SZGR2

Summary ?

GeneID	2332
Symbol	FMR1
Synonyms	FMRP\|FRAXA\|POF\|POF1
Description	fragile X mental retardation 1
Reference	MIM:309550\|HGNC:HGNC:3775\|Ensembl:ENSG00000102081\|HPRD:02398\|Vega:OTTHUMG00000022606
Gene type	protein-coding
Map location	Xq27.3
Sherlock p-value	0.675
Fetal beta	-0.109
Support	Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
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,schizophrenic,schizophrenias,schizotypal	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

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
CP	0.91	0.50
KCNJ13	0.90	0.41
CLIC6	0.90	0.45
TTR	0.89	0.54
F5	0.88	0.33
SLC13A4	0.88	0.27
PRLR	0.85	0.20
SLC5A5	0.85	0.24
ABCA4	0.84	0.30
TRPV4	0.82	0.31

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
EPHB6	-0.17	-0.36
IER5L	-0.16	-0.53
CIDEA	-0.15	-0.49
RND1	-0.15	-0.37
ARL4D	-0.15	-0.48
LNX1	-0.14	-0.41
CACNB3	-0.14	-0.38
MEF2C	-0.14	-0.59
LDB2	-0.14	-0.46
EFNA5	-0.14	-0.51

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003723	RNA binding	IEA		-
GO:0003729	mRNA binding	TAS		7692601
GO:0005515	protein binding	IPI		10556305 \|16407062
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007417	central nervous system development	IEA	Brain (GO term level: 6)	-
GO:0006810	transport	IEA		-
GO:0051028	mRNA transport	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005625	soluble fraction	TAS		8401578
GO:0005634	nucleus	IEA		-
GO:0005654	nucleoplasm	TAS		10888599
GO:0005730	nucleolus	TAS		16407062
GO:0005737	cytoplasm	TAS		16407062
GO:0042788	polysomal ribosome	TAS		12837692

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CYFIP1	FLJ45151 \| P140SRA-1 \| SHYC \| SRA1	cytoplasmic FMR1 interacting protein 1	-	HPRD,BioGRID	11438699
CYFIP2	PIR121	cytoplasmic FMR1 interacting protein 2	-	HPRD,BioGRID	11438699
FMR1	FMRP \| FRAXA \| MGC87458 \| POF \| POF1	fragile X mental retardation 1	Affinity Capture-Western	BioGRID	10567518
FXR1	-	fragile X mental retardation, autosomal homolog 1	-	HPRD,BioGRID	7489725 \|8668200
FXR2	FMR1L2	fragile X mental retardation, autosomal homolog 2	-	HPRD,BioGRID	7489725 \|8668200 \|10567518
MAP1B	DKFZp686E1099 \| DKFZp686F1345 \| FLJ38954 \| FUTSCH \| MAP5	microtubule-associated protein 1B	FMR1 (FMRP) interacts with MAP1B mRNA. This interaction was modeled on a demonstrated interaction between FMR1 from an unspecified species and human MAP1B mRNA.	BIND	15381419
NCL	C23 \| FLJ45706	nucleolin	Affinity Capture-Western	BioGRID	10567518
NUFIP1	NUFIP \| bA540M5.1	nuclear fragile X mental retardation protein interacting protein 1	-	HPRD,BioGRID	10556305
NUFIP2	182-FIP \| 82-FIP \| FIP-82 \| FLJ10976 \| KIAA1321 \| MGC117262 \| PIG1	nuclear fragile X mental retardation protein interacting protein 2	-	HPRD,BioGRID	12837692
RANBP9	RANBPM	RAN binding protein 9	FMR1 (FMRP) interacts with RANBP9 (RanBPM).	BIND	15381419
UBE2I	C358B7.1 \| P18 \| UBC9	ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)	-	HPRD,BioGRID	11367701

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
DAVICIONI PAX FOXO1 SIGNATURE IN ARMS UP	59	38	All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP	255	177	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN	463	290	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS DN	431	263	All SZGR 2.0 genes in this pathway
LAIHO COLORECTAL CANCER SERRATED DN	86	47	All SZGR 2.0 genes in this pathway
SLEBOS HEAD AND NECK CANCER WITH HPV UP	84	43	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN	485	334	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS UP	169	127	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL	330	217	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 DN	584	395	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP	424	268	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP	203	135	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS	217	138	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS DN	97	53	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR DN	185	116	All SZGR 2.0 genes in this pathway
PYEON CANCER HEAD AND NECK VS CERVICAL UP	193	95	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D	882	506	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-101	1620	1626	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124/506	544	550	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	544	550	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-125/351	595	601	1A	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	595	601	1A	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-129-5p	523	530	1A,m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	523	530	1A,m8	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-130/301	2009	2015	1A	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
				hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-132/212	1885	1891	1A	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	1885	1891	1A	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-136	2113	2119	m8	hsa-miR-136	ACUCCAUUUGUUUUGAUGAUGGA
miR-139	1621	1628	1A,m8	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-141/200a	776	782	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	776	782	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-144	1619	1626	1A,m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-148/152	756	763	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-153	1753	1759	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-181	1550	1556	1A	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-182	1510	1517	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-19	1584	1590	1A	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
				hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-194	1886	1892	m8	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-194	1886	1892	m8	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-200bc/429	468	474	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-203.1	426	432	1A	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-205	1276	1282	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-221/222	631	638	1A,m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	631	638	1A,m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-23	1273	1279	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
				hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-24*	88	95	1A,m8	hsa-miR-189	GUGCCUACUGAGCUGAUAUCAGU
miR-25/32/92/363/367	1738	1745	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-323	2064	2070	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-324-3p	273	279	1A	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-324-5p	584	590	1A	hsa-miR-324-5p	CGCAUCCCCUAGGGCAUUGGUGU
miR-335	1665	1671	m8	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-369-3p	574	580	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	574	580	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-377	493	499	m8	hsa-miR-377	AUCACACAAAGGCAACUUUUGU
miR-410	1298	1304	m8	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-410	1298	1304	m8	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-448	1753	1759	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-448	1753	1759	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-450	523	529	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-485-3p	534	540	m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-490	1090	1096	1A	hsa-miR-490	CAACCUGGAGGACUCCAUGCUG
miR-496	2237	2243	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-543	621	627	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-9	75	81	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	1511	1517	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: FMR1