18
# samples 124
** MAII scorelog2(12/540*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: AFF3 [Title/Abstract] AND NPAS2 [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
TgeneNPAS2

GO:0045893

positive regulation of transcription, DNA-templated

11441146

TgeneNPAS2

GO:0051775

response to redox state

11441146


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
TCGARVLUADTCGA-97-8174-01AAFF3chr2

100623094

-NPAS2chr2

101604541

+
* 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-shitENST00000409236ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000409236ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000409236ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000356421ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000356421ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000356421ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000317233ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000317233ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000317233ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000409579ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shitENST00000409579ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000409579ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-3CDSENST00000483600ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-3CDSENST00000483600ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-intronENST00000483600ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+

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FusionProtFeatures for AFF3_NPAS2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
AFF3

P51826

NPAS2

Q99743

Transcriptional activator which forms a core componentof the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes throughthe generation of approximately 24 hour circadian rhythms in geneexpression, which are translated into rhythms in metabolism andbehavior. It is derived from the Latin roots 'circa' (about) and'diem' (day) and acts as an important regulator of a wide array ofphysiological functions including metabolism, sleep, bodytemperature, blood pressure, endocrine, immune, cardiovascular,and renal function. Consists of two major components: the centralclock, residing in the suprachiasmatic nucleus (SCN) of the brain,and the peripheral clocks that are present in nearly every tissueand organ system. Both the central and peripheral clocks can bereset by environmental cues, also known as Zeitgebers (German for'timegivers'). The predominant Zeitgeber for the central clock islight, which is sensed by retina and signals directly to the SCN.The central clock entrains the peripheral clocks through neuronaland hormonal signals, body temperature and feeding-related cues,aligning all clocks with the external light/dark cycle. Circadianrhythms allow an organism to achieve temporal homeostasis with itsenvironment at the molecular level by regulating gene expressionto create a peak of protein expression once every 24 hours tocontrol when a particular physiological process is most activewith respect to the solar day. Transcription and translation ofcore clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2,PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythmgeneration, whereas delays imposed by post-translationalmodifications (PTMs) are important for determining the period(tau) of the rhythms (tau refers to the period of a rhythm and isthe length, in time, of one complete cycle). A diurnal rhythm issynchronized with the day/night cycle, while the ultradian andinfradian rhythms have a period shorter and longer than 24 hours,respectively. Disruptions in the circadian rhythms contribute tothe pathology of cardiovascular diseases, cancer, metabolicsyndromes and aging. A transcription/translation feedback loop(TTFL) forms the core of the molecular circadian clock mechanism.Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 orARNTL2/BMAL2, form the positive limb of the feedback loop, act inthe form of a heterodimer and activate the transcription of coreclock genes and clock-controlled genes (involved in key metabolicprocesses), harboring E-box elements (5'-CACGTG-3') within theirpromoters. The core clock genes: PER1/2/3 and CRY1/2 which aretranscriptional repressors form the negative limb of the feedbackloop and interact with the CLOCK|NPAS2-ARNTL/BMAL1|ARNTL2/BMAL2heterodimer inhibiting its activity and thereby negativelyregulating their own expression. This heterodimer also activatesnuclear receptors NR1D1/2 and RORA/B/G, which form a secondfeedback loop and which activate and repress ARNTL/BMAL1transcription, respectively. The NPAS2-ARNTL/BMAL1 heterodimerpositively regulates the expression of MAOA, F7 and LDHA andmodulates the circadian rhythm of daytime contrast sensitivity byregulating the rhythmic expression of adenylate cyclase type 1(ADCY1) in the retina. NPAS2 plays an important role in sleephomeostasis and in maintaining circadian behaviors in normallight/dark and feeding conditions and in the effectivesynchronization of feeding behavior with scheduled foodavailability. Regulates the gene transcription of key metabolicpathways in the liver and is involved in DNA damage response byregulating several cell cycle and DNA repair genes.{ECO:0000269|PubMed:11441146, ECO:0000269|PubMed:11441147,ECO:0000269|PubMed:14645221, ECO:0000269|PubMed:18439826,ECO:0000269|PubMed:18819933}.

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 AFF3_NPAS2


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 AFF3_NPAS2


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
AFF3MLLT3, CDK9, PIP4K2ANPAS2EP300, NCOA3, KAT2B, CREBBP, RXRA, RARA, ARNTL, HSP90AA1, HESX1, RHOXF1, ZSCAN1, TRAF4, RPL6, ARNT2, ARNTL2, CRX, EFS, HGS, RASSF7, SHMT2, CLOCK, CRY1, CSNK2B, DEC1, RORC, CRY2


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 AFF3_NPAS2


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 AFF3_NPAS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFF3C0003873Rheumatoid Arthritis2CTD_human
HgeneAFF3C0236969Substance-Related Disorders1CTD_human
TgeneNPAS2C0005586Bipolar Disorder5PSYGENET
TgeneNPAS2C0085159Seasonal Affective Disorder4PSYGENET
TgeneNPAS2C0011581Depressive disorder2PSYGENET
TgeneNPAS2C0004352Autistic Disorder1CTD_human
TgeneNPAS2C0011570Mental Depression1PSYGENET
TgeneNPAS2C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneNPAS2C0036337Schizoaffective Disorder1PSYGENET
TgeneNPAS2C0036341Schizophrenia1PSYGENET