ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for FGFR2

Gene summary

Gene information	Gene symbol	FGFR2
	Gene ID	2263
	Gene name	fibroblast growth factor receptor 2
	Synonyms	BBDS\|BEK\|BFR-1\|CD332\|CEK3\|CFD1\|ECT1\|JWS\|K-SAM\|KGFR\|TK14\|TK25
	Cytomap	10q26.13
	Type of gene	protein-coding
	Description	fibroblast growth factor receptor 2BEK fibroblast growth factor receptorbacteria-expressed kinasekeratinocyte growth factor receptorprotein tyrosine kinase, receptor like 14
	Modification date	20200322
	UniProtAcc	A0A087WY21, A0A087X2D1, A0A0A0MR25, A0A141AXF0, A0A141AXF1, A0A141AXF2, A0A141AXF3, A0A141AXF4, A0A141AXF5, A0A141AXF6, A0A141AXF7, A0A141AXF8, A0A1B0GWF4, A0A1B0GYB8, A0A1B0GYP7, A0A1W2PQT9, A0A5S6RJB7, B5A960, B5A961, B5A962, B5A963, D2CGD1, D3DRD3, D3DRD4, D3DRD5, D3DRD6, D3DRD9, D3DRE0, E2I6F9, E7EVR7, H7BXU9, H7C265, L8E779, L8E8R5, P21802, S4R381, S4R3B2,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
FGFR2	GO:0008284	positive regulation of cell proliferation	8663044
FGFR2	GO:0008543	fibroblast growth factor receptor signaling pathway	8663044\|15629145
FGFR2	GO:0018108	peptidyl-tyrosine phosphorylation	15629145\|16844695
FGFR2	GO:0046777	protein autophosphorylation	15629145

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Gene structures and expression levels for FGFR2

Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

ENSG00000066468

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	DOWN	ENST00000638709.1	FGFR2-227:protein_coding:FGFR2	5.442680e+02	-8.574386e-01	1.787583e-13	3.646273e-11
CB	DOWN	ENST00000357555.9	FGFR2-205:protein_coding:FGFR2	4.568169e+01	-1.220406e+00	4.324465e-06	5.188369e-05
CB	DOWN	ENST00000369061.8	FGFR2-213:protein_coding:FGFR2	7.072644e+02	-1.575505e+00	3.870783e-04	2.321079e-03
TC	DOWN	ENST00000636922.1	FGFR2-226:non_stop_decay:FGFR2	1.163448e+01	-1.618116e+00	3.533089e-10	5.566983e-08
TC	DOWN	ENST00000491475.1	FGFR2-221:retained_intron:FGFR2	1.348197e+01	-1.148397e+00	2.102483e-08	1.667873e-06
TC	DOWN	ENST00000613324.4	FGFR2-225:protein_coding:FGFR2	2.766281e+02	-8.642345e-01	5.618642e-07	2.535584e-05
TC	DOWN	ENST00000611527.1	FGFR2-223:protein_coding:FGFR2	1.245197e+01	-1.054893e+00	1.047337e-05	2.684321e-04
TC	DOWN	ENST00000369061.8	FGFR2-213:protein_coding:FGFR2	3.933624e+02	-1.937780e+00	1.010732e-03	9.985796e-03

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for FGFR2

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_110244	chr10	121479855:121480021:121483698:121483803:121485395:121485532	121483698:121483803
exon_skip_121055	chr10	121538592:121538715:121551290:121551459:121564502:121564579	121551290:121551459
exon_skip_132506	chr10	121517370:121517463:121518682:121518829:121519979:121520169	121518682:121518829
exon_skip_132835	chr10	121564502:121564579:121565637:121565704:121593709:121593764	121565637:121565704
exon_skip_167389	chr10	121519979:121520169:121538592:121538715:121551290:121551459	121538592:121538715
exon_skip_242373	chr10	121517334:121517463:121518682:121518829:121519979:121520167	121518682:121518829
exon_skip_253745	chr10	121551290:121551459:121564502:121564579:121593709:121593764	121564502:121564579
exon_skip_259053	chr10	121496532:121496722:121498495:121498605:121500826:121500947	121498495:121498605
exon_skip_268632	chr10	121551290:121551459:121593709:121593967:121597962:121597966	121593709:121593967
exon_skip_270896	chr10	121515117:121515319:121517319:121517463:121518682:121518829	121517319:121517463
exon_skip_42079	chr10	121564502:121564579:121565438:121565704:121593709:121593764	121565438:121565704
exon_skip_62481	chr10	121517334:121517463:121518682:121518829:121519979:121520169	121518682:121518829
exon_skip_70260	chr10	121538592:121538715:121551290:121551459:121593709:121593764	121551290:121551459
exon_skip_73681	chr10	121519979:121520169:121526155:121526194:121526729:121526954	121526155:121526194

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for FGFR2

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000358487	121483698	121483803	Frame-shift
ENST00000358487	121538592	121538715	Frame-shift
ENST00000358487	121551290	121551459	Frame-shift
ENST00000358487	121565438	121565704	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000358487	121565438	121565704	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000358487	121551290	121551459	Frame-shift
ENST00000358487	121498495	121498605	In-frame
ENST00000358487	121565438	121565704	In-frame

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Infer the effects of exon skipping event on protein functional features for FGFR2

p-ENSG00000066468_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000358487	4272	821	121565438	121565704	383	648	36	125

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000358487	4272	821	121565438	121565704	383	648	36	125

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000358487	4272	821	121565438	121565704	383	648	36	125
ENST00000358487	4272	821	121498495	121498605	1835	1944	520	557

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P21802	36	125	37	152	Alternative sequence	ID=VSP_019608;Note=In isoform 20. EPPTKYQISQPEVYVAAPGESLEVRCLLKDAAVISWTKDGVHLGPNNRTVLIGEYLQIKGATPRDSGLYACTASRTVDSETWYFMVNVTDAISSGDDEDDTDGAEDFVSENSNNKR->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P21802	36	125	37	125	Alternative sequence	ID=VSP_002964;Note=In isoform 4%2C isoform 21 and isoform 22. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:2377625;Dbxref=PMID:14702039,PMID:2377625
P21802	36	125	22	821	Chain	ID=PRO_0000016783;Note=Fibroblast growth factor receptor 2
P21802	36	125	62	107	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P21802	36	125	25	125	Domain	Note=Ig-like C2-type 1
P21802	36	125	83	83	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	123	123	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	57	57	Natural variant	ID=VAR_042204;Note=Polymorphism. S->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17344846,ECO:0000269\|PubMed:26429889;Dbxref=dbSNP:rs56226109,PMID:17344846,PMID:26429889
P21802	36	125	105	105	Natural variant	ID=VAR_004112;Note=In CS. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11781872,ECO:0000269\|PubMed:8946174;Dbxref=dbSNP:rs1434545235,PMID:11781872,PMID:8946174
P21802	36	125	22	377	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P21802	36	125	37	152	Alternative sequence	ID=VSP_019608;Note=In isoform 20. EPPTKYQISQPEVYVAAPGESLEVRCLLKDAAVISWTKDGVHLGPNNRTVLIGEYLQIKGATPRDSGLYACTASRTVDSETWYFMVNVTDAISSGDDEDDTDGAEDFVSENSNNKR->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P21802	36	125	37	125	Alternative sequence	ID=VSP_002964;Note=In isoform 4%2C isoform 21 and isoform 22. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:2377625;Dbxref=PMID:14702039,PMID:2377625
P21802	36	125	22	821	Chain	ID=PRO_0000016783;Note=Fibroblast growth factor receptor 2
P21802	36	125	62	107	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P21802	36	125	25	125	Domain	Note=Ig-like C2-type 1
P21802	36	125	83	83	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	123	123	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	57	57	Natural variant	ID=VAR_042204;Note=Polymorphism. S->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17344846,ECO:0000269\|PubMed:26429889;Dbxref=dbSNP:rs56226109,PMID:17344846,PMID:26429889
P21802	36	125	105	105	Natural variant	ID=VAR_004112;Note=In CS. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11781872,ECO:0000269\|PubMed:8946174;Dbxref=dbSNP:rs1434545235,PMID:11781872,PMID:8946174
P21802	36	125	22	377	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
P21802	36	125	37	152	Alternative sequence	ID=VSP_019608;Note=In isoform 20. EPPTKYQISQPEVYVAAPGESLEVRCLLKDAAVISWTKDGVHLGPNNRTVLIGEYLQIKGATPRDSGLYACTASRTVDSETWYFMVNVTDAISSGDDEDDTDGAEDFVSENSNNKR->G;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P21802	36	125	37	125	Alternative sequence	ID=VSP_002964;Note=In isoform 4%2C isoform 21 and isoform 22. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:2377625;Dbxref=PMID:14702039,PMID:2377625
P21802	36	125	22	821	Chain	ID=PRO_0000016783;Note=Fibroblast growth factor receptor 2
P21802	36	125	62	107	Disulfide bond	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00114
P21802	36	125	25	125	Domain	Note=Ig-like C2-type 1
P21802	36	125	83	83	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	123	123	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	36	125	57	57	Natural variant	ID=VAR_042204;Note=Polymorphism. S->L;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:17344846,ECO:0000269\|PubMed:26429889;Dbxref=dbSNP:rs56226109,PMID:17344846,PMID:26429889
P21802	36	125	105	105	Natural variant	ID=VAR_004112;Note=In CS. Y->C;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11781872,ECO:0000269\|PubMed:8946174;Dbxref=dbSNP:rs1434545235,PMID:11781872,PMID:8946174
P21802	36	125	22	377	Topological domain	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255
P21802	520	557	255	821	Alternative sequence	ID=VSP_002966;Note=In isoform 14. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1313574;Dbxref=PMID:1313574
P21802	520	557	366	821	Alternative sequence	ID=VSP_002974;Note=In isoform 19. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:1309608,ECO:0000303\|PubMed:7866434;Dbxref=PMID:1309608,PMID:7866434
P21802	520	557	550	554	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PVF
P21802	520	557	556	558	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PVF
P21802	520	557	22	821	Chain	ID=PRO_0000016783;Note=Fibroblast growth factor receptor 2
P21802	520	557	481	770	Domain	Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00159
P21802	520	557	525	541	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2PVF
P21802	520	557	549	549	Mutagenesis	Note=Constitutive kinase activity. N->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17803937;Dbxref=PMID:17803937
P21802	520	557	526	526	Natural variant	ID=VAR_023788;Note=In FSPC%3B constitutive kinase activity. K->E;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:16061565,ECO:0000269\|PubMed:17803937;Dbxref=dbSNP:rs121918507,PMID:16061565,PMID:17803937
P21802	520	557	549	549	Natural variant	ID=VAR_017276;Note=In CS%3B constitutive kinase activity. N->H;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11781872,ECO:0000269\|PubMed:17803937;Dbxref=dbSNP:rs1057519045,PMID:11781872,PMID:17803937
P21802	520	557	399	821	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255

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3'-UTR located exon skipping events that lost miRNA binding sites in FGFR2

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for FGFR2

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for FGFR2

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FGFR2

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for FGFR2

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
IFG	ESRP1	exon_skip_253745	4.017192e-01	3.779828e-02
IFG	ESRP1	exon_skip_42079	-4.858796e-01	8.759325e-03

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RelatedDrugs for FGFR2

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P21802	approved	DB00039	Palifermin	biotech	P21802
P21802	approved\|investigational\|withdrawn	DB01041	Thalidomide	small molecule	P21802
P21802	approved\|investigational	DB01109	Heparin	small molecule	P21802
P21802	approved	DB08896	Regorafenib	small molecule	P21802
P21802	approved\|investigational	DB08901	Ponatinib	small molecule	P21802
P21802	approved\|investigational	DB09078	Lenvatinib	small molecule	P21802
P21802	approved	DB09079	Nintedanib	small molecule	P21802
P21802	approved\|investigational	DB12010	Fostamatinib	small molecule	P21802

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RelatedDiseases for FGFR2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for FGFR2

Gene structures and expression levels for FGFR2

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for FGFR2

Open reading frame (ORF) annotation in the exon skipping event for FGFR2

Infer the effects of exon skipping event on protein functional features for FGFR2

3'-UTR located exon skipping events that lost miRNA binding sites in FGFR2

SNVs in the skipped exons for FGFR2

AD stage-associated exon skippint events for FGFR2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for FGFR2

Correlation with RNA binding proteins (RBPs) for FGFR2

RelatedDrugs for FGFR2

RelatedDiseases for FGFR2