SZGR2

Summary ?

GeneID	9969
Symbol	MED13
Synonyms	ARC250\|DRIP250\|HSPC221\|THRAP1\|TRAP240
Description	mediator complex subunit 13
Reference	MIM:603808\|HGNC:HGNC:22474\|Ensembl:ENSG00000108510\|HPRD:07229\|Vega:OTTHUMG00000179251
Gene type	protein-coding
Map location	17q23.2
Pascal p-value	0.079
Fetal beta	1.795
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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.	1
Expression	Meta-analysis of gene expression	P value: 1.38

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg20376447	17	60143446	MED13	1.18E-9	-0.029	1.28E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs12620093	chr2	69393712	MED13	9969		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
DMXL1	0.93	0.95
NF1	0.93	0.95
GARNL1	0.92	0.92
ATG2B	0.92	0.93
CXorf39	0.92	0.92
DMXL2	0.91	0.92
AC010896.1	0.91	0.95
APPL1	0.91	0.92
SEL1L	0.91	0.94
C9orf5	0.91	0.92

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FXYD1	-0.59	-0.58
AF347015.21	-0.58	-0.56
C1orf61	-0.57	-0.70
C1orf54	-0.57	-0.62
HIGD1B	-0.57	-0.59
MT-CO2	-0.55	-0.56
CSAG1	-0.55	-0.55
VAMP5	-0.55	-0.53
AC098691.2	-0.55	-0.59
EIF4EBP3	-0.54	-0.57

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	IDA		12218053
GO:0016455	RNA polymerase II transcription mediator activity	IDA		10198638
GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	NAS		10235266
GO:0042809	vitamin D receptor binding	NAS		10235266
GO:0046966	thyroid hormone receptor binding	IDA		10198638
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006367	transcription initiation from RNA polymerase II promoter	IDA		12218053
GO:0006350	transcription	IEA		-
GO:0030521	androgen receptor signaling pathway	IDA		12218053
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IDA		12037571
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000119	mediator complex	IDA		10198638
GO:0005634	nucleus	IDA		10235267

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN UP	177	113	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS D UP	38	23	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER UP	181	108	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL	326	213	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
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 17Q21 Q25 AMPLICON	335	181	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN	228	146	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR UP	178	111	All SZGR 2.0 genes in this pathway
DURCHDEWALD SKIN CARCINOGENESIS DN	264	168	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER CLUSTER 5	18	11	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	3084	3090	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-128	760	766	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
				hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-129-5p	3818	3824	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	3818	3824	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-134	263	270	1A,m8	hsa-miR-134^brain	UGUGACUGGUUGACCAGAGGG
miR-135	2742	2748	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
				hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
				hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
				hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
				hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-136	329	335	1A	hsa-miR-136	ACUCCAUUUGUUUUGAUGAUGGA
miR-137	538	544	m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-140	2893	2899	m8	hsa-miR-140^brain	AGUGGUUUUACCCUAUGGUAG
miR-142-5p	3623	3629	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-144	3083	3090	1A,m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-145	3525	3531	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-145	3525	3531	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-146	1450	1456	1A	hsa-miR-146a	UGAGAACUGAAUUCCAUGGGUU
miR-146	1450	1456	1A	hsa-miR-146b^brain	UGAGAACUGAAUUCCAUAGGCU
miR-15/16/195/424/497	1595	1601	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-153	2737	2743	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	3622	3628	1A	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-18	2796	2802	1A	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	2796	2802	1A	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-183	3740	3746	1A	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-19	1531	1538	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	1531	1538	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-194	1017	1023	1A	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-196	1664	1670	1A	hsa-miR-196a	UAGGUAGUUUCAUGUUGUUGG
miR-196	1664	1670	1A	hsa-miR-196b	UAGGUAGUUUCCUGUUGUUGG
miR-200bc/429	2659	2665	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-205	3628	3634	m8	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-208	565	572	1A,m8	hsa-miR-208	AUAAGACGAGCAAAAAGCUUGU
miR-217	582	588	1A	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-24	288	294	1A	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-26	1641	1647	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
				hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
				hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
				hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-27	2761	2768	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	2761	2768	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-299-5p	2892	2898	1A	hsa-miR-299-5p	UGGUUUACCGUCCCACAUACAU
miR-323	3034	3040	m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-324-3p	3657	3663	1A	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-34b	521	527	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-369-3p	603	609	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-369-3p	603	609	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	222	229	1A,m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-375	3717	3723	1A	hsa-miR-375	UUUGUUCGUUCGGCUCGCGUGA
miR-379	1662	1668	m8	hsa-miR-379^brain	UGGUAGACUAUGGAACGUA
miR-381	390	396	m8	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-410	894	900	m8	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
				hsa-miR-410	AAUAUAACACAGAUGGCCUGU
				hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-433-3p	3850	3856	1A	hsa-miR-433^brain	AUCAUGAUGGGCUCCUCGGUGU
miR-448	2737	2743	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-485-3p	2776	2783	1A,m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-493-5p	742	748	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
				hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
				hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-499	566	572	1A	hsa-miR-499	UUAAGACUUGCAGUGAUGUUUAA
miR-543	1015	1021	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: MED13