SZGR2

Summary ?

GeneID	51176
Symbol	LEF1
Synonyms	LEF-1\|TCF10\|TCF1ALPHA\|TCF7L3
Description	lymphoid enhancer binding factor 1
Reference	MIM:153245\|HGNC:HGNC:6551\|Ensembl:ENSG00000138795\|HPRD:01075\|Vega:OTTHUMG00000131809
Gene type	protein-coding
Map location	4q25
Pascal p-value	0.166
Fetal beta	-0.823

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg19737633	4	109087912	LOC641518;LEF1	1.177E-4	-0.381	0.029	DMG:Wockner_2014

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003677	DNA binding	IEA		-
GO:0003682	chromatin binding	IEA		-
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	IEA		-
GO:0005515	protein binding	IPI		9751710 \|12192039
GO:0008301	DNA bending activity	ISS		-
GO:0016563	transcription activator activity	IEA		-
GO:0043565	sequence-specific DNA binding	IDA		9308964
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0021542	dentate gyrus development	IEA	neuron (GO term level: 12)	-
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0001756	somitogenesis	IEA		-
GO:0001890	placenta development	IEA		-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006350	transcription	IEA		-
GO:0016055	Wnt receptor signaling pathway	IEA		-
GO:0048468	cell development	IEA		-
GO:0030111	regulation of Wnt receptor signaling pathway	IEA		-
GO:0042475	odontogenesis of dentine-containing tooth	IEA		-
GO:0030879	mammary gland development	IEA		-
GO:0030326	embryonic limb morphogenesis	IEA		-
GO:0048341	paraxial mesoderm formation	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0045843	negative regulation of striated muscle development	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IC		9308964
GO:0005634	nucleus	IEA		-
GO:0005667	transcription factor complex	IEA		-
GO:0005730	nucleolus	IDA		18029348
GO:0005737	cytoplasm	IDA		18029348
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ALX4	FPP \| KIAA1788 \| PFM \| PFM1 \| PFM2	ALX homeobox 4	-	HPRD,BioGRID	11696550
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	-	HPRD	8757136 \|12556497
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	Affinity Capture-Western Two-hybrid	BioGRID	8757136 \|12748295 \|15684397
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	LEF-1 interacts with Beta-catenin. This interaction was modeled on a demonstrated interaction between human LEF-1 and mouse Beta-catenin.	BIND	15525529
EP300	KAT3B \| p300	E1A binding protein p300	-	HPRD,BioGRID	12446687
KPNA1	IPOA5 \| NPI-1 \| RCH2 \| SRP1	karyopherin alpha 1 (importin alpha 5)	-	HPRD	8631802
KPNA2	IPOA1 \| QIP2 \| RCH1 \| SRP1alpha	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	-	HPRD	8631802
MITF	MI \| WS2A \| bHLHe32	microphthalmia-associated transcription factor	-	HPRD,BioGRID	12032083
NLK	DKFZp761G1211 \| FLJ21033	nemo-like kinase	Affinity Capture-Western	BioGRID	12556497
NLK	DKFZp761G1211 \| FLJ21033	nemo-like kinase	-	HPRD	12901858
NOTCH1	TAN1 \| hN1	Notch homolog 1, translocation-associated (Drosophila)	-	HPRD,BioGRID	11604490
PIAS4	FLJ12419 \| MGC35296 \| PIASY \| Piasg \| ZMIZ6	protein inhibitor of activated STAT, 4	-	HPRD,BioGRID	11731474
RUNX1	AML1 \| AML1-EVI-1 \| AMLCR1 \| CBFA2 \| EVI-1 \| PEBP2aB	runt-related transcription factor 1	Reconstituted Complex	BioGRID	12551949
RUNX2	AML3 \| CBFA1 \| CCD \| CCD1 \| MGC120022 \| MGC120023 \| OSF2 \| PEA2aA \| PEBP2A1 \| PEBP2A2 \| PEBP2aA \| PEBP2aA1	runt-related transcription factor 2	Reconstituted Complex	BioGRID	12551949
RUVBL1	ECP54 \| INO80H \| NMP238 \| PONTIN \| Pontin52 \| RVB1 \| TIH1 \| TIP49 \| TIP49A	RuvB-like 1 (E. coli)	Affinity Capture-Western	BioGRID	9843967
SMAD1	BSP1 \| JV4-1 \| JV41 \| MADH1 \| MADR1	SMAD family member 1	-	HPRD,BioGRID	10890911
SMAD2	JV18 \| JV18-1 \| MADH2 \| MADR2 \| MGC22139 \| MGC34440 \| hMAD-2 \| hSMAD2	SMAD family member 2	-	HPRD,BioGRID	10890911
SMAD3	DKFZp586N0721 \| DKFZp686J10186 \| HSPC193 \| HsT17436 \| JV15-2 \| MADH3 \| MGC60396	SMAD family member 3	Lef1 interacts with Smad3. This interaction was modeled on a demonstrated interaction between mouse Lef1 and Smad3 from an unspecified species.	BIND	15750622
SMAD3	DKFZp586N0721 \| DKFZp686J10186 \| HSPC193 \| HsT17436 \| JV15-2 \| MADH3 \| MGC60396	SMAD family member 3	-	HPRD,BioGRID	10890911
SMAD4	DPC4 \| JIP \| MADH4	SMAD family member 4	-	HPRD,BioGRID	10890911
SMAD7	CRCS3 \| FLJ16482 \| MADH7 \| MADH8	SMAD family member 7	Affinity Capture-Western	BioGRID	15684397
THOC4	ALY \| BEF	THO complex 4	Reconstituted Complex	BioGRID	9119228
TLE1	ESG \| ESG1 \| GRG1	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	-	HPRD,BioGRID	9751710
TLE1	ESG \| ESG1 \| GRG1	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	LEF-1 interacts with TLE1. This interaction was modeled on a demonstrated interaction between LEF-1 from an unspecified species and human TLE1.	BIND	9751710
TRA@	FLJ22602 \| MGC117436 \| MGC22624 \| MGC23964 \| MGC71411 \| TCRA \| TCRD \| TRA	T cell receptor alpha locus	-	HPRD	1827423 \|9119227\|9119227
UBTF	NOR-90 \| UBF	upstream binding transcription factor, RNA polymerase I	-	HPRD,BioGRID	12748295

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG WNT SIGNALING PATHWAY	151	112	All SZGR 2.0 genes in this pathway
KEGG ADHERENS JUNCTION	75	53	All SZGR 2.0 genes in this pathway
KEGG MELANOGENESIS	102	80	All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER	328	259	All SZGR 2.0 genes in this pathway
KEGG COLORECTAL CANCER	62	47	All SZGR 2.0 genes in this pathway
KEGG ENDOMETRIAL CANCER	52	45	All SZGR 2.0 genes in this pathway
KEGG PROSTATE CANCER	89	75	All SZGR 2.0 genes in this pathway
KEGG THYROID CANCER	29	26	All SZGR 2.0 genes in this pathway
KEGG BASAL CELL CARCINOMA	55	44	All SZGR 2.0 genes in this pathway
KEGG ACUTE MYELOID LEUKEMIA	60	47	All SZGR 2.0 genes in this pathway
KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC	76	59	All SZGR 2.0 genes in this pathway
BIOCARTA GSK3 PATHWAY	27	26	All SZGR 2.0 genes in this pathway
BIOCARTA PITX2 PATHWAY	15	15	All SZGR 2.0 genes in this pathway
BIOCARTA WNT PATHWAY	26	24	All SZGR 2.0 genes in this pathway
WNT SIGNALING	89	71	All SZGR 2.0 genes in this pathway
PID CMYB PATHWAY	84	61	All SZGR 2.0 genes in this pathway
PID BETA CATENIN NUC PATHWAY	80	60	All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP	201	125	All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS UP	137	94	All SZGR 2.0 genes in this pathway
RODRIGUES NTN1 TARGETS UP	17	11	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP	233	161	All SZGR 2.0 genes in this pathway
HUMMEL BURKITTS LYMPHOMA UP	43	27	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LPS UP	431	237	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS UP	214	155	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL DN	226	132	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 48HR DN	64	39	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 96HR DN	75	50	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B	392	251	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN 2FC DN	21	13	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS MODERATELY UP	109	69	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP	292	168	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
MORI PRE BI LYMPHOCYTE UP	80	54	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
PARK HSC MARKERS	44	31	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR DN	63	41	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
HU GENOTOXIN ACTION DIRECT VS INDIRECT 24HR	55	38	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR UP	156	101	All SZGR 2.0 genes in this pathway
ZHENG BOUND BY FOXP3	491	310	All SZGR 2.0 genes in this pathway
ZHENG FOXP3 TARGETS IN T LYMPHOCYTE DN	37	29	All SZGR 2.0 genes in this pathway
SANSOM WNT PATHWAY REQUIRE MYC	58	43	All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3	97	72	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
NADELLA PRKAR1A TARGETS DN	8	8	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
MCGARVEY SILENCED BY METHYLATION IN COLON CANCER	42	29	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
RUIZ TNC TARGETS UP	153	107	All SZGR 2.0 genes in this pathway
LEE DIFFERENTIATING T LYMPHOCYTE	200	115	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G6 UP	65	43	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP	207	143	All SZGR 2.0 genes in this pathway
GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA DN	56	39	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 UP	87	50	All SZGR 2.0 genes in this pathway
KASLER HDAC7 TARGETS 1 UP	194	133	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-26	978	984	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	978	984	1A	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-34/449	190	197	1A,m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-363	31	38	1A,m8	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-381	612	619	1A,m8	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-505	81	87	1A	hsa-miR-505	GUCAACACUUGCUGGUUUCCUC
miR-93.hd/291-3p/294/295/302/372/373/520	975	981	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: LEF1