SZGR2

Summary ?

GeneID	6628
Symbol	SNRPB
Synonyms	CCMS\|COD\|SNRPB1\|Sm-B/B'\|SmB/B'\|SmB/SmB'\|snRNP-B
Description	small nuclear ribonucleoprotein polypeptides B and B1
Reference	MIM:182282\|HGNC:HGNC:11153\|Ensembl:ENSG00000125835\|HPRD:01655\|Vega:OTTHUMG00000031694
Gene type	protein-coding
Map location	20p13
Pascal p-value	0.061
Sherlock p-value	0.053
Fetal beta	0.7
DMG	2 (# studies)

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.	2
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).	2

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg04435241	20	2442475	SNRPB	1.779E-4	0.268	0.034	DMG:Wockner_2014
cg11521799	20	2451663	SNRPB	4.71E-8	-0.015	1.27E-5	DMG:Jaffe_2016

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
DPP9	0.86	0.88
ZNF687	0.86	0.86
ATG2A	0.84	0.88
NUP210	0.84	0.87
MED15	0.84	0.86
POLG	0.84	0.85
FOXRED2	0.83	0.86
RPAP1	0.83	0.87
CORO2B	0.83	0.84
UPF1	0.83	0.85

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.21	-0.63	-0.66
SYCP3	-0.61	-0.70
C1orf54	-0.60	-0.65
GNG11	-0.58	-0.62
AF347015.31	-0.57	-0.55
MT-CO2	-0.56	-0.55
AL050337.1	-0.56	-0.63
CLEC2B	-0.55	-0.63
HIGD1B	-0.54	-0.53
NOSTRIN	-0.53	-0.51

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ASCC2	ASC1p100	activating signal cointegrator 1 complex subunit 2	Two-hybrid	BioGRID	16169070
C14orf1	ERG28 \| NET51	chromosome 14 open reading frame 1	Two-hybrid	BioGRID	16169070
CLNS1A	CLCI \| CLNS1B \| ICln	chloride channel, nucleotide-sensitive, 1A	Affinity Capture-Western	BioGRID	11713266
COIL	CLN80 \| p80-coilin	coilin	-	HPRD,BioGRID	11641277
CTDP1	CCFDN \| FCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	-	HPRD	12560496
DDX20	DKFZp434H052 \| DP103 \| GEMIN3	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	-	HPRD,BioGRID	10601333
DHX9	DDX9 \| LKP \| NDHII \| RHA	DEAH (Asp-Glu-Ala-His) box polypeptide 9	-	HPRD	11149922
DYNC1H1	DHC1 \| DHC1a \| DKFZp686P2245 \| DNCH1 \| DNCL \| DNECL \| DYHC \| Dnchc1 \| HL-3 \| KIAA0325 \| p22	dynein, cytoplasmic 1, heavy chain 1	Affinity Capture-MS	BioGRID	17353931
EFTUD2	DKFZp686E24196 \| FLJ44695 \| KIAA0031 \| Snrp116 \| Snu114 \| U5-116KD	elongation factor Tu GTP binding domain containing 2	Affinity Capture-MS	BioGRID	17353931
FNBP4	DKFZp686M14102 \| DKFZp779I1064 \| FBP30 \| FLJ41904 \| KIAA1014	formin binding protein 4	Protein-peptide	BioGRID	11604498
GEMIN4	DKFZp434B131 \| DKFZp434D174 \| HC56 \| HCAP1 \| HHRF-1 \| p97	gem (nuclear organelle) associated protein 4	Affinity Capture-MS	BioGRID	17353931
GEMIN4	DKFZp434B131 \| DKFZp434D174 \| HC56 \| HCAP1 \| HHRF-1 \| p97	gem (nuclear organelle) associated protein 4	-	HPRD	10725331
GEMIN5	DKFZp586M1824 \| MGC142174	gem (nuclear organelle) associated protein 5	-	HPRD	11714716
GEMIN6	FLJ23459	gem (nuclear organelle) associated protein 6	Gemin6 interacts with SmB.	BIND	11748230
GEMIN6	FLJ23459	gem (nuclear organelle) associated protein 6	Gemin6 interacts with SNRPB (SmB)	BIND	15939020
GEMIN7	SIP3	gem (nuclear organelle) associated protein 7	GEMIN7 interacts with SNRPB (SmB)	BIND	12065586
HTATSF1	TAT-SF1 \| dJ196E23.2	HIV-1 Tat specific factor 1	Affinity Capture-MS	BioGRID	17353931
KHK	-	ketohexokinase (fructokinase)	Affinity Capture-MS	BioGRID	17353931
LGALS1	DKFZp686E23103 \| GAL1 \| GBP	lectin, galactoside-binding, soluble, 1	Affinity Capture-Western	BioGRID	11522829
LSM11	FLJ38273	LSM11, U7 small nuclear RNA associated	-	HPRD	12975319
PRPF8	HPRP8 \| PRP8 \| PRPC8 \| RP13	PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)	Affinity Capture-MS	BioGRID	17353931
PSMA3	HC8 \| MGC12306 \| MGC32631 \| PSC3	proteasome (prosome, macropain) subunit, alpha type, 3	Two-hybrid	BioGRID	16169070
RBBP6	DKFZp686P0638 \| DKFZp761B2423 \| MY038 \| P2P-R \| PACT \| RBQ-1 \| SNAMA	retinoblastoma binding protein 6	Sm interacts with PACT.	BIND	9010216
SART3	DSAP1 \| KIAA0156 \| MGC138188 \| P100 \| RP11-13G14 \| TIP110 \| p110 \| p110(nrb)	squamous cell carcinoma antigen recognized by T cells 3	Affinity Capture-MS	BioGRID	17353931
SF3A2	PRP11 \| PRPF11 \| SAP62 \| SF3a66	splicing factor 3a, subunit 2, 66kDa	Affinity Capture-MS	BioGRID	12234937
SMN1	BCD541 \| SMA \| SMA1 \| SMA2 \| SMA3 \| SMA4 \| SMA@ \| SMN \| SMNT \| T-BCD541	survival of motor neuron 1, telomeric	SMN interacts with SmB'.	BIND	15494309
SMN1	BCD541 \| SMA \| SMA1 \| SMA2 \| SMA3 \| SMA4 \| SMA@ \| SMN \| SMNT \| T-BCD541	survival of motor neuron 1, telomeric	-	HPRD	11720283
SMN1	BCD541 \| SMA \| SMA1 \| SMA2 \| SMA3 \| SMA4 \| SMA@ \| SMN \| SMNT \| T-BCD541	survival of motor neuron 1, telomeric	-	HPRD,BioGRID	9323129\|11720283
SMN2	BCD541 \| C-BCD541 \| FLJ76644 \| MGC20996 \| MGC5208 \| SMNC	survival of motor neuron 2, centromeric	-	HPRD	9323129
SNRNP200	ASCC3L1 \| BRR2 \| HELIC2 \| U5-200KD	small nuclear ribonucleoprotein 200kDa (U5)	Affinity Capture-MS	BioGRID	17353931
SNRPD3	SMD3	small nuclear ribonucleoprotein D3 polypeptide 18kDa	-	HPRD,BioGRID	10025403
SNUPN	KPNBL \| RNUT1 \| Snurportin1	snurportin 1	Reconstituted Complex	BioGRID	12095920
STXBP2	Hunc18b \| MUNC18-2 \| UNC18-2 \| UNC18B \| pp10122	syntaxin binding protein 2	-	HPRD	11748230
STXBP3	MUNC18-3 \| MUNC18C \| PSP \| UNC-18C	syntaxin binding protein 3	-	HPRD	12065586
TOP3B	FLJ39376	topoisomerase (DNA) III beta	-	HPRD,BioGRID	11549288
WBP4	FBP21 \| MGC117310	WW domain binding protein 4 (formin binding protein 21)	-	HPRD	9724750
WBP4	FBP21 \| MGC117310	WW domain binding protein 4 (formin binding protein 21)	Protein-peptide	BioGRID	11604498
WDR77	HKMT1069 \| MEP50 \| MGC2722 \| Nbla10071 \| RP11-552M11.3 \| p44	WD repeat domain 77	-	HPRD,BioGRID	11756452

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG SPLICEOSOME	128	72	All SZGR 2.0 genes in this pathway
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS	140	100	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF NON CODING RNA	49	29	All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	140	77	All SZGR 2.0 genes in this pathway
REACTOME SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS	11	5	All SZGR 2.0 genes in this pathway
REACTOME RNA POL II TRANSCRIPTION	105	54	All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING	161	86	All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING	111	58	All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING MINOR PATHWAY	45	19	All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRONLESS PRE MRNA	23	10	All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION	210	127	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA	330	155	All SZGR 2.0 genes in this pathway
REACTOME CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION	44	22	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP	430	232	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP	722	443	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP	530	342	All SZGR 2.0 genes in this pathway
SCHLOSSER MYC TARGETS AND SERUM RESPONSE UP	47	32	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
MEINHOLD OVARIAN CANCER LOW GRADE DN	20	16	All SZGR 2.0 genes in this pathway
FURUKAWA DUSP6 TARGETS PCI35 UP	74	32	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
PUJANA XPRSS INT NETWORK	168	103	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	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
PUJANA BRCA CENTERED NETWORK	117	72	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE DN	75	43	All SZGR 2.0 genes in this pathway
MORI EMU MYC LYMPHOMA BY ONSET TIME UP	110	69	All SZGR 2.0 genes in this pathway
IIZUKA LIVER CANCER PROGRESSION L1 G1 DN	12	6	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS	185	114	All SZGR 2.0 genes in this pathway
NING CHRONIC OBSTRUCTIVE PULMONARY DISEASE DN	121	79	All SZGR 2.0 genes in this pathway
SHIPP DLBCL VS FOLLICULAR LYMPHOMA UP	45	30	All SZGR 2.0 genes in this pathway
NADLER HYPERGLYCEMIA AT OBESITY	58	35	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP	428	266	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR UP	148	96	All SZGR 2.0 genes in this pathway
GAVIN FOXP3 TARGETS CLUSTER T7	98	63	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER UP	285	167	All SZGR 2.0 genes in this pathway
MALONEY RESPONSE TO 17AAG DN	79	45	All SZGR 2.0 genes in this pathway
MUELLER PLURINET	299	189	All SZGR 2.0 genes in this pathway
TOOKER GEMCITABINE RESISTANCE UP	79	40	All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE UP	212	128	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6	456	285	All SZGR 2.0 genes in this pathway
ZHAN V1 LATE DIFFERENTIATION GENES DN	15	13	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G123 UP	45	21	All SZGR 2.0 genes in this pathway
YOSHIOKA LIVER CANCER EARLY RECURRENCE UP	40	23	All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2	277	172	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP	72	53	All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP	143	100	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	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 ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT	572	352	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS LOW SERUM	100	51	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
JUBAN TARGETS OF SPI1 AND FLI1 DN	92	60	All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE	45	33	All SZGR 2.0 genes in this pathway

Gene Page: SNRPB