SZGR2

Summary ?

GeneID	23367
Symbol	LARP1
Synonyms	LARP
Description	La ribonucleoprotein domain family member 1
Reference	MIM:612059\|HGNC:HGNC:29531\|Ensembl:ENSG00000155506\|HPRD:11225\|Vega:OTTHUMG00000130191
Gene type	protein-coding
Map location	5q33.2
Pascal p-value	0.117
Sherlock p-value	0.045
Fetal beta	-0.353
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00459
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.01718

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4864466	chr4	54403975	LARP1	23367		0.1		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
TCF20	0.94	0.97
CHD8	0.94	0.96
UBTF	0.93	0.94
SETD2	0.93	0.95
RNASEN	0.93	0.94
CDC2L5	0.93	0.95
YLPM1	0.92	0.95
SCAPER	0.92	0.93
GON4L	0.92	0.95
TRIO	0.92	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.79	-0.90
MT-CO2	-0.76	-0.88
AF347015.27	-0.74	-0.85
IFI27	-0.74	-0.86
HIGD1B	-0.74	-0.88
FXYD1	-0.74	-0.85
COPZ2	-0.73	-0.81
S100B	-0.73	-0.82
AF347015.33	-0.73	-0.82
MT-CYB	-0.73	-0.84

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003723	RNA binding	IEA		-
GO:0005515	protein binding	IPI		17353931

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
LIU SOX4 TARGETS DN	309	191	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 UP	146	86	All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS DN	68	49	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS TOP50 UP	38	27	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP	368	234	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN	335	193	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN	180	101	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
SCHLOSSER MYC AND SERUM RESPONSE SYNERGY	32	22	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
MCCLUNG COCAINE REWARD 5D	79	62	All SZGR 2.0 genes in this pathway
DASU IL6 SIGNALING SCAR UP	30	21	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS DN	292	189	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
MELLMAN TUT1 TARGETS UP	19	11	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS UP	221	135	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE M G1	148	95	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	All SZGR 2.0 genes in this pathway
HOLLEMAN DAUNORUBICIN B ALL UP	10	9	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	2202	2209	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124.1	914	920	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	914	920	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	914	920	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-129-5p	3471	3477	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	3471	3477	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-143	2384	2391	1A,m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-144	2203	2209	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-153	412	418	m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-214	548	554	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-214	548	554	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-26	3337	3344	1A,m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
				hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
				hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
				hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
				hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
				hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-30-5p	2502	2508	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-326	675	682	1A,m8	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-369-3p	3352	3359	1A,m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	3353	3360	1A,m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-381	3349	3355	m8	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-410	267	273	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-496	3329	3335	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-9	594	600	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: LARP1