SZGR2

Summary ?

GeneID	9208
Symbol	LRRFIP1
Synonyms	FLAP-1\|FLAP1\|FLIIAP1\|GCF-2\|GCF2\|HUFI-1\|TRIP
Description	leucine rich repeat (in FLII) interacting protein 1
Reference	MIM:603256\|HGNC:HGNC:6702\|Ensembl:ENSG00000124831\|HPRD:04460\|Vega:OTTHUMG00000133339
Gene type	protein-coding
Map location	2q37.3
Pascal p-value	0.252
Sherlock p-value	0.598
Fetal beta	0.657
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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).	2
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Expression	Meta-analysis of gene expression	P value: 1.613
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg22734058	2	238578491	LRRFIP1	9.96E-6	0.679	0.013	DMG:Wockner_2014
cg20732367	2	238601467	LRRFIP1	2.118E-4	-0.358	0.036	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs9306764	chrX	22142353	LRRFIP1	9208		0.01		trans

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
VCP	0.96	0.96
SEC31A	0.95	0.96
DDB1	0.95	0.96
DLSTP	0.95	0.94
CHMP7	0.95	0.96
PSMD3	0.95	0.94
EDC3	0.95	0.95
KIAA0406	0.94	0.95
KIAA1967	0.94	0.95
CSNK2A1	0.94	0.95

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.84	-0.91
AF347015.31	-0.84	-0.90
AF347015.33	-0.83	-0.89
AF347015.27	-0.83	-0.90
AF347015.8	-0.82	-0.90
MT-CYB	-0.81	-0.88
FXYD1	-0.81	-0.88
AF347015.21	-0.78	-0.92
AF347015.15	-0.78	-0.87
AF347015.2	-0.78	-0.88

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003674	molecular_function	ND		-
GO:0003677	DNA binding	IEA		-
GO:0003725	double-stranded RNA binding	TAS		9671805
GO:0005515	protein binding	IPI		9671805
GO:0016564	transcription repressor activity	NAS		9705290
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006357	regulation of transcription from RNA polymerase II promoter	TAS		9705290
GO:0008150	biological_process	ND		-
GO:0016481	negative regulation of transcription	NAS		9705290
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005856	cytoskeleton	TAS		9671805
GO:0005575	cellular_component	ND		-
GO:0005634	nucleus	NAS		9705290
GO:0005737	cytoplasm	TAS		9671805

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
WANG LMO4 TARGETS UP	372	227	All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS DN	186	114	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP	404	246	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL DN	275	168	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D DN	143	83	All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL UP	95	64	All SZGR 2.0 genes in this pathway
DITTMER PTHLH TARGETS DN	73	51	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 2HR UP	27	19	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN	214	133	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN	329	219	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN	508	354	All SZGR 2.0 genes in this pathway
LANDIS BREAST CANCER PROGRESSION UP	44	27	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA FOREVER DN	31	23	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 UP	150	93	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM UP	176	111	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER UP	227	137	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
LIU COMMON CANCER GENES	79	47	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY DN	382	224	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 40 MCF10A	19	11	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND DN	225	163	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 10	30	17	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS DN	31	23	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
SARTIPY BLUNTED BY INSULIN RESISTANCE UP	19	17	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP	268	157	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP	280	183	All SZGR 2.0 genes in this pathway
BILD HRAS ONCOGENIC SIGNATURE	261	166	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE DN	274	165	All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP	250	168	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP	259	185	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
CHEN LIVER METABOLISM QTL CIS	93	40	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL	216	130	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B	549	316	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR UP	199	143	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	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
let-7/98	621	627	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-132/212	146	153	1A,m8	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	146	153	1A,m8	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-192/215	526	532	m8	hsa-miR-192	CUGACCUAUGAAUUGACAGCC
miR-192/215	526	532	m8	hsa-miR-215	AUGACCUAUGAAUUGACAGAC
miR-194	148	154	m8	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA

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: LRRFIP1