SZGR2

Summary ?

GeneID	5930
Symbol	RBBP6
Synonyms	MY038\|P2P-R\|PACT\|RBQ-1\|SNAMA
Description	retinoblastoma binding protein 6
Reference	MIM:600938\|HGNC:HGNC:9889\|Ensembl:ENSG00000122257\|HPRD:02964\|Vega:OTTHUMG00000096991
Gene type	protein-coding
Map location	16p12.2
Pascal p-value	0.015
Fetal beta	0.885
DMG	2 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	3
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	3
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.01775

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg05920643	16	24552079	RBBP6	2.747E-4	-0.539	0.038	DMG:Wockner_2014
cg27501380	16	24551577	RBBP6		-0.028	0.3	DMG:Nishioka_2013
cg16050957	16	24550743	RBBP6		-0.029	0.39	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs16829545	chr2	151977407	RBBP6	5930	6.838E-5	trans
rs10491487	chr5	80323367	RBBP6	5930	0.01	trans
rs11115542	chr12	83419258	RBBP6	5930	0.09	trans
rs10862560	chr12	83419667	RBBP6	5930	0.17	trans
rs2403055	chr12	83421514	RBBP6	5930	0.17	trans
rs16955618	chr15	29937543	RBBP6	5930	6.414E-5	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
SMARCA5	0.92	0.91
CDC73	0.87	0.88
STAG2	0.86	0.88
ARL13B	0.86	0.83
NARG2	0.85	0.82
TMX1	0.84	0.76
SFRS2IP	0.84	0.81
PPIL4	0.84	0.84
HAUS6	0.84	0.84
RAD21	0.84	0.83

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
CXCL14	-0.53	-0.66
IFI27	-0.51	-0.65
MT-CO2	-0.51	-0.62
AF347015.31	-0.50	-0.62
FXYD1	-0.50	-0.62
ENHO	-0.49	-0.64
MYL3	-0.49	-0.60
AF347015.21	-0.48	-0.59
HIGD1B	-0.48	-0.61
AC018755.7	-0.47	-0.58

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003676	nucleic acid binding	IEA		-
GO:0005515	protein binding	TAS		8595913
GO:0004842	ubiquitin-protein ligase activity	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016567	protein ubiquitination	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000151	ubiquitin ligase complex	IEA		-
GO:0005634	nucleus	IEA		-

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
GAZDA DIAMOND BLACKFAN ANEMIA MYELOID DN	38	25	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN	244	147	All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA DN	104	59	All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS DN	186	114	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN	335	193	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS LIGHTYELLOW UP	11	8	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
HOEBEKE LYMPHOID STEM CELL UP	95	64	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LPS UP	431	237	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP	530	342	All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID WITH 7Q DELETION UP	67	37	All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP	584	356	All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP	390	236	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
PUJANA CHEK2 PCC NETWORK	779	480	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION UP	69	55	All SZGR 2.0 genes in this pathway
CHEN NEUROBLASTOMA COPY NUMBER GAINS	50	35	All SZGR 2.0 genes in this pathway
DORSAM HOXA9 TARGETS DN	32	22	All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE DN	245	154	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
PARK HSC MARKERS	44	31	All SZGR 2.0 genes in this pathway
STONER ESOPHAGEAL CARCINOGENESIS DN	7	6	All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION	405	264	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR UP	105	73	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN	123	76	All SZGR 2.0 genes in this pathway
MMS MOUSE LYMPH HIGH 4HRS UP	36	20	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	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
ZHENG BOUND BY FOXP3	491	310	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY GAMMA AND UV RADIATION	88	65	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE UP	226	164	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP	673	430	All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN	593	372	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN	591	366	All SZGR 2.0 genes in this pathway
DE YY1 TARGETS DN	92	64	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN	249	165	All SZGR 2.0 genes in this pathway
CHEN HOXA5 TARGETS 9HR UP	223	132	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS UP	163	100	All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE DN	181	97	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 9 11 TRANSLOCATION	130	87	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS UP	221	135	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR UP	55	41	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	All SZGR 2.0 genes in this pathway
BILANGES SERUM AND RAPAMYCIN SENSITIVE GENES	68	35	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	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-103/107	106	112	1A	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	106	112	1A	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-142-5p	155	161	1A	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-15/16/195/424/497	123	129	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-224	20	26	1A	hsa-miR-224	CAAGUCACUAGUGGUUCCGUUUA
miR-320	153	159	1A	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-496	60	66	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-93.hd/291-3p/294/295/302/372/373/520	110	116	1A	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: RBBP6