SZGR2

Summary ?

GeneID	8087
Symbol	FXR1
Synonyms	FXR1P
Description	FMR1 autosomal homolog 1
Reference	MIM:600819\|HGNC:HGNC:4023\|Ensembl:ENSG00000114416\|HPRD:02892\|Vega:OTTHUMG00000158138
Gene type	protein-coding
Map location	3q28
Pascal p-value	1.075E-10
Sherlock p-value	0.087
Fetal beta	0.731
DMG	2 (# 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:PGC128	Genome-wide Association Study	A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	2
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	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.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,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

CV:PGC128

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg27437944	3	180630533	FXR1		-0.027	0.51	DMG:Nishioka_2013
cg19678270	3	180630780	FXR1	6.27E-8	-0.01	1.56E-5	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1324669	chr13	107872446	FXR1	8087	0.01	trans
rs9949772	chr18	31042632	FXR1	8087	0.13	trans
rs17145698	chrX	40218345	FXR1	8087	0.08	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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003723	RNA binding	TAS		7781595
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007519	skeletal muscle development	IEA	neuron (GO term level: 8)	-
GO:0006915	apoptosis	TAS		9642279
GO:0007275	multicellular organismal development	IEA		-
GO:0030154	cell differentiation	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005844	polysome	TAS		9817930
GO:0005730	nucleolus	TAS		10888599
GO:0005737	cytoplasm	TAS		7781595

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
C14orf1	ERG28 \| NET51	chromosome 14 open reading frame 1	Two-hybrid	BioGRID	16169070
C1orf103	FLJ11269 \| RIF1 \| RP11-96K19.1	chromosome 1 open reading frame 103	Two-hybrid	BioGRID	16169070
CRMP1	DPYSL1 \| DRP-1 \| DRP1	collapsin response mediator protein 1	Two-hybrid	BioGRID	16169070
CYFIP1	FLJ45151 \| P140SRA-1 \| SHYC \| SRA1	cytoplasmic FMR1 interacting protein 1	Affinity Capture-Western	BioGRID	11438699
CYFIP2	PIR121	cytoplasmic FMR1 interacting protein 2	-	HPRD,BioGRID	11438699
FMR1	FMRP \| FRAXA \| MGC87458 \| POF \| POF1	fragile X mental retardation 1	-	HPRD,BioGRID	7489725 \|8668200
FXR1	-	fragile X mental retardation, autosomal homolog 1	-	HPRD,BioGRID	7489725
FXR2	FMR1L2	fragile X mental retardation, autosomal homolog 2	-	HPRD,BioGRID	7489725 \|8668200
GBP2	-	guanylate binding protein 2, interferon-inducible	Two-hybrid	BioGRID	16169070
KIAA1377	-	KIAA1377	Two-hybrid	BioGRID	16169070
LUC7L2	CGI-59 \| CGI-74 \| FLJ10657 \| LUC7B2	LUC7-like 2 (S. cerevisiae)	Two-hybrid	BioGRID	16169070
PRSS23	MGC5107 \| SIG13 \| SPUVE \| ZSIG13	protease, serine, 23	Two-hybrid	BioGRID	16169070

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
ONKEN UVEAL MELANOMA DN	526	357	All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS DN	352	225	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP	404	246	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC UP	185	126	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 6HR DN	167	100	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN	459	276	All SZGR 2.0 genes in this pathway
GRAHAM CML QUIESCENT VS NORMAL DIVIDING UP	57	33	All SZGR 2.0 genes in this pathway
GRAHAM NORMAL QUIESCENT VS NORMAL DIVIDING UP	66	47	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP	633	376	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN UP	177	113	All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP	584	356	All SZGR 2.0 genes in this pathway
IVANOV MUTATED IN COLON CANCER	13	9	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	483	336	All SZGR 2.0 genes in this pathway
AMUNDSON RESPONSE TO ARSENITE	217	143	All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 LASER DN	50	38	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
BENPORATH ES 1	379	235	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 60 HELA	46	32	All SZGR 2.0 genes in this pathway
DING LUNG CANCER EXPRESSION BY COPY NUMBER	100	62	All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO UP	205	126	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
DORSAM HOXA9 TARGETS DN	32	22	All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR UP	78	56	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C8	72	56	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP	314	201	All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS	138	91	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY DN	145	88	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN	215	132	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR UP	178	111	All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 8G	95	62	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN	270	181	All SZGR 2.0 genes in this pathway
HONMA DOCETAXEL RESISTANCE	34	23	All SZGR 2.0 genes in this pathway
SPIRA SMOKERS LUNG CANCER UP	38	24	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP	518	299	All SZGR 2.0 genes in this pathway
ZHAN VARIABLE EARLY DIFFERENTIATION GENES DN	30	19	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G3 UP	188	121	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP	207	143	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE M G1	148	95	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN	336	211	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
BILANGES RAPAMYCIN SENSITIVE VIA TSC1 AND TSC2	73	37	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-132/212	581	587	m8	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	581	587	m8	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-145	524	530	1A	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-182	64	71	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-199	523	529	1A	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	523	529	1A	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-200bc/429	627	633	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-25/32/92/363/367	815	822	1A,m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-30-3p	706	713	1A,m8	hsa-miR-30a-3p	CUUUCAGUCGGAUGUUUGCAGC
miR-30-3p	706	713	1A,m8	hsa-miR-30e-3p	CUUUCAGUCGGAUGUUUACAGC
miR-30-5p	18	24	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-31	63	69	1A	hsa-miR-31	AGGCAAGAUGCUGGCAUAGCUG
miR-320	648	654	1A	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-324-3p	575	582	1A,m8	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-493-5p	55	61	1A	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-7	856	862	1A	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-9	67	73	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	65	71	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: FXR1