ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for EGFR

Gene summary

Gene information	Gene symbol	EGFR
	Gene ID	1956
	Gene name	epidermal growth factor receptor
	Synonyms	ERBB\|ERBB1\|HER1\|NISBD2\|PIG61\|mENA
	Cytomap	7p11.2
	Type of gene	protein-coding
	Description	epidermal growth factor receptoravian erythroblastic leukemia viral (v-erb-b) oncogene homologcell growth inhibiting protein 40cell proliferation-inducing protein 61epidermal growth factor receptor tyrosine kinase domainerb-b2 receptor tyrosine kinas
	Modification date	20200329
	UniProtAcc	A0A068JCC9, A0A068JD88, A0A1W2PRR9, A0A1Y0DMK7, A2VCQ7, A7VMV4, A7VN05, A7VN06, A7VN07, B6RC65, B6RC66, C9JYS6, E2I6F5, E7BSV0, E9PFD7, F1JTL6, G9MC26, G9MC81, I3WA68, I3WA72, I3WA73, L0R6G1, P00533, Q147T7, Q30BI0, Q4H1F3, Q504U8, Q68GS6, Q75MF2, Q8NDU8, Q8WZA5, Q9H3C8, Q9H3D0,
	Context	- 32495567(Effects of Huangpu Tongqiao Capsules on EGFR-PLCgamma signal pathway of hippocampus in rats with Alzheimer's disease)

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

Gene	GO ID	GO term	PubMed ID
EGFR	GO:0001934	positive regulation of protein phosphorylation	20551055
EGFR	GO:0007165	signal transduction	10572067
EGFR	GO:0007166	cell surface receptor signaling pathway	7736574
EGFR	GO:0007173	epidermal growth factor receptor signaling pathway	7736574\|12435727
EGFR	GO:0008283	cell proliferation	17115032
EGFR	GO:0008284	positive regulation of cell proliferation	7736574
EGFR	GO:0010750	positive regulation of nitric oxide mediated signal transduction	12828935
EGFR	GO:0018108	peptidyl-tyrosine phosphorylation	22732145
EGFR	GO:0030307	positive regulation of cell growth	15467833
EGFR	GO:0042177	negative regulation of protein catabolic process	17115032
EGFR	GO:0042327	positive regulation of phosphorylation	15082764
EGFR	GO:0043406	positive regulation of MAP kinase activity	10572067
EGFR	GO:0045739	positive regulation of DNA repair	17115032
EGFR	GO:0045740	positive regulation of DNA replication	17115032
EGFR	GO:0045944	positive regulation of transcription by RNA polymerase II	20551055
EGFR	GO:0050679	positive regulation of epithelial cell proliferation	10572067
EGFR	GO:0050999	regulation of nitric-oxide synthase activity	12828935
EGFR	GO:0070141	response to UV-A	18483258
EGFR	GO:0070374	positive regulation of ERK1 and ERK2 cascade	20551055
EGFR	GO:0071392	cellular response to estradiol stimulus	20551055
EGFR	GO:1900020	positive regulation of protein kinase C activity	22732145
EGFR	GO:1903078	positive regulation of protein localization to plasma membrane	22732145

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Gene structures and expression levels for EGFR

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.

ENSG00000146648

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
DLPFC	UP	ENST00000455089.5	EGFR-207:protein_coding:EGFR	1.854481e+00	1.885384e+00	9.270677e-04	3.209616e-02
CB	UP	ENST00000455089.5	EGFR-207:protein_coding:EGFR	8.590210e-01	1.198051e+00	1.351011e-02	4.432763e-02

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 EGFR

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_225129	chr7	55143305:55143488:55146606:55146740:55151294:55151362	55146606:55146740

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 EGFR

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
ENST00000275493	55146606	55146740	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

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

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

p-ENSG00000146648_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
ENST00000275493	9838	1210	55146606	55146740	603	736	142	186

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

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

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
P00533	142	186	145	152	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UV7
P00533	142	186	183	185	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5XWD
P00533	142	186	25	1210	Chain	ID=PRO_0000016665;Note=Epidermal growth factor receptor
P00533	142	186	157	187	Disulfide bond	Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:1IVO,ECO:0000244\|PDB:1MOX,ECO:000024
P00533	142	186	175	175	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000244\|PDB:1IVO,ECO:0000244\|PDB:3NJP,ECO:0000269\|PubMed:12297050,ECO:0000269\|PubMed:12731890,ECO:0000269\|P
P00533	142	186	159	161	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UV7
P00533	142	186	164	166	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:4UV7
P00533	142	186	170	173	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1MOX
P00533	142	186	30	297	Natural variant	ID=VAR_066493;Note=Variant EGFR vIII%3B found in a lung cancer sample%3B somatic mutation%3B induces lung cancer when exogenously expressed. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16672372;Dbxref=PMID:16672372
P00533	142	186	75	300	Repeat	Note=Approximate
P00533	142	186	25	645	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

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

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

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 EGFR

- 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 EGFR

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 EGFR

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 EGFR

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for EGFR

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

UniProtAcc	DrugBank ID	Drug name	Drug activity	Drug type	Drug status
P00533	approved	DB00002	Cetuximab	biotech	P00533
P00533	approved\|investigational	DB00072	Trastuzumab	biotech	P00533
P00533	approved\|vet_approved	DB00281	Lidocaine	small molecule	P00533
P00533	approved\|investigational	DB00317	Gefitinib	small molecule	P00533
P00533	approved\|investigational	DB00530	Erlotinib	small molecule	P00533
P00533	approved\|investigational	DB01259	Lapatinib	small molecule	P00533
P00533	approved\|investigational	DB01269	Panitumumab	biotech	P00533
P00533	approved	DB05294	Vandetanib	small molecule	P00533
P00533	approved	DB08916	Afatinib	small molecule	P00533
P00533	approved	DB09330	Osimertinib	small molecule	P00533
P00533	approved\|investigational	DB09559	Necitumumab	biotech	P00533
P00533	approved\|investigational	DB11828	Neratinib	small molecule	P00533
P00533	approved\|investigational	DB11963	Dacomitinib	small molecule	P00533
P00533	approved\|investigational	DB12010	Fostamatinib	small molecule	P00533
P00533	approved\|investigational	DB12267	Brigatinib	small molecule	P00533

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RelatedDiseases for EGFR

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 EGFR

Gene structures and expression levels for EGFR

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

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

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

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

SNVs in the skipped exons for EGFR

AD stage-associated exon skippint events for EGFR

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

Correlation with RNA binding proteins (RBPs) for EGFR

RelatedDrugs for EGFR

RelatedDiseases for EGFR