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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: TMED2 (NCBI Gene ID:10959)

Gene Summary

Gene Summary

Gene Information	Gene Name: TMED2
	Gene ID: 10959
	Gene Symbol	TMED2
	Gene ID	10959
	Gene Name	transmembrane p24 trafficking protein 2
	Synonyms	P24A\|RNP24\|p24\|p24b1\|p24beta1
	Cytomap	12q24.31
	Type of Gene	protein-coding
	Description	transmembrane emp24 domain-containing protein 2coated vesicle membrane proteinmembrane protein p24Ap24 family protein beta-1transmembrane emp24 domain trafficking protein 2
	Modification date	20200313
	UniProtAcc	Q15363

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

GO ID	GO term
GO:0006417	Regulation of translation
GO:0006413	Translational initiation
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
Hgene	TMED2	GO:0006886	intracellular protein transport	20427317
Hgene	TMED2	GO:0034260	negative regulation of GTPase activity	10761932
Hgene	TMED2	GO:0072659	protein localization to plasma membrane	20361938

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
TMED2	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'TMED2[title] AND translation [title] AND human.'

Gene	Title	PMID
TMED2	.	.

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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
ENST00000262225	124074888	124074996	In-frame

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)
ENST00000262225	124074888	124074996	2569	480	587	201	124	160

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.
Q15363	124	160	21	201	Chain	ID=PRO_0000010381;Note=Transmembrane emp24 domain-containing protein 2
Q15363	124	160	21	168	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q15363	124	160	1	181	Region	Note=Interaction with F2RL1;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17693410;Dbxref=PMID:17693410
Q15363	124	160	118	157	Region	Note=Required for TMED10 and TMED2 cis-Golgi network localization
Q15363	124	160	117	167	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255

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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
KIRP	TMED2	-1.31893777335992	0.000713176093995571

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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
DLBC	TMED2	hsa-miR-30a-5p	88	0.331290471785384	0.0233863014717027
KICH	TMED2	hsa-miR-30a-5p	88	-0.327872444011685	0.00332077402304602
PCPG	TMED2	hsa-miR-30c-5p	86	0.410832521908471	0.000192345442558435

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
MESO	TMED2	-0.062529651	0.037023001
PAAD	TMED2	0.192415156	0.045775891
THYM	TMED2	0.175888302	0.046430552
SARC	TMED2	0.294605444	0.046497195

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with TMED2 (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
THYM	Cell metabolism gene	TMED2	GFPT1	0.846835651	1.07E-34
THYM	Cell metabolism gene	TMED2	ALG10	0.848458387	5.91E-35
THYM	Cell metabolism gene	TMED2	LMAN1	0.866256999	5.72E-38
THYM	Epifactor	TMED2	AEBP2	0.816049412	2.39E-30
THYM	IUPHAR	TMED2	TNFRSF10A	0.802347062	1.15E-28
THYM	IUPHAR	TMED2	ATP2A2	0.82922002	4.20E-32
THYM	TF	TMED2	ADNP2	0.810586297	1.16E-29
THYM	TF	TMED2	AEBP2	0.816049412	2.39E-30
THYM	TF	TMED2	ZNF664	0.839119518	1.60E-33
THYM	TSG	TMED2	TNFRSF10A	0.802347062	1.15E-28
UCS	Cell metabolism gene	TMED2	GFPT1	0.846835651	1.07E-34
UCS	Cell metabolism gene	TMED2	ALG10	0.848458387	5.91E-35
UCS	Cell metabolism gene	TMED2	LMAN1	0.866256999	5.72E-38
UCS	Epifactor	TMED2	AEBP2	0.816049412	2.39E-30
UCS	IUPHAR	TMED2	TNFRSF10A	0.802347062	1.15E-28
UCS	IUPHAR	TMED2	ATP2A2	0.82922002	4.20E-32
UCS	TF	TMED2	ADNP2	0.810586297	1.16E-29
UCS	TF	TMED2	AEBP2	0.816049412	2.39E-30
UCS	TF	TMED2	ZNF664	0.839119518	1.60E-33
UCS	TSG	TMED2	TNFRSF10A	0.802347062	1.15E-28
UVM	Cell metabolism gene	TMED2	SLC25A32	0.800097014	5.46E-19
UVM	IUPHAR	TMED2	SLC25A32	0.800097014	5.46E-19
UVM	IUPHAR	TMED2	IDE	0.801650418	4.15E-19
UVM	IUPHAR	TMED2	SLC35E3	0.8059063	1.94E-19
UVM	IUPHAR	TMED2	SLC30A6	0.822449824	8.43E-21
UVM	TSG	TMED2	DNAJA3	0.802324021	3.69E-19

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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
PRAD	TMED2	TMED9	1.52305630485258	0.000110686569292389
KIRP	TMED2	TMED7	-4.96458336532143	0.000177780166268349
THCA	TMED2	TMED7	-1.18842245190368	0.000184004079391529
KIRP	TMED2	NOTCH1	2.42717060781601	0.000334546435624361
LIHC	TMED2	TMED9	1.27624924626935	0.000837680065881122
KIRP	TMED2	SCFD1	1.71013810252937	0.00133262807503343
STAD	TMED2	SCFD1	1.98803301799122	0.00192895717918873
PRAD	TMED2	ARF1	1.25327075473145	0.00224782609453915
COAD	TMED2	TMED7	-2.76841912505026	0.00390031933784485
BLCA	TMED2	TMED10	-1.75880699412505	0.00391769409179688
LUSC	TMED2	NOTCH2	-2.40370704331476	0.00765883184752251
BLCA	TMED2	TMED4	-2.63520977431679	0.00823211669921875
LIHC	TMED2	TMED10	-10.9431952070679	0.0105240117726964
STAD	TMED2	NOTCH1	1.53524076803986	0.0111397774890065
BLCA	TMED2	ARF1	-2.85492040338458	0.014068603515625
BLCA	TMED2	SCFD1	-2.80983082393531	0.0229873657226562
HNSC	TMED2	NOTCH2	-2.74060158635258	0.0301271170746986
KICH	TMED2	TMED10	-1.5749810971249	0.0318078398704529
BRCA	TMED2	TMED4	-2.0648208914464	1.06097090545132e-08
HNSC	TMED2	TMED3	-1.91925251290308	1.37760207508109e-06
KIRP	TMED2	TMED3	-1.73469503524547	1.80229544639588e-05
KIRC	TMED2	ARF1	-1.3497769633198	1.88365218821087e-07
THCA	TMED2	TMED10	-3.09421108482075	2.69027427455582e-07
BRCA	TMED2	LMAN1	1.86923174354104	2.92764034831899e-11
KIRC	TMED2	NOTCH1	-2.64675932514903	3.2413838720108e-06
LIHC	TMED2	LMAN1	-1.28943371397605	3.4520382341717e-07
KICH	TMED2	LMAN1	1.44685942277428	5.38825988769531e-05
BRCA	TMED2	TMED9	-3.09752077578269	5.68656170814884e-20
KICH	TMED2	SCFD1	1.7973677375698	7.49826431274414e-05
KICH	TMED2	NOTCH2	2.1975198671307	8.34465026855468e-07

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

PPI interactors with TMED2

GORASP2, GORASP1, GOLGA2, Gorasp1, ELAVL1, TMED4, SDHB, LMAN1, TMED9, SEC23B, UBL4A, AKT2, TMED10, TMED3, CHST8, ERGIC1, HNRNPUL1, HSD17B12, RPS10, TM9SF4, ATP1A1, EIF3I, LMAN2, RAB1A, RAB1B, LOC101929876, RPS26, SRPRB, MED20, TCTN3, CEP128, TCTN1, Tmed10, FAF2, PTAR1, GOLGB1, TMED7, DNAJC30, USP22, FGFRL1, ATP9A, PNPT1, TMED1, LIPG, OSBPL6, ATP8B2, ATP12A, TMED5, PTPRO, LNX1, ESR2, AGR2, RECQL4, KIAA1429, KRAS, CYB5R3, TOMM6, NOD2, CALR3, FANCD2, M, ORF7b, RAB5A, EMC1, EMC2, MMGT1, nsp4, nsp5, nsp6, ORF6, E, ESR1, ORF8, ORF7a, HSCB, CIT, PRC1, FASN, NR3C1, DNAJC25, PMAIP1, DDRGK1, CALU, LRRC59, PDIA4, SEC61B, SYNE3, VAPA, FGF3, CDK5RAP3, HERC5, CTXN1, ZDHHC13, CYBA, ERGIC2, SMPD2, PA2G4, MAGT1, UQCRH, ERGIC3, SPPL2B, EMC7, TMEM106B, CNR2, KLF16, KLF8,

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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
TMED2	SKCM	chr12	124071410	124071410	C	T	Silent	p.S99S	2
TMED2	BRCA	chr12	124074976	124074976	G	A	Missense_Mutation	p.R154Q	2
TMED2	UCEC	chr12	124071385	124071385	A	G	Missense_Mutation	p.K91R	2
TMED2	SKCM	chr12	124081261	124081261	C	T	Silent	p.V197V	2
TMED2	UCEC	chr12	124071422	124071422	A	T	Silent	p.P103	2
TMED2	BRCA	chr12	124081212	124081212	T	A	Missense_Mutation	p.V181D	2
TMED2	UCEC	chr12	124081218	124081223	TGACAT	-	In_Frame_Del	p.TL184in_frame_del	2
TMED2	STAD	chr12	124069277	124069277	T	C	Missense_Mutation	p.C32R	2
TMED2	STAD	chr12	124074954	124074954	G	A	Missense_Mutation	p.E147K	2
TMED2	STAD	chr12	124074934	124074934	C	T	Missense_Mutation	p.A140V	2
TMED2	KIRC	chr12	124069276	124069276	G	A	Silent	p.E31E	2
TMED2	SARC	chr12	124069230	124069230	C	T	Missense_Mutation	p.A16V	2
TMED2	UCEC	chr12	124071320	124071320	T	G	Missense_Mutation	p.I69M	2
TMED2	UCEC	chr12	124071330	124071330	G	A	Missense_Mutation	p.D73N	2
TMED2	UCEC	chr12	124071336	124071336	G	T	Nonsense_Mutation	p.E75*	2
TMED2	LUAD	chr12	124071432	124071432	A	T	Missense_Mutation	p.M107L	1
TMED2	LUSC	chr12	124074954	124074954	G	T	Nonsense_Mutation	p.E147*	1
TMED2	MESO	chr12	124069211	124069211	C	G	Missense_Mutation		1
TMED2	SKCM	chr12	124081262	124081262	C	T	Missense_Mutation	p.R198W	1
TMED2	CHOL	chr12	124069354	124069354	C	T	Silent		1
TMED2	MESO	chr12	124069211	124069211	C	G	Missense_Mutation	p.L10V	1
TMED2	SKCM	chr12	124081200	124081200	C	T	Missense_Mutation	p.A177V	1
TMED2	CHOL	chr12	124071376	124071376	G	T	Missense_Mutation		1
TMED2	SARC	chr12	124071371	124071371	G	T	Translation_Start_Site		1
TMED2	CHOL	chr12	124071376	124071376	G	T	Missense_Mutation	p.G88V	1
TMED2	SARC	chr12	124071360	124071360	G	T	Missense_Mutation		1
TMED2	HNSC	chr12	124069243	124069243	C	G	Silent		1
TMED2	SARC	chr12	124069230	124069230	C	T	Missense_Mutation		1
TMED2	HNSC	chr12	124069243	124069243	C	G	Silent	p.G20G	1
TMED2	SARC	chr12	124069231	124069231	C	T	Silent		1
TMED2	UCEC	chr12	124081218	124081223	TGACAT	-	In_Frame_Del	p.TL184del	1
TMED2	KIRC	chr12	124069310	124069310	A	G	Missense_Mutation	p.M43V	1
TMED2	SARC	chr12	124069231	124069231	C	T	Silent	p.A16A	1
TMED2	BLCA	chr12	124069350	124069350	A	G	Missense_Mutation		1
TMED2	LIHC	chr12	124069288	124069288	G	T	Missense_Mutation		1
TMED2	SARC	chr12	124069231	124069231	C	T	Silent	p.A16	1
TMED2	BLCA	chr12	124069350	124069350	A	G	Missense_Mutation	p.D56G	1

Copy number variation (CNV) of TMED2
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across TMED2
* 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
91451	STAD	TCGA-BR-8364-01A	CLIP1	chr12	122861936	-	TMED2	chr12	124081152	+
91451	N/A	AX188335	CMTM4	chr16	66697019	+	TMED2	chr12	124081799	-
91451	N/A	BE858941	MDK	chr11	46405298	-	TMED2	chr12	124081861	-
91451	BRCA	TCGA-LD-A7W6-01A	PCBP2	chr12	53862616	+	TMED2	chr12	124082475	+
91451	N/A	EC573613	RP11-445O3.2	chr5	4546969	+	TMED2	chr12	124082289	+
91452	N/A	AX184750	TMED2	chr12	124081799	+	CMTM4	chr16	66697019	-
102664	LUAD	TCGA-86-6851-01A	TMED2	chr12	124074996	+	FAM101A	chr12	124796364	+
101073	N/A	AX395954	TMED2	chr12	124082631	+	LGR5	chr12	71978829	-
92317	BRCA	TCGA-A8-A08L-01A	TMED2	chr12	124074996	+	MTCP1	chrX	154293812	-
91452	N/A	DA857875	TMED2	chr12	124069276	+	PARM1	chr4	75858327	+
98007	N/A	BM752192	TMED2	chr12	124082124	+	PPIA	chr7	44836280	+
100924	N/A	AX341547	TMED2	chr12	124081633	+	PPP2R5E	chr14	63840897	+
91452	N/A	AA469160	TMED2	chr12	124083129	+	SYN3	chr22	33082398	-
100772	STAD	TCGA-BR-A4PE-01A	TMED2	chr12	124074996	+	TGIF1	chr18	3456352	+
91452	N/A	AA533651	TMED2	chr12	124081419	+	TMED2	chr12	124081353	-
91452	N/A	AI791655	TMED2	chr12	124081353	+	TMED2	chr12	124081419	-
91452	N/A	BQ776227	TMED2	chr12	124071308	-	TMED2	chr12	124069247	+
100388	N/A	CF125471	TMED2	chr12	124071482	+	WLS	chr1	68698039	-

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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
KIRP	TMED2	0.00384037036160169	0.11
LUAD	TMED2	0.0347211684342591	0.94

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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
KIRP	TMED2	0.0277689923128327	0.89
THYM	TMED2	0.00825935614471309	0.27

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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
C0151744	Myocardial Ischemia	1	CTD_human