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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: LIN28A (NCBI Gene ID:79727)

Gene Summary

Gene Summary

Gene Information	Gene Name: LIN28A
	Gene ID: 79727
	Gene Symbol	LIN28A
	Gene ID	79727
	Gene Name	lin-28 homolog A
	Synonyms	CSDD1\|LIN-28\|LIN28\|ZCCHC1\|lin-28A
	Cytomap	1p36.11
	Type of Gene	protein-coding
	Description	protein lin-28 homolog ARNA-binding protein LIN-28zinc finger CCHC domain-containing protein 1zinc finger, CCHC domain containing 1
	Modification date	20200322
	UniProtAcc	Q9H9Z2

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

GO ID	GO term
GO:0017148	Negative regulation of translation
GO:0006417	Regulation of translation
GO:0045727	Positive regulation of translation
GO:0002181	Cytoplasmic 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
LIN28A	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'LIN28A[title] AND translation [title] AND human.'

Gene	Title	PMID
LIN28A	.	.

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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

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

adj.pval

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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

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
CHOL	LIN28A	2	1	0.0307534966364818	0.336634022038567	0.180231439393939	0.738846976201091	1.39816591559567
UCEC	LIN28A	2	1	0.00979615515967982	0.300294871194379	0.162620254339553	-0.142074603530491	0.217911091033772

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
DLBC	LIN28A	2	3	0.0347861002651992	0.400917226890756	0.655519387755102	1.19961877533234	0.71080406945

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
LIHC	LIN28A	-0.012374055	0.014429177

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with LIN28A (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
CHOL	IUPHAR	LIN28A	HTR1E	0.816682041	7.93E-12
CHOL	IUPHAR	LIN28A	GPR6	0.821783138	4.57E-12
CHOL	IUPHAR	LIN28A	FABP2	0.844440793	3.12E-13
CHOL	IUPHAR	LIN28A	TAAR6	0.866785238	1.41E-14
CHOL	TF	LIN28A	MSGN1	0.866785238	1.41E-14
TGCT	Epifactor	LIN28A	DPPA3	0.800010972	5.45E-36
TGCT	Epifactor	LIN28A	AURKA	0.805430673	8.23E-37
TGCT	IUPHAR	LIN28A	AURKA	0.805430673	8.23E-37
TGCT	Kinase	LIN28A	AURKA	0.805430673	8.23E-37
TGCT	TF	LIN28A	ARID3B	0.852059184	3.82E-45
TGCT	TF	LIN28A	FOXH1	0.861177873	4.12E-47

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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
LIHC	LIN28A	POU5F1	-4.77673145264574	0.000263325268073385
KIRC	LIN28A	TRIM71	-1.72374332356924	0.000294681332419049
PRAD	LIN28A	SOX2	-3.9477998039979	0.000791075079951539
THCA	LIN28A	KLF4	-2.81921715489122	0.00112615620207012
HNSC	LIN28A	POU5F1	-1.82253221062701	0.0014147440645047
LIHC	LIN28A	SALL4	1.10911208584394	0.00323738381247511
CHOL	LIN28A	TUT1	-3.79709296246396	0.00390625
LUSC	LIN28A	TUT1	-1.06977079427873	0.00418864341551449
KIRP	LIN28A	TRIM71	-1.87622711327744	0.00527895997429013
KICH	LIN28A	NANOG	1.35500397586069	0.00672554969787598
PRAD	LIN28A	SALL4	1.08843829166211	0.00907687285353705
COAD	LIN28A	SOX2	1.09282234082593	0.0110453069210053
CHOL	LIN28A	ZCCHC6	-7.22209762803066	0.02734375
STAD	LIN28A	NANOG	-3.94900325489234	0.028887763494347
READ	LIN28A	TUT1	-2.74832504699882	0.03125
CHOL	LIN28A	ZCCHC11	2.70414463340831	0.0390625
PRAD	LIN28A	TUT1	1.84422223754928	1.02977929185394e-06
STAD	LIN28A	SOX2	-6.13634024860629	1.11940316855908e-05
BLCA	LIN28A	KLF4	-3.15022273927776	1.1444091796875e-05
LUSC	LIN28A	KLF4	-1.10280265474584	2.3637790353623e-06
LUAD	LIN28A	KLF4	-5.02800387455212	2.93315225525545e-10
LUSC	LIN28A	SOX2	4.04311665476673	2.9495431998617e-08
COAD	LIN28A	TUT1	-2.36693462096329	2.98023223876954e-07
COAD	LIN28A	KLF4	-1.60505850394383	2.98023223876954e-08
THCA	LIN28A	ZCCHC6	1.60276948837993	3.35959958932981e-05
THCA	LIN28A	ZCCHC11	-1.02904440345021	4.22574981970489e-05
HNSC	LIN28A	SALL4	-2.53591748937606	4.35534275311512e-09
LIHC	LIN28A	ZCCHC6	-1.61500566300055	4.44908704487695e-07
KIRC	LIN28A	POU5F1	1.60944809981704	4.4523606197609e-12
THCA	LIN28A	SALL4	-2.55166038010611	4.87027791984247e-06
LUAD	LIN28A	TUT1	-2.125133012661	5.3012005084452e-06
LIHC	LIN28A	KLF4	3.97988748432668	6.01468343739179e-07
LUAD	LIN28A	TRIM71	-5.14884793069944	8.51355532875163e-11
KIRC	LIN28A	ZCCHC6	-2.2526040296022	9.9540413319149e-05

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

PPI interactors with LIN28A

DOT1L, ZFP36, AATF, BRIX1, BYSL, NOA1, CDC5L, DDX50, DHX57, FASTKD2, FBL, GADD45GIP1, H1F0, HNRNPUL2, HP1BP3, ICT1, KRI1, KRR1, LARP4, TRIM71, LTV1, METTL17, MEPCE, NCBP1, NHP2, NOB1, NOC3L, NOL6, NOP10, PHAX, POP1, PRPF19, DHX8, ZC3HAV1, PURA, PTCD1, SNRPG, PRPF3, DDX41, TCOF1, ZBTB11, STRBP, RALY, SNRPB, IFIT5, EBNA1BP2, UPF1, SF3B2, NCBP2, SRRT, SRP72, SNRPB2, LARP7, KPNA4, PWP1, SNRNP70, RBM28, RBM34, HNRNPAB, RRP12, RRS1, SNRPF, SREK1, SNRPA, SRP14, SRRM1, PPAN, SURF6, TGS1, TSR1, RRP9, XRN2, ZC3H11A, CCBL2, DHX36, DKC1, HNRNPA3, IGF2BP3, LARP1, LARP4B, NHP2L1, NOP2, SND1, SSB, ZDHHC17, L1TD1, TRIM25, MIRLET7A1, MIR363, UBE3A, EZH2, USP28, ZNF275, FBXL19-AS1, MIRLET7A2, MIRLET7A3, MIRLET7B, MIRLET7C, MIRLET7D, MIRLET7E, MIRLET7F1, MIRLET7F2, MIRLET7G, MIRLET7I, MIR98, MIR1-1, MIR1-2, MIR7-1, MIR7-2, MIR7-3, MIR9-1, MIR9-2, MIR10B, MIR15A, MIR15B, MIR16-1, MIR16-2, MIR17, MIR18A, MIR18B, MIR19A, MIR19B1, MIR19B2, MIR20A, MIR20B, MIR21, MIR25, MIR29A, MIR29B1, MIR29B2, MIR29C, MIR31, MIR34A, MIR34B, MIR34C, MIR92A2, MIR93, MIR106A, MIR106B, MIR107, MIR122, MIR128-1, MIR128-2, MIR138-1, MIR138-2, MIR140, MIR141, MIR143, MIR145, MIR155, MIR199A1, MIR199A2, MIR200A, MIR200B, MIR200C, MIR205, MIR206, MIR214, MIR221, MIR222, MIR429, MIR451A, FASN, RPL35A, PABPC1, PABPC4, MED18, RPL35, RPS19, RPL23A, HIST1H2AI, TUBA1B, YBX1, RPL6, IGF2BP1, RPL29, RPL31, HIST1H1E, DCD, ADNP, WDR43, LIN28B, REXO4, ZCCHC3, ZNF768, RBM19, DDX24, MRPL32, ZNF346, CMSS1, MPHOSPH10, RSL24D1, RPS3, PURB, MRPL1, MRPL9, PRDM10, MRPL21, RPS17, ZC3H8, MRPL57, FTSJ3, MRPL10, U2SURP, CDK12, SRSF12, ZFR, FBLL1, SRP68, GPATCH11, SF3B1, NIP7, MRPL30, MRPL27, MRPL47, RSL1D1, MRPL3, MRPL15, APOBEC3C, LARP1B, RPS10, RPS15, CHERP, ZNF384, UNC50, RSBN1, NOC4L, MRPL13, RPL26L1, MRPL22, HIST1H1C, MRPL20, STAU1, MRPL2, GLE1, MRPL50, CCDC86, MRPL28, RPL36AL, DDX18, HNRNPC, MRPS30, C8orf33, ZNF668, SCAF1, MRPL16, PRR3, MRPL24, RPS5, RPL17, ZNF22, GLYR1, HIST1H1T, THUMPD1, MAK16, MRPS9, APOBEC3F, PABPC4L, MOV10, SRSF1, STK38, FARS2, RPS2, DDX31, STAU2, RBM17, RPL3, H2AFX, CDKN2AIP, THUMPD3, ZNF672, SKIV2L, RPS26, MRPS18B, MRPL42, NIFK, BCAS2, GNL2, XRN1, DDX10, MRPS27, MRPS25, NOM1, NOP14, RPLP0, ZNF770, CASC3, DUSP11, MRPL4, EPB41L5, RPS4Y2, MRPS15, MRPS24, C1orf35, RRP1B, YBX3, ZFP91, MRPS34, PUM1, CRNKL1, BUD13, DDX56, GTPBP4, RPL7L1, BMS1, SUGP2, DDX55, SRSF5, RPLP2, TRUB2, DDX28, MRPS16, PAK1IP1, RPL10A, ABT1, SPATS2L, ERAL1, RPS24, LUC7L, PDCD11, ZCCHC6, YTHDF1, ZNF629, PUM2, RPL27, RPL26, NKRF, NSA2, HIST2H2AC, WBSCR16, FAM111A, DIMT1, PTCD3, NAT10, ZNF574, APOBEC3B, MRPL40, MRPL38, ZNF512, PRPF4B, RPSA, RPL37A, FAM120A, DHX30, MRPS31, ZNF16, UTP3, DDX54, MRPL17, MRPS18A, MRPS14, MRPS7, TOE1, RPS27A, MTERF3, CTCF, MRPS26, NCL, RPS14, RPL4, MRPS10, DICER1, ZNF638, RPL9, RPL8, RPL15, CACTIN, NGDN, CEBPZ, RSBN1L, TTC37, RPF2, GLTSCR2, RPS20, C7orf50, RPF1, HELZ, KIAA0020, SRSF10, HJURP, MRPL46, ZCRB1, PRKRA, RPL18, DAP3, MRPS35, WHSC1, CLK3, NGRN, RRP15, IREB2, NOL10, NOC2L, MRPL55, YTHDC1, DIS3L2, NOP9, MRPL11, MRPS18C, SUPV3L1, YTHDC2, HERC5, TPPP, RBM39, CCDC137, IMP3, PRKRIR, FAM207A, RPS3A, RPS13, RPL11, MRPL48, PTBP1, Pcbp1,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
LIN28A	chr1	26737932	C	G	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant

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
LIN28A	LUAD	chr1	26738039	26738039	C	T	Missense_Mutation	p.A65V	5
LIN28A	SKCM	chr1	26751942	26751942	G	A	Missense_Mutation	p.G126E	4
LIN28A	UCEC	chr1	26751952	26751952	G	A	Missense_Mutation	p.M129I	3
LIN28A	HNSC	chr1	26752814	26752814	G	C	Missense_Mutation	p.Q165H	3
LIN28A	SKCM	chr1	26751877	26751877	G	A	Silent	p.L104L	2
LIN28A	SKCM	chr1	26751920	26751920	G	A	Missense_Mutation	p.G119R	2
LIN28A	UCEC	chr1	26737393	26737393	T	C	Missense_Mutation	p.V4A	2
LIN28A	LIHC	chr1	26751824	26751824	T	A	Missense_Mutation		2
LIN28A	BLCA	chr1	26752761	26752761	C	T	Missense_Mutation	p.H148Y	2
LIN28A	UCEC	chr1	26752893	26752893	C	T	Nonsense_Mutation	p.R192*	2
LIN28A	BLCA	chr1	26752886	26752886	C	G	Silent	p.T189T	2
LIN28A	SKCM	chr1	26752889	26752889	C	T	Silent	p.Y190Y	2
LIN28A	LIHC	chr1	26752785	26752785	C	-	Frame_Shift_Del	p.P156fs	2
LIN28A	LIHC	chr1	26752791	26752791	C	-	Frame_Shift_Del	p.P158fs	2
LIN28A	CESC	chr1	26752837	26752837	C	G	Nonsense_Mutation	p.S173*	2
LIN28A	STAD	chr1	26752823	26752823	C	T	Silent	p.S168S	2
LIN28A	STAD	chr1	26751895	26751895	C	T	Silent	p.T110T	2
LIN28A	KIRC	chr1	26737960	26737960	C	T	Missense_Mutation	p.H39Y	1
LIN28A	BLCA	chr1	26752886	26752886	C	G	Silent		1
LIN28A	LUAD	chr1	26751806	26751806	A	G	Missense_Mutation	p.M81V	1
LIN28A	COAD	chr1	26751862	26751862	G	C	Missense_Mutation	p.K99N	1
LIN28A	THYM	chr1	26737968	26737968	G	T	Silent		1
LIN28A	LGG	chr1	26751871	26751871	G	T	Missense_Mutation	p.K102N	1
LIN28A	BLCA	chr1	26737974	26737974	C	T	Silent		1
LIN28A	COAD	chr1	26752734	26752734	T	A	Missense_Mutation	p.C139S	1
LIN28A	LIHC	chr1	26751794	26751794	A	G	Missense_Mutation		1
LIN28A	BLCA	chr1	26752802	26752802	C	G	Missense_Mutation		1
LIN28A	HNSC	chr1	26751932	26751932	C	T	Missense_Mutation		1
LIN28A	HNSC	chr1	26752814	26752814	G	C	Missense_Mutation		1
LIN28A	LIHC	chr1	26751824	26751824	T	A	Missense_Mutation	p.L87M	1
LIN28A	HNSC	chr1	26752798	26752798	A	C	Missense_Mutation		1
LIN28A	BLCA	chr1	26737974	26737974	C	T	Silent	p.I43I	1
LIN28A	SKCM	chr1	26751818	26751818	C	T	Missense_Mutation	p.R85W	1
LIN28A	HNSC	chr1	26752828	26752828	T	C	Missense_Mutation		1
LIN28A	BLCA	chr1	26752802	26752802	C	G	Missense_Mutation	p.C161W	1
LIN28A	SKCM	chr1	26752948	26752948	G	A	Silent	p.210	1
LIN28A	HNSC	chr1	26752798	26752798	A	C	Missense_Mutation	p.K160T	1
LIN28A	LIHC	chr1	26737998	26737998	G	-	Frame_Shift_Del	p.M51fs	1
LIN28A	CESC	chr1	26751847	26751847	G	T	Missense_Mutation		1
LIN28A	SKCM	chr1	26737876	26737876	G	A	Splice_Site		1
LIN28A	HNSC	chr1	26752828	26752828	T	C	Missense_Mutation	p.M170T	1
LIN28A	LUAD	chr1	26751830	26751830	G	A	Missense_Mutation	p.E89K	1
LIN28A	CESC	chr1	26752837	26752837	C	G	Nonsense_Mutation		1
LIN28A	HNSC	chr1	26751932	26751932	C	T	Missense_Mutation	p.R123W	1
LIN28A	BLCA	chr1	26752761	26752761	C	T	Missense_Mutation		1
LIN28A	LUAD	chr1	26751900	26751900	C	T	Missense_Mutation	p.P112L	1
LIN28A	COAD	chr1	26737993	26737993	C	T	Missense_Mutation	p.R50C	1
LIN28A	STAD	chr1	26751934	26751934	G	A	Silent	p.R123R	1

Copy number variation (CNV) of LIN28A
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across LIN28A
* 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
77985	HNSC	TCGA-DQ-7591-01A	EIF4G3	chr1	21267984	-	LIN28A	chr1	26737877	+
73161	TGCT	TCGA-2G-AAFV-01A	LIN28A	chr1	26738073	+	CD52	chr1	26646662	+
44745	TGCT	TCGA-2G-AAGN	LIN28A	chr1	26843881	+	EXO1	chr1	242055823	+
44745	TGCT	TCGA-2G-AAGS	LIN28A	chr1	26843880	+	EXO1	chr1	242055823	+
44745	TGCT	TCGA-2G-AAGT	LIN28A	chr1	26755054	+	EXO1	chr1	242055827	+
44745	TGCT	TCGA-2G-AAL7	LIN28A	chr1	26755049	+	EXO1	chr1	242055823	+
44745	TGCT	TCGA-VF-A8A8	LIN28A	chr1	26755050	+	EXO1	chr1	242055823	+
77987	LUAD	TCGA-55-8085-01A	RPS6KA1	chr1	26885428	+	LIN28A	chr1	26751794	+

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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

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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
KIRC	LIN28A	0.0496402132709137	1
BRCA	LIN28A	0.0415644596454657	1
PCPG	LIN28A	0.0270651489908984	0.89

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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