SZGR2

Summary ?

GeneID	26994
Symbol	RNF11
Synonyms	CGI-123\|SID1669
Description	ring finger protein 11
Reference	MIM:612598\|HGNC:HGNC:10056\|Ensembl:ENSG00000123091\|HPRD:09955\|Vega:OTTHUMG00000008190
Gene type	protein-coding
Map location	1p32
Pascal p-value	0.219
Fetal beta	-1.177
eGene	Myers' cis & trans Meta

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0972

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1146358	chr1	116657767	RNF11	26994	0.17	trans
rs1620334	chr1	205697844	RNF11	26994	0.03	trans
rs823123	chr1	205725345	RNF11	26994	0.04	trans
rs823066	chr1	205771172	RNF11	26994	0.02	trans
rs11120206	chr1	206610593	RNF11	26994	0.09	trans
rs17012898	chr2	33601648	RNF11	26994	0.03	trans
rs17012916	chr2	33606031	RNF11	26994	0.04	trans
rs17012924	chr2	33612474	RNF11	26994	0.08	trans
rs2716734	chr2	39947720	RNF11	26994	9.419E-4	trans
rs2716736	chr2	39947946	RNF11	26994	9.419E-4	trans
rs10928499	chr2	135332354	RNF11	26994	0.06	trans
rs17044826	chr3	66620522	RNF11	26994	0.05	trans
rs16850133	chr3	140030776	RNF11	26994	0.13	trans
rs17023105	chr4	96074164	RNF11	26994	1.101E-4	trans
rs10516959	chr4	96088848	RNF11	26994	2.69E-4	trans
rs16869878	chr5	2523760	RNF11	26994	0	trans
rs467856	chr5	3128168	RNF11	26994	0	trans
rs6451640	chr5	20088127	RNF11	26994	0.11	trans
rs17103639	chr5	145081858	RNF11	26994	0.18	trans
snp_a-2169623		0	RNF11	26994	0	trans
rs13175086	chr5	174691428	RNF11	26994	0.07	trans
rs2016128	chr6	42442743	RNF11	26994	0	trans
rs9376870	chr6	145206590	RNF11	26994	0.09	trans
rs4947631	chr7	50603378	RNF11	26994	0.01	trans
rs870686	chr8	25253521	RNF11	26994	0.03	trans
rs10503771	chr8	25304019	RNF11	26994	0.02	trans
rs2513775	chr8	95111616	RNF11	26994	0.15	trans
rs12352894	chr9	38197383	RNF11	26994	0.17	trans
rs6559219		0	RNF11	26994	0.06	trans
rs12255258	chr10	106306927	RNF11	26994	5.656E-4	trans
rs4944475	chr11	83985410	RNF11	26994	0.01	trans
rs7298298	chr12	17810638	RNF11	26994	0	trans
rs998923	chr13	35507810	RNF11	26994	0.19	trans
rs4943304	chr13	36058065	RNF11	26994	0.04	trans
rs2518660	chr14	31271351	RNF11	26994	0.17	trans
rs4609787	chr15	61796043	RNF11	26994	0.09	trans
rs10512600	chr17	72812978	RNF11	26994	0.02	trans
rs17078828	chr18	65948765	RNF11	26994	0.05	trans
rs6040607	chr20	11371092	RNF11	26994	0.13	trans
rs225434	chr21	43724740	RNF11	26994	6.467E-4	trans
rs362166	chr22	35461382	RNF11	26994	0.18	trans
rs1882710	chrX	149894355	RNF11	26994	0.19	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
TAF7	0.94	0.93
COPS3	0.94	0.94
GTF2B	0.94	0.93
PSMD14	0.94	0.92
CCT4	0.94	0.95
MRPL44	0.93	0.93
ARF4	0.93	0.92
CCT2	0.93	0.94
CCT8	0.92	0.91
MRPL3	0.92	0.92

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.33	-0.72	-0.80
MT-CO2	-0.72	-0.77
AF347015.8	-0.71	-0.79
MT-CYB	-0.71	-0.79
AF347015.26	-0.71	-0.82
AF347015.15	-0.71	-0.80
AF347015.2	-0.70	-0.79
AF347015.27	-0.70	-0.77
AF347015.31	-0.68	-0.74
HLA-F	-0.68	-0.75

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003677	DNA binding	TAS		10673045
GO:0005515	protein binding	IDA		14755250
GO:0008270	zinc ion binding	TAS		10673045
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042787	protein ubiquitination during ubiquitin-dependent protein catabolic process	IDA		14755250
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000151	ubiquitin ligase complex	IDA		14755250

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
EPS15	AF-1P \| AF1P \| MLLT5	epidermal growth factor receptor pathway substrate 15	Two-hybrid	BioGRID	14755250
EPS15	AF-1P \| AF1P \| MLLT5	epidermal growth factor receptor pathway substrate 15	RNF11 interacts with EPS15.	BIND	14755250
ITCH	AIF4 \| AIP4 \| NAPP1 \| dJ468O1.1	itchy E3 ubiquitin protein ligase homolog (mouse)	RNF11 interacts with AIP4.	BIND	14559117
RPS27A	CEP80 \| HUBCEP80 \| UBA80 \| UBCEP1 \| UBCEP80	ribosomal protein S27a	RNF11 interacts with RPS27A.	BIND	14755250
RPS27A	CEP80 \| HUBCEP80 \| UBA80 \| UBCEP1 \| UBCEP80	ribosomal protein S27a	Two-hybrid	BioGRID	14755250
SMURF2	DKFZp686F0270 \| MGC138150	SMAD specific E3 ubiquitin protein ligase 2	RNF11 interacts with Smurf2.	BIND	14562029
STAMBP	AMSH \| MGC126516 \| MGC126518	STAM binding protein	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	14755250
STAMBP	AMSH \| MGC126516 \| MGC126518	STAM binding protein	RNF11 interacts with AMSH.	BIND	14755250
STAMBPL1	ALMalpha \| AMSH-FP \| AMSH-LP \| FLJ31524 \| KIAA1373 \| bA399O19.2	STAM binding protein-like 1	Two-hybrid	BioGRID	14755250
UBC	HMG20	ubiquitin C	RNF11 interacts with UbC.	BIND	14755250
UBC	HMG20	ubiquitin C	Two-hybrid	BioGRID	14755250
UBE2D1	E2(17)KB1 \| SFT \| UBC4/5 \| UBCH5 \| UBCH5A	ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)	RNF11 interacts with UbcH5a.	BIND	14562029
UBE2D2	E2(17)KB2 \| PUBC1 \| UBC4 \| UBC4/5 \| UBCH5B	ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)	RNF11 interacts with UbcH5b.	BIND	14562029
UBE2D3	E2(17)KB3 \| MGC43926 \| MGC5416 \| UBC4/5 \| UBCH5C	ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)	RNF11 interacts with UbcH5c.	BIND	14562029
ZNF350	ZBRK1 \| ZFQR	zinc finger protein 350	RNF11 interacts with ZBRK1.	BIND	14755250
ZNF350	ZBRK1 \| ZFQR	zinc finger protein 350	Two-hybrid	BioGRID	14755250

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA DN	136	86	All SZGR 2.0 genes in this pathway
NAM FXYD5 TARGETS DN	18	11	All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS UP	332	228	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP	177	110	All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN	310	188	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN	800	473	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL	326	213	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP	176	115	All SZGR 2.0 genes in this pathway
GOLDRATH HOMEOSTATIC PROLIFERATION	171	102	All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS UP	88	64	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 DN	1237	837	All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF TROGLITAZONE DN	42	24	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF DN	84	50	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 6	189	112	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED	1022	619	All SZGR 2.0 genes in this pathway
AMUNDSON POOR SURVIVAL AFTER GAMMA RADIATION 8G	95	62	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN	270	181	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
BASSO HAIRY CELL LEUKEMIA DN	80	66	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS DN	210	128	All SZGR 2.0 genes in this pathway
RAGHAVACHARI PLATELET SPECIFIC GENES	70	46	All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS DN	207	139	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	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
KIM ALL DISORDERS CALB1 CORR UP	548	370	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-124.1	526	532	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	526	532	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	526	532	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-129-5p	465	471	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	465	471	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-130/301	682	688	1A	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-141/200a	280	286	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	280	286	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-186	393	399	m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-19	487	494	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
				hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-199	452	458	m8	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	452	458	m8	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-24	62	68	m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-362	997	1003	1A	hsa-miR-362	AAUCCUUGGAACCUAGGUGUGAGU
miR-369-3p	549	555	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-381	1170	1176	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-384	326	332	1A	hsa-miR-384	AUUCCUAGAAAUUGUUCAUA
miR-384	326	332	1A	hsa-miR-384	AUUCCUAGAAAUUGUUCAUA
miR-496	200	206	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-544	639	645	m8	hsa-miR-544	AUUCUGCAUUUUUAGCAAGU
miR-9	68	74	1A	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: RNF11