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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: PATL2 (NCBI Gene ID:197135)

Gene Summary

Gene Summary

Gene Information	Gene Name: PATL2
	Gene ID: 197135
	Gene Symbol	PATL2
	Gene ID	197135
	Gene Name	PAT1 homolog 2
	Synonyms	OOMD4\|Pat1a\|hPat1a
	Cytomap	15q21.1
	Type of Gene	protein-coding
	Description	protein PAT1 homolog 2PAT1-like protein 2protein PAT1 homolog aprotein associated with topoisomerase II homolog 2
	Modification date	20200313
	UniProtAcc	C9JE40

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: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
PATL2	(355.7 - 733]

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Translation Studies in PubMed

We searched PubMed using 'PATL2[title] AND translation [title] AND human.'

Gene	Title	PMID
PATL2	.	.

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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	FC	adj.pval
LUAD	PATL2	-2.53293713200388	0.0219209391678432

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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

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
PAAD	PATL2	-0.09558218	0.015366231

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with PATL2 (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
TGCT	Cell metabolism gene	PATL2	PSMB9	0.815163641	2.37E-38
TGCT	CGC	PATL2	CIITA	0.801053747	3.81E-36
TGCT	CGC	PATL2	RHOH	0.813884267	3.82E-38
TGCT	CGC	PATL2	CD74	0.815010812	2.51E-38
TGCT	CGC	PATL2	BIRC3	0.815104923	2.42E-38
TGCT	CGC	PATL2	JAK3	0.833040724	1.95E-41
TGCT	CGC	PATL2	P2RY8	0.853622398	1.80E-45
TGCT	CGC	PATL2	WAS	0.856144588	5.22E-46
TGCT	CGC	PATL2	IKZF1	0.861945603	2.77E-47
TGCT	Epifactor	PATL2	SP140	0.812930066	5.44E-38
TGCT	Epifactor	PATL2	GFI1	0.860660167	5.37E-47
TGCT	Epifactor	PATL2	IKZF1	0.861945603	2.77E-47
TGCT	IUPHAR	PATL2	RIPK3	0.800159863	5.18E-36
TGCT	IUPHAR	PATL2	CSF2RB	0.800796566	4.16E-36
TGCT	IUPHAR	PATL2	CIITA	0.801053747	3.81E-36
TGCT	IUPHAR	PATL2	CXCR6	0.801719603	3.02E-36
TGCT	IUPHAR	PATL2	FGR	0.804761122	1.04E-36
TGCT	IUPHAR	PATL2	GPR132	0.805775649	7.28E-37
TGCT	IUPHAR	PATL2	GZMA	0.807951779	3.35E-37
TGCT	IUPHAR	PATL2	TAP1	0.808494781	2.75E-37
TGCT	IUPHAR	PATL2	CTLA4	0.808542326	2.71E-37
TGCT	IUPHAR	PATL2	PDCD1	0.810945076	1.13E-37
TGCT	IUPHAR	PATL2	SP140	0.812930066	5.44E-38
TGCT	IUPHAR	PATL2	CD74	0.815010812	2.51E-38
TGCT	IUPHAR	PATL2	BIRC3	0.815104923	2.42E-38
TGCT	IUPHAR	PATL2	PSMB9	0.815163641	2.37E-38
TGCT	IUPHAR	PATL2	GPR18	0.817413839	1.01E-38
TGCT	IUPHAR	PATL2	IL2RG	0.819875541	3.93E-39
TGCT	IUPHAR	PATL2	CD27	0.822989273	1.17E-39
TGCT	IUPHAR	PATL2	MCOLN2	0.826109506	3.37E-40
TGCT	IUPHAR	PATL2	GPR65	0.827774081	1.72E-40
TGCT	IUPHAR	PATL2	CD247	0.82934526	9.06E-41
TGCT	IUPHAR	PATL2	IL10RA	0.830213552	6.34E-41
TGCT	IUPHAR	PATL2	GZMK	0.832164899	2.82E-41
TGCT	IUPHAR	PATL2	JAK3	0.833040724	1.95E-41
TGCT	IUPHAR	PATL2	CD2	0.835495142	6.90E-42
TGCT	IUPHAR	PATL2	PTPN22	0.838356	2.01E-42
TGCT	IUPHAR	PATL2	CXCR3	0.839351173	1.30E-42
TGCT	IUPHAR	PATL2	PYHIN1	0.843031985	2.54E-43
TGCT	IUPHAR	PATL2	CD3E	0.844617042	1.24E-43
TGCT	IUPHAR	PATL2	CD6	0.844894995	1.09E-43
TGCT	IUPHAR	PATL2	ITGB7	0.849136458	1.53E-44
TGCT	IUPHAR	PATL2	AIM2	0.849962987	1.04E-44
TGCT	IUPHAR	PATL2	GPR171	0.851997439	3.94E-45
TGCT	IUPHAR	PATL2	P2RY8	0.853622398	1.80E-45
TGCT	IUPHAR	PATL2	ITGAL	0.860802427	4.99E-47
TGCT	IUPHAR	PATL2	NLRC3	0.872864495	7.54E-50
TGCT	IUPHAR	PATL2	CD37	0.87294174	7.21E-50
TGCT	IUPHAR	PATL2	NLRC5	0.896744097	2.15E-56
TGCT	Kinase	PATL2	RIPK3	0.800159863	5.18E-36
TGCT	Kinase	PATL2	FGR	0.804761122	1.04E-36
TGCT	Kinase	PATL2	JAK3	0.833040724	1.95E-41
TGCT	TF	PATL2	STAT4	0.802661635	2.18E-36
TGCT	TF	PATL2	RUNX3	0.812061548	7.50E-38
TGCT	TF	PATL2	SP140	0.812930066	5.44E-38
TGCT	TF	PATL2	TBX21	0.844996978	1.04E-43
TGCT	TF	PATL2	ZNF831	0.856288092	4.86E-46
TGCT	TF	PATL2	GFI1	0.860660167	5.37E-47
TGCT	TF	PATL2	IKZF1	0.861945603	2.77E-47
TGCT	TSG	PATL2	DOK3	0.811829093	8.17E-38
TGCT	TSG	PATL2	RUNX3	0.812061548	7.50E-38
TGCT	TSG	PATL2	TNFAIP8L2	0.817443134	1.00E-38
TGCT	TSG	PATL2	RASSF5	0.833380147	1.69E-41
TGCT	TSG	PATL2	PYHIN1	0.843031985	2.54E-43
TGCT	TSG	PATL2	DENND2D	0.846107989	6.26E-44
TGCT	TSG	PATL2	AIM2	0.849962987	1.04E-44
TGCT	TSG	PATL2	IKZF1	0.861945603	2.77E-47
UVM	CGC	PATL2	B2M	0.837293224	3.78E-22
UVM	IUPHAR	PATL2	NLRC5	0.801854795	4.01E-19
UVM	IUPHAR	PATL2	AIM2	0.808103596	1.30E-19
UVM	IUPHAR	PATL2	TAP1	0.809213828	1.06E-19
UVM	TF	PATL2	STAT1	0.816094256	2.92E-20
UVM	TF	PATL2	IRF1	0.830404624	1.66E-21
UVM	TSG	PATL2	GBP1	0.807837913	1.37E-19
UVM	TSG	PATL2	AIM2	0.808103596	1.30E-19
UVM	TSG	PATL2	STAT1	0.816094256	2.92E-20
UVM	TSG	PATL2	IRF1	0.830404624	1.66E-21

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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
LUAD	PATL2	LSM1	-2.25310461629053	0.000250126280442223
THCA	PATL2	LSM4	-1.7720393464767	0.00053867884007499
HNSC	PATL2	LSM5	-2.42626046370549	0.0014147440645047
ESCA	PATL2	LSM7	-2.31243124209969	0.0029296875
THCA	PATL2	LSM7	-1.257555185578	0.00448578010535268
ESCA	PATL2	LSM5	-2.94289921304876	0.009765625
KIRC	PATL2	DCP2	1.26475649682567	0.0124189994647713
ESCA	PATL2	LSM4	-1.10763832306386	0.013671875
STAD	PATL2	LSM5	-2.04224010610308	0.0148032568395138
THCA	PATL2	LSM1	-1.2467434703155	0.0168973193592333
HNSC	PATL2	LSM2	-1.16751559143959	0.0177602205276344
HNSC	PATL2	XRN1	1.48932008251589	0.0217607007634797
LIHC	PATL2	LSM7	-1.74964110437643	0.0251194595851845
COAD	PATL2	LSM7	2.30429568056628	1.2814998626709e-06
BRCA	PATL2	LSM5	-3.47385312153922	1.5252788990783e-09
STAD	PATL2	LSM4	-7.46687657673868	2.26888805627823e-05
COAD	PATL2	LSM4	2.16462365278872	2.27093696594239e-05
BRCA	PATL2	LSM2	-2.87365292130904	3.37458938836032e-08
BRCA	PATL2	LSM4	-2.45028637685104	3.44605555708978e-29
KIRC	PATL2	LSM4	1.00210951357873	3.97470828213212e-07
LUAD	PATL2	LSM4	-1.48392189129577	4.20890892730867e-05
KICH	PATL2	LSM2	1.66342090505246	5.24520874023437e-06
LUAD	PATL2	LSM5	-4.9594264060254	5.68692060030821e-07
LIHC	PATL2	LSM2	-2.21541388815629	7.4950933254918e-06
THCA	PATL2	DDX6	-4.18593714762416	8.3083675979354e-06

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

PPI interactors with PATL2

DNAH5, RRBP1,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
PATL2	chr15	44958010	A	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001624\|3_prime_UTR_variant	SO:0001624\|3_prime_UTR_variant
PATL2	chr15	44958652	T	C	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
PATL2	chr15	44958673	G	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
PATL2	chr15	44960683	G	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
PATL2	chr15	44961176	A	G	single_nucleotide_variant	Pathogenic	Oocyte_maturation_defect_4	SO:0001575\|splice_donor_variant	SO:0001575\|splice_donor_variant
PATL2	chr15	44961294	C	T	single_nucleotide_variant	Uncertain_significance	Oocyte_maturation_defect_4	SO:0001583\|missense_variant	SO:0001583\|missense_variant
PATL2	chr15	44961589	A	G	single_nucleotide_variant	Uncertain_significance	Oocyte_maturation_defect_4	SO:0001583\|missense_variant	SO:0001583\|missense_variant
PATL2	chr15	44962012	C	T	single_nucleotide_variant	Uncertain_significance	Oocyte_maturation_defect_4	SO:0001583\|missense_variant	SO:0001583\|missense_variant
PATL2	chr15	44962067	G	A	single_nucleotide_variant	Likely_pathogenic	Oocyte_maturation_defect_4	SO:0001587\|nonsense	SO:0001587\|nonsense
PATL2	chr15	44964221	A	T	single_nucleotide_variant	Likely_pathogenic	Oocyte_maturation_defect_4	SO:0001583\|missense_variant,SO:0001627\|intron_variant	SO:0001583\|missense_variant,SO:0001627\|intron_variant
PATL2	chr15	44964304	A	C	single_nucleotide_variant	Likely_pathogenic	Oocyte_maturation_defect_4	SO:0001583\|missense_variant,SO:0001623\|5_prime_UTR_variant,SO:0001627\|intron_variant	SO:0001583\|missense_variant,SO:0001623\|5_prime_UTR_variant,SO:0001627\|intron_variant
PATL2	chr15	44964312	A	T	single_nucleotide_variant	Pathogenic	Oocyte_maturation_defect_4	SO:0001587\|nonsense,SO:0001623\|5_prime_UTR_variant,SO:0001627\|intron_variant	SO:0001587\|nonsense,SO:0001623\|5_prime_UTR_variant,SO:0001627\|intron_variant
PATL2	chr15	44964623	G	A	single_nucleotide_variant	Likely_pathogenic	Oocyte_maturation_defect_2\|Oocyte_maturation_defect_4	SO:0001587\|nonsense,SO:0001623\|5_prime_UTR_variant	SO:0001587\|nonsense,SO:0001623\|5_prime_UTR_variant
PATL2	chr15	44966389	T	C	single_nucleotide_variant	Benign	Oocyte_maturation_defect_4	SO:0001583\|missense_variant,SO:0001627\|intron_variant	SO:0001583\|missense_variant,SO:0001627\|intron_variant
PATL2	chr15	44966429	CTGGAACAGGAGGG	C	Deletion	Pathogenic	Oocyte_maturation_defect_4	SO:0001574\|splice_acceptor_variant,SO:0001627\|intron_variant	SO:0001574\|splice_acceptor_variant,SO:0001627\|intron_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
PATL2	BRCA	chr15	44965451	44965451	G	A	Missense_Mutation	p.S143L	4
PATL2	UCEC	chr15	44960623	44960623	C	T	Missense_Mutation	p.E428K	4
PATL2	ACC	chr15	44964347	44964347	C	A	Missense_Mutation	p.A175S	3
PATL2	BRCA	chr15	44962197	44962197	G	A	Missense_Mutation	p.P249L	3
PATL2	PRAD	chr15	44966389	44966389	T	C	Missense_Mutation	p.M88V	3
PATL2	ESCA	chr15	44960587	44960587	G	A	Missense_Mutation	p.P440S	2
PATL2	LIHC	chr15	44960660	44960660	T	-	Frame_Shift_Del	p.K415fs	2
PATL2	ESCA	chr15	44961491	44961491	G	A	Nonsense_Mutation	p.Q351*	2
PATL2	CESC	chr15	44965451	44965451	G	A	Missense_Mutation		2
PATL2	UCEC	chr15	44961567	44961567	C	T	Silent	p.R325	2
PATL2	UCEC	chr15	44961718	44961718	C	T	Missense_Mutation	p.R307Q	2
PATL2	SARC	chr15	44961245	44961245	G	T	Missense_Mutation		2
PATL2	UCEC	chr15	44962208	44962208	C	T	Silent	p.K245	2
PATL2	UCEC	chr15	44966425	44966425	C	T	Missense_Mutation	p.A76T	2
PATL2	COAD	chr15	44962250	44962250	G	A	Silent	p.D231D	1
PATL2	LIHC	chr15	44964221	44964221	A	G	Missense_Mutation	p.Y217H	1
PATL2	TGCT	chr15	44958652	44958652	T	C	Missense_Mutation		1
PATL2	COAD	chr15	44964622	44964622	C	T	Missense_Mutation	p.R160Q	1
PATL2	LIHC	chr15	44961589	44961589	A	G	Missense_Mutation	p.I318T	1
PATL2	THYM	chr15	44968674	44968674	T	C	Silent		1
PATL2	THYM	chr15	44964267	44964267	C	T	Silent	p.V201V	1
PATL2	LIHC	chr15	44964626	44964626	G	-	Frame_Shift_Del	p.Q159fs	1
PATL2	THYM	chr15	44965491	44965491	G	A	Missense_Mutation	p.P130S	1
PATL2	ESCA	chr15	44961491	44961491	G	A	Nonsense_Mutation	p.Q351X	1
PATL2	LIHC	chr15	44966409	44966409	G	-	Frame_Shift_Del	p.P81fs	1
PATL2	THYM	chr15	44968674	44968674	T	C	Silent	p.E5E	1
PATL2	KIRC	chr15	44964245	44964245	C	A	Missense_Mutation	p.A209S	1
PATL2	LIHC	chr15	44959362	44959362	C	-	Frame_Shift_Del	p.E469fs	1
PATL2	KIRC	chr15	44962242	44962242	A	G	Missense_Mutation	p.L234P	1
PATL2	CESC	chr15	44958662	44958662	G	T	Missense_Mutation		1
PATL2	KIRC	chr15	44965468	44965468	G	A	Silent	p.F137F	1
PATL2	SARC	chr15	44958658	44958658	G	T	Missense_Mutation		1
PATL2	COAD	chr15	44961211	44961211	C	T	Silent	p.L397L	1
PATL2	KIRC	chr15	44964348	44964349	-	G	Frame_Shift_Ins	p.P174fs	1
PATL2	COAD	chr15	44961988	44961988	C	A	Missense_Mutation	p.G288V	1
PATL2	LIHC	chr15	44961753	44961753	T	C	Silent		1
PATL2	SARC	chr15	44959356	44959356	G	A	Silent		1
PATL2	COAD	chr15	44962066	44962066	C	T	Missense_Mutation	p.R262Q	1
PATL2	LIHC	chr15	44967716	44967716	G	T	Missense_Mutation		1
PATL2	SARC	chr15	44958658	44958658	G	T	Missense_Mutation	p.S515R	1

Copy number variation (CNV) of PATL2
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across PATL2
* 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
56255	CESC	TCGA-IR-A3LA-01A	B2M	chr15	45003811	+	PATL2	chr15	44968763	-
56255	STAD	TCGA-VQ-A92D	FMN1	chr15	33357157	-	PATL2	chr15	44968763	-
56255	STAD	TCGA-VQ-A92D-01A	FMN1	chr15	33357158	-	PATL2	chr15	44968763	-
56255	Non-Cancer	TCGA-BH-A1EV-11A	MYEF2	chr15	48458130	-	PATL2	chr15	44968763	-
62921	N/A	GW493008	PATL2	chr15	44996699	+	DSC2	chr18	28645946	+
85147	N/A	FN074041	PATL2	chr15	45002141	-	SOGA3	chr6	127774986	-

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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
LUAD	PATL2	0.00626661449126391	0.17
BRCA	PATL2	0.00797186031052162	0.21
LIHC	PATL2	0.0167227035987587	0.42
PAAD	PATL2	0.0248622880283459	0.6
GBM	PATL2	0.0275015584212043	0.63
KIRP	PATL2	2.33850900583492e-07	6.5e-06

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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
LUSC	PATL2	0.0412335731340031	1
KIRP	PATL2	0.0273014551289126	0.87
COAD	PATL2	0.0207114141303662	0.68

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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
C4540284	OOCYTE MATURATION DEFECT 4	2	UNIPROT