SZGR2

Summary ?

GeneID	5649
Symbol	RELN
Synonyms	ETL7\|LIS2\|PRO1598\|RL
Description	reelin
Reference	MIM:600514\|HGNC:HGNC:9957\|Ensembl:ENSG00000189056\|HPRD:02742\|Vega:OTTHUMG00000157247
Gene type	protein-coding
Map location	7q22
Pascal p-value	0.039
Sherlock p-value	0.426
TADA p-value	0.033
Fetal beta	0.052
eGene	Myers' cis & trans
Support	CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	2	Link to SZGene
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 31

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
RELN	chr7	103194134	T	C	NM_005045 NM_173054	p.1981Y>C p.1981Y>C	missense missense			Schizophrenia	DNM:Fromer_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs2502827	chr1	176044216	RELN	5649	0.14	trans
rs3845734	chr2	171125572	RELN	5649	0.12	trans
rs7584986	chr2	184111432	RELN	5649	5.384E-5	trans
rs1368303	chr5	147672388	RELN	5649	0.09	trans
snp_a-2055204		0	RELN	5649	0.2	trans
rs17104720	chr14	77127308	RELN	5649	0.04	trans
rs16955618	chr15	29937543	RELN	5649	6.42E-7	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
AL161668.2	0.84	0.85
ERBB2	0.84	0.84
GNA12	0.84	0.84
ARAF	0.82	0.79
HEATR2	0.81	0.77
SMO	0.81	0.77
ASAP3	0.81	0.76
ZNF687	0.80	0.74
CHST14	0.80	0.79
PAK4	0.80	0.77

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.21	-0.40	-0.46
C5orf53	-0.39	-0.37
SYCP3	-0.37	-0.40
LY96	-0.37	-0.45
CLEC2B	-0.36	-0.42
SPHAR	-0.36	-0.47
RERGL	-0.36	-0.42
GPR160	-0.36	-0.39
KMO	-0.35	-0.36
AF347015.27	-0.35	-0.36

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004252	serine-type endopeptidase activity	IEA	glutamate (GO term level: 7)	-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0008233	peptidase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007155	cell adhesion	IEA		-
GO:0007275	multicellular organismal development	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0005578	proteinaceous extracellular matrix	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG FOCAL ADHESION	201	138	All SZGR 2.0 genes in this pathway
KEGG ECM RECEPTOR INTERACTION	84	53	All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY	29	29	All SZGR 2.0 genes in this pathway
PID LIS1 PATHWAY	28	22	All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN	391	222	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS BLUE UP	136	80	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS G UP	238	135	All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER DN	37	22	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA PROGRESSION RISK	74	44	All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP	100	75	All SZGR 2.0 genes in this pathway
KANG GIST WITH PDGFRA UP	50	27	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
WATTEL AUTONOMOUS THYROID ADENOMA DN	55	29	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
MORI SMALL PRE BII LYMPHOCYTE UP	86	57	All SZGR 2.0 genes in this pathway
CHESLER BRAIN D6MIT150 QTL TRANS	9	7	All SZGR 2.0 genes in this pathway
PETROVA ENDOTHELIUM LYMPHATIC VS BLOOD UP	131	87	All SZGR 2.0 genes in this pathway
RAMALHO STEMNESS DN	74	55	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP	249	170	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP	428	266	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS DN	142	94	All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS UP	24	14	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP	282	183	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN	540	340	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
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP	149	85	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C CLUSTER UP	38	26	All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE D7 DN	40	22	All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE 35D DN	49	34	All SZGR 2.0 genes in this pathway
VANASSE BCL2 TARGETS UP	40	25	All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE DN	72	47	All SZGR 2.0 genes in this pathway
HOFFMANN SMALL PRE BII TO IMMATURE B LYMPHOCYTE DN	50	33	All SZGR 2.0 genes in this pathway
HOFFMANN IMMATURE TO MATURE B LYMPHOCYTE DN	50	36	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME3 AND H3K27ME3	142	103	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
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA3 DN	69	38	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP	207	143	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3	210	148	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 2	86	50	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 5	30	22	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
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
HOELZEL NF1 TARGETS UP	139	93	All SZGR 2.0 genes in this pathway
CHANGOLKAR H2AFY TARGETS DN	40	26	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP	266	142	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	All SZGR 2.0 genes in this pathway
NABA ECM GLYCOPROTEINS	196	99	All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME	275	148	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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-128	156	163	1A,m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	156	163	1A,m8	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-138	902	909	1A,m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-15/16/195/424/497	507	513	m8	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-205	96	102	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-218	301	308	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-27	157	164	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	157	164	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-34/449	778	784	1A	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-378	82	88	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU
miR-544	536	543	1A,m8	hsa-miR-544	AUUCUGCAUUUUUAGCAAGU

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: RELN