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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:NCK2-NFYC (FusionGDB2 ID:57609)

Fusion Gene Summary for NCK2-NFYC

Fusion gene summary

Fusion gene information	Fusion gene name: NCK2-NFYC
	Fusion gene ID: 57609
		Hgene	Tgene
	Gene symbol	NCK2	NFYC
	Gene ID	8440	4802
	Gene name	NCK adaptor protein 2	nuclear transcription factor Y subunit gamma
	Synonyms	GRB4\|NCKbeta	CBF-C\|CBFC\|H1TF2A\|HAP5\|HSM\|NF-YC
	Cytomap	2q12.2	1p34.2
	Type of gene	protein-coding	protein-coding
	Description	cytoplasmic protein NCK2SH2/SH3 adaptor protein NCK-betagrowth factor receptor-bound protein 4noncatalytic region of tyrosine kinase, beta	nuclear transcription factor Y subunit gammaCAAT box DNA-binding protein subunit CCCAAT binding factor subunit CCCAAT transcription binding factor subunit gammahistone H1 transcription factor large subunit 2Anuclear transcription factor Y subunit Cn
	Modification date	20200327	20200313
	UniProtAcc	O43639	Q13952
	Ensembl transtripts involved in fusion gene	ENST00000233154, ENST00000451463, ENST00000522586, ENST00000393349,	ENST00000308733, ENST00000372651, ENST00000372652, ENST00000372653, ENST00000372654, ENST00000425457, ENST00000427410, ENST00000440226, ENST00000447388, ENST00000456393, ENST00000483091,
Fusion gene scores	* DoF score	15 X 7 X 9=945	16 X 10 X 7=1120
	# samples	20	18
	** MAII score	log2(20/945*10)=-2.24031432933371 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(18/1120*10)=-2.63742992061529 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NCK2 [Title/Abstract] AND NFYC [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	NCK2(106433070)-NFYC(41213205), # samples:1
Anticipated loss of major functional domain due to fusion event.

* 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	NCK2	GO:0033137	negative regulation of peptidyl-serine phosphorylation	16835242
Hgene	NCK2	GO:0045944	positive regulation of transcription by RNA polymerase II	10026169
Hgene	NCK2	GO:1903912	negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation	16835242
Tgene	NFYC	GO:0006355	regulation of transcription, DNA-templated	15243141

Fusion gene breakpoints across NCK2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across NFYC (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	Non-Cancer	TCGA-HU-A4GC-11A	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+

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Fusion Gene ORF analysis for NCK2-NFYC

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
5UTR-3CDS	ENST00000233154	ENST00000308733	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000372651	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000372652	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000372653	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000372654	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000425457	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000427410	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000440226	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000447388	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000233154	ENST00000456393	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000308733	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000372651	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000372652	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000372653	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000372654	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000425457	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000427410	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000440226	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000447388	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000451463	ENST00000456393	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000308733	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000372651	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000372652	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000372653	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000372654	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000425457	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000427410	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000440226	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000447388	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-3CDS	ENST00000522586	ENST00000456393	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-intron	ENST00000233154	ENST00000483091	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-intron	ENST00000451463	ENST00000483091	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
5UTR-intron	ENST00000522586	ENST00000483091	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000308733	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000372651	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000372652	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000372653	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000372654	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000425457	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000427410	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000440226	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000447388	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-3CDS	ENST00000393349	ENST00000456393	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+
intron-intron	ENST00000393349	ENST00000483091	NCK2	chr2	106433070	+	NFYC	chr1	41213205	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

No-coding score

Coding score

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Fusion Genomic Features for NCK2-NFYC

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
NCK2	chr2	106433070	+	NFYC	chr1	41213205	+	0.002680822	0.99731916
NCK2	chr2	106433070	+	NFYC	chr1	41213205	+	0.002680822	0.99731916

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for NCK2-NFYC

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:106433070/:41213205)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
NCK2 O43639	NFYC Q13952
FUNCTION: Adapter protein which associates with tyrosine-phosphorylated growth factor receptors or their cellular substrates. Maintains low levels of EIF2S1 phosphorylation by promoting its dephosphorylation by PP1. Plays a role in ELK1-dependent transcriptional activation in response to activated Ras signaling. {ECO:0000269\|PubMed:10026169, ECO:0000269\|PubMed:16835242}.	FUNCTION: Component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors.

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
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.

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

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Fusion Gene Sequence for NCK2-NFYC

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for NCK2-NFYC

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- 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

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Related Drugs for NCK2-NFYC

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for NCK2-NFYC

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source