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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: SERP1 (NCBI Gene ID:27230)

Gene Summary

Gene Summary

Gene Information	Gene Name: SERP1
	Gene ID: 27230
	Gene Symbol	SERP1
	Gene ID	27230
	Gene Name	stress associated endoplasmic reticulum protein 1
	Synonyms	RAMP4
	Cytomap	3q25.1
	Type of Gene	protein-coding
	Description	stress-associated endoplasmic reticulum protein 1ribosome associated membrane protein 4ribosome-attached membrane protein 4
	Modification date	20200313
	UniProtAcc	Q9Y6X1

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0006417	Regulation of translation
GO:0005840	Ribosome
GO:0045727	Positive regulation of translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
SERP1	(355.7 - 733]

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Translation Studies in PubMed

We searched PubMed using 'SERP1[title] AND translation [title] AND human.'

Gene	Title	PMID
SERP1	.	.

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Exon Skipping Events

Skipped exons in TCGA and GTEx 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.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events 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.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000479209	150263489	150263565	Frame-shift

Exon skipping position in the amino acid sequence.

ENST

Exon skip start (DNA)

Exon Skip end (DNA)

Len(transcript seq)

Exon skip start (mRNA)

Exon Skip end (mRNA)

Len(amino acid seq)

Exon skip start (AA)

Exon Skip end (AA)

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc

Exon skip start (AA)

Exon Skip end (AA)

Function feature start (AA)

Function feature end (AA)

Functional feature type

Functional feature desc.

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
LIHC	SERP1	-1.18382388675902	0.0117519726237409
KIRP	SERP1	1.16553853677872	3.54833900928498e-07

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type	Gene	miRNA	TargetScan binding score (Context++ score percentile)	Coefficient	Pvalue
OV	SERP1	hsa-miR-27b-3p	87	-0.361137197985145	0.00886879603833395

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
TGCT	SERP1	-0.068751282	0.04618177

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with SERP1 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type

Gene group

Translation factor

Correlated gene

Coefficient

Pvalue

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
KIRP	SERP1	SEC61A1	-3.20496014730735	0.00016188295558095
HNSC	SERP1	VAMP2	1.8022226059167	0.000163285275220915
LIHC	SERP1	VAMP2	1.63645169970466	0.000341801925418751
KICH	SERP1	UBE2J2	1.73001793038243	0.000489473342895508
LUAD	SERP1	HMOX1	-1.13208899876975	0.000946439675051467
COAD	SERP1	SEC61G	-5.41038695520821	0.00144392251968384
LUAD	SERP1	UBE2J2	-3.76603754902323	0.0018074900119541
LUAD	SERP1	SEC61B	-2.32114007409432	0.00280308004336457
KIRP	SERP1	HMOX1	2.65582910063891	0.00294740917161107
STAD	SERP1	SEC61A1	-1.88998846847012	0.00294740917161107
CHOL	SERP1	CYB5A	-3.80733178330297	0.00390625
CHOL	SERP1	XBP1	-8.46435000705812	0.00390625
CHOL	SERP1	SEC61B	-2.97215588829574	0.0078125
PRAD	SERP1	SEC61G	-2.16268367639515	0.0312569736289674
STAD	SERP1	SEC61G	-1.56324112840461	0.0358188794925809
CHOL	SERP1	SEC61G	-2.00137220268497	0.0390625
KICH	SERP1	SEC61B	-4.0943425800432	0.0393387079238892
LUSC	SERP1	SEC61B	-2.12105887233033	0.0405499559725146
COAD	SERP1	STX5	1.25117900731569	0.0463311672210694
THCA	SERP1	HMOX1	-2.15494121531135	1.10352030163672e-06
KIRC	SERP1	VAMP2	-3.14478000511798	1.24447204814406e-10
LUAD	SERP1	CYB5A	-1.32168806444923	1.40840364087473e-09
LUSC	SERP1	STX1A	-5.29589817678553	2.02303326988093e-08
BRCA	SERP1	SEC61B	-1.78158851602912	2.17107710907341e-07
BRCA	SERP1	HMOX1	-2.62880267149677	2.26546920634303e-06
KIRC	SERP1	SEC61A1	-1.52636476875725	2.2690774310224e-06
KICH	SERP1	SEC61G	-1.52816791741908	2.66432762145996e-05
KIRP	SERP1	STX1A	-1.34096364095222	2.84211710095406e-05
HNSC	SERP1	CYB5A	1.70037180409334	2.97245203455532e-05
BRCA	SERP1	SEC61G	-2.36615187420152	3.3703497882398e-23
LUSC	SERP1	HMOX1	-2.81385558928862	3.49701144711369e-07
KIRC	SERP1	SEC61B	-1.17237328013735	3.8520824094777e-05
KICH	SERP1	VAMP2	-2.9047502444867	4.17232513427734e-07
KIRP	SERP1	CYB5A	-2.1023128658139	4.6566128730774e-10
COAD	SERP1	SEC61A1	-2.98853358461324	5.1647424697876e-05
PRAD	SERP1	SEC61A1	1.73121902517327	5.60797254840577e-07
KICH	SERP1	CYB5A	-1.79698101619284	5.96046447753906e-08
LIHC	SERP1	HMOX1	-2.59010775031154	7.18311440405189e-08
BRCA	SERP1	STX1A	-1.92137354863472	9.64837825071027e-18

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with SERP1

SCNN1B, SCNN1G, SCNN1A, APP, VKORC1, LOC100355886, BAG6, ASNA1, DNAJB1, HSPA4, HSPA8, SGTA, TMEM79, LMNA, GLP1R, CD74, TNFRSF9, CYBRD1, SAR1A, SLC35C2, AQP6, BIK, AQP8, STX4, CD79A, STX1A, STX2, APH1A, MTIF3, FAM210B, FAM209A, CRB3, TMEM14B, SLC10A6, EBP, HIATL1, LPPR1, TMEM56, KCNF1, GPX8, SSMEM1, TMEM52B, SEC11C, BSCL2, REEP4, GKN1, GPR37L1, HSD17B13, JAGN1, FRMD3, FAM174A, IL3RA, GJB3, GJB5, LHFPL5, ALG3, KIR3DL3, SLC22A1, SLC22A2, DDX58,

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Mutations

Clinically associated variants from ClinVar.

Gene

Chr

Position

RefSeq

VarSeq

RefSeeq

VarType

Pathogenic

Disease

VarInfo

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
SERP1	LIHC	chr3	150263506	150263506	A	-	Frame_Shift_Del	p.F48fs	4
SERP1	UCEC	chr3	150263564	150263564	C	A	Missense_Mutation	p.R29I	2
SERP1	CESC	chr3	150263566	150263566	C	T	Splice_Site		2
SERP1	UCEC	chr3	150263456	150263456	G	T	Missense_Mutation	p.S65Y	2
SERP1	KIRC	chr3	150263555	150263555	G	A	Missense_Mutation	p.P32L	1
SERP1	LIHC	chr3	150262283	150262283	T	C	Missense_Mutation	p.I55V	1
SERP1	LUSC	chr3	150263869	150263869	G	A	Silent	p.I18I	1
SERP1	LUSC	chr3	150263884	150263884	C	A	Missense_Mutation	p.K13N	1
SERP1	SARC	chr3	150301010	150301010	G	T	Silent		1
SERP1	BLCA	chr3	150263499	150263499	A	C	Missense_Mutation		1
SERP1	SKCM	chr3	150263527	150263527	C	T	Nonsense_Mutation	p.W41*	1
SERP1	BLCA	chr3	150263499	150263499	A	C	Missense_Mutation	p.C51G	1
SERP1	SKCM	chr3	150263528	150263528	C	T	Nonsense_Mutation	p.W41*	1
SERP1	STAD	chr3	150263978	150263978	C	A	Translation_Start_Site		1
SERP1	CESC	chr3	150264652	150264652	C	T	RNA	NULL	1
SERP1	STAD	chr3	150263861	150263861	C	G	Missense_Mutation		1
SERP1	CESC	chr3	150263566	150263566	C	T	Splice_Site	e2-1	1

Copy number variation (CNV) of SERP1
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across SERP1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
85839	N/A	CB054155	C15orf41	chr15	36952190	+	SERP1	chr3	150262005	+
85839	N/A	EC582035	CCSER1	chr4	92399933	-	SERP1	chr3	150261975	+
85839	N/A	AI675212	DLEU1	chr13	51235176	+	SERP1	chr3	150262131	+
85839	N/A	AA075049	GABRG1	chr4	46100453	+	SERP1	chr3	150262286	-
85839	SKCM	TCGA-ER-A19W-06A	MBNL1	chr3	152150709	+	SERP1	chr3	150284893	-
88292	N/A	BG388672	SERP1	chr3	150190248	-	KIAA1217	chr10	23987824	-
83776	STAD	TCGA-BR-8284-01A	SERP1	chr3	150284688	-	MBNL1	chr3	152132730	+
92973	N/A	BF340136	SERP1	chr3	150259785	-	MPPED1	chr22	43841809	-
91495	N/A	BQ183150	SERP1	chr3	150263938	+	SRPK2	chr7	104773523	+
95902	N/A	BF344624	SERP1	chr3	150262008	-	UBAP1L	chr15	65398996	-
82324	N/A	BE161616	SERP1	chr3	150261195	-	UNK	chr17	73787306	+
85839	BRCA	TCGA-E2-A1II-01A	SIAH2	chr3	150480220	-	SERP1	chr3	150284893	-
85839	STAD	TCGA-BR-A4PE-01A	SPINT1	chr15	41137227	+	SERP1	chr3	150284893	-

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
SARC	SERP1	0.00825385173920196	0.23
KIRP	SERP1	0.0113073821305981	0.31
STAD	SERP1	0.0161372068646909	0.42
THCA	SERP1	0.0175524955783627	0.44

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
THCA	SERP1	0.0397219177605554	1
LGG	SERP1	0.00023745087473138	0.0078
BRCA	SERP1	0.0474351081923072	1
SKCM	SERP1	0.041442491101604	1
UCEC	SERP1	0.000435696938972913	0.014

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Related Drugs

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

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID

Disease Name

# PubMeds

Disease source