SZGR2

Summary ?

GeneID	9782
Symbol	MATR3
Synonyms	ALS21\|MPD2\|VCPDM
Description	matrin 3
Reference	MIM:164015\|HGNC:HGNC:6912\|Ensembl:ENSG00000015479\|Ensembl:ENSG00000280987\|HPRD:05270\|Vega:OTTHUMG00000129229 Vega:OTTHUMG00000189583
Gene type	protein-coding
Map location	5q31.2
Pascal p-value	0.335
Sherlock p-value	0.814
DEG p-value	DEG:Sanders_2014:DS1_p=0.123:DS1_beta=0.039900:DS2_p=8.19e-01:DS2_beta=-0.010:DS2_FDR=9.17e-01
Fetal beta	1.28

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
DEG:Sanders_2013	Microarray	Whole-genome gene expression profiles using microarrays on lymphoblastoid cell lines (LCLs) from 413 cases and 446 controls.
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0717

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
VCPIP1	0.94	0.96
SEL1L	0.93	0.94
EXOC6B	0.93	0.95
KIAA1219	0.93	0.95
TBL1XR1	0.93	0.95
RAB3GAP2	0.93	0.95
ZYG11B	0.92	0.94
SNX30	0.92	0.93
APPL1	0.92	0.94
KIAA1128	0.92	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
S100A16	-0.63	-0.68
CST3	-0.63	-0.69
FXYD1	-0.62	-0.68
TLCD1	-0.62	-0.67
ENHO	-0.61	-0.71
HIGD1B	-0.61	-0.68
RAB34	-0.61	-0.69
RHOC	-0.61	-0.70
METRN	-0.60	-0.68
EIF4EBP3	-0.60	-0.65

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0003676	nucleic acid binding	IEA		-
GO:0003723	RNA binding	IEA		-
GO:0005515	protein binding	IPI		17353931
GO:0005198	structural molecule activity	TAS		2033075
GO:0008270	zinc ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005622	intracellular	IEA		-
GO:0005634	nucleus	IEA		-
GO:0005637	nuclear inner membrane	TAS		2033075
GO:0016363	nuclear matrix	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP	408	247	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS DN	431	263	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE UP	423	283	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP	430	232	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN	281	186	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	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
GAUSSMANN MLL AF4 FUSION TARGETS A UP	191	128	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
FALVELLA SMOKERS WITH LUNG CANCER	80	52	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP	424	268	All SZGR 2.0 genes in this pathway
BYSTROEM CORRELATED WITH IL5 DN	64	47	All SZGR 2.0 genes in this pathway
CHESLER BRAIN HIGHEST EXPRESSION	40	29	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI DN	172	107	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL SHORT TERM	32	15	All SZGR 2.0 genes in this pathway
KEEN RESPONSE TO ROSIGLITAZONE DN	106	68	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
MONNIER POSTRADIATION TUMOR ESCAPE UP	393	244	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS UP	425	253	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS UP	74	45	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP	518	299	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE DN	841	431	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 2 UP	54	31	All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 3 UP	170	97	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
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN	553	343	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4	227	149	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-1/206	406	413	1A,m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-129-5p	160	167	1A,m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	160	167	1A,m8	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-141/200a	151	157	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	151	157	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-200bc/429	684	691	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-203.1	812	818	m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-21	252	258	1A	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	252	258	1A	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-216	498	504	m8	hsa-miR-216	UAAUCUCAGCUGGCAACUGUG
miR-24	423	429	m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-26	716	722	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	716	722	1A	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-30-5p	920	926	m8	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-329	772	778	1A	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-382	265	271	m8	hsa-miR-382^brain	GAAGUUGUUCGUGGUGGAUUCG
miR-409-3p	405	411	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-450	160	166	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-500	519	525	m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-543	53	59	1A	hsa-miR-543	AAACAUUCGCGGUGCACUUCU

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: MATR3