SZGR2

Summary ?

GeneID	4691
Symbol	NCL
Synonyms	C23
Description	nucleolin
Reference	MIM:164035\|HGNC:HGNC:7667\|HPRD:01245\|
Gene type	protein-coding
Map location	2q37.1
Pascal p-value	0.062
Sherlock p-value	0.159
Fetal beta	0.246
eGene	Meta
Support	Ascano FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizotypy,schizophrenias,schizotypal	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0143

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
AC116610.1	1.00	1.00
ZNHIT1	0.87	0.75
COX8A	0.86	0.75
TRAPPC5	0.86	0.76
NDUFB7	0.85	0.71
NDUFA11	0.85	0.70
MRP63	0.85	0.74
C7orf59	0.85	0.72
C19orf70	0.85	0.75
NDUFA2	0.84	0.73

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
BAT2D1	-0.44	-0.41
RBM25	-0.41	-0.44
MYH9	-0.40	-0.37
ZC3H13	-0.39	-0.37
UPF2	-0.38	-0.34
ZNHIT6	-0.37	-0.34
MACF1	-0.37	-0.34
SFRS12	-0.37	-0.41
MDN1	-0.36	-0.33
SLC6A6	-0.36	-0.34

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:0003677	DNA binding	IEA		-
GO:0003723	RNA binding	TAS		2737305
GO:0005515	protein binding	IEA		-
GO:0008022	protein C-terminus binding	IPI		16403913
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001525	angiogenesis	IDA		16403913
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005730	nucleolus	IDA		12944467
GO:0005730	nucleolus	IEA		-
GO:0005938	cell cortex	IDA		16403913

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ADAP1	CENTA1 \| GCS1L \| p42IP4	ArfGAP with dual PH domains 1	-	HPRD,BioGRID	12565890
CD3E	FLJ18683 \| T3E \| TCRE	CD3e molecule, epsilon (CD3-TCR complex)	Reconstituted Complex	BioGRID	11115514
CSNK2A1	CK2A1 \| CKII	casein kinase 2, alpha 1 polypeptide	-	HPRD	2192260\|8663258
CSNK2A2	CK2A2 \| CSNK2A1 \| FLJ43934	casein kinase 2, alpha prime polypeptide	Affinity Capture-Western Biochemical Activity Far Western	BioGRID	8663258
CYFIP1	FLJ45151 \| P140SRA-1 \| SHYC \| SRA1	cytoplasmic FMR1 interacting protein 1	Affinity Capture-Western	BioGRID	11438699
FMR1	FMRP \| FRAXA \| MGC87458 \| POF \| POF1	fragile X mental retardation 1	Affinity Capture-Western	BioGRID	10567518
GZMA	CTLA3 \| HFSP	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	-	HPRD	1860869
MDK	FLJ27379 \| MK \| NEGF2	midkine (neurite growth-promoting factor 2)	-	HPRD,BioGRID	12147681
MYB	Cmyb \| c-myb \| c-myb_CDS \| efg	v-myb myeloblastosis viral oncogene homolog (avian)	Affinity Capture-Western	BioGRID	10660576
MYBL1	A-MYB \| AMYB \| MGC120059 \| MGC120061	v-myb myeloblastosis viral oncogene homolog (avian)-like 1	Affinity Capture-Western Far Western	BioGRID	10660576
MYC	bHLHe39 \| c-Myc	v-myc myelocytomatosis viral oncogene homolog (avian)	Ncl (nucleolin) interacts with Myc (c-Myc).	BIND	15674325
NPM1	B23 \| MGC104254 \| NPM	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	-	HPRD,BioGRID	8620867 \|10503877
NR3C1	GCCR \| GCR \| GR \| GRL	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	-	HPRD,BioGRID	8530516 \|11162542
PPARGC1A	LEM6 \| PGC-1(alpha) \| PGC-1v \| PGC1 \| PGC1A \| PPARGC1	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	-	HPRD	10983978
PPP1CB	MGC3672 \| PP-1B \| PPP1CD	protein phosphatase 1, catalytic subunit, beta isoform	Affinity Capture-Western	BioGRID	12185196
PRKCZ	PKC-ZETA \| PKC2	protein kinase C, zeta	-	HPRD,BioGRID	9388266
S100A11	MLN70 \| S100C	S100 calcium binding protein A11	-	HPRD,BioGRID	14623863
SFRS12	DKFZp564B176 \| MGC133045 \| SRrp508 \| SRrp86	splicing factor, arginine/serine-rich 12	-	HPRD	14559993
SP1	-	Sp1 transcription factor	Affinity Capture-Western	BioGRID	14623863
SSB	LARP3 \| La	Sjogren syndrome antigen B (autoantigen La)	Affinity Capture-MS Affinity Capture-Western	BioGRID	12096904
SWAP70	FLJ39540 \| HSPC321 \| KIAA0640 \| SWAP-70	SWAP-70 protein	-	HPRD,BioGRID	9642267
TERT	EST2 \| TCS1 \| TP2 \| TRT \| hEST2	telomerase reverse transcriptase	Affinity Capture-Western Reconstituted Complex	BioGRID	15371412
TERT	EST2 \| TCS1 \| TP2 \| TRT \| hEST2	telomerase reverse transcriptase	nucleolin interacts with hTERT.	BIND	15371412
TOP1	TOPI	topoisomerase (DNA) I	Top1 interacts with Nucleolin	BIND	10967121
TOP1	TOPI	topoisomerase (DNA) I	-	HPRD,BioGRID	8567649 \|9512561 \|10967121
TP53	FLJ92943 \| LFS1 \| TRP53 \| p53	tumor protein p53	-	HPRD,BioGRID	12138209
TROVE2	RO60 \| SSA2	TROVE domain family, member 2	-	HPRD	12096904

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION	59	36	All SZGR 2.0 genes in this pathway
BIOCARTA SARS PATHWAY	10	5	All SZGR 2.0 genes in this pathway
PID AURORA B PATHWAY	39	24	All SZGR 2.0 genes in this pathway
PID MYC ACTIV PATHWAY	79	62	All SZGR 2.0 genes in this pathway
PID TELOMERASE PATHWAY	68	48	All SZGR 2.0 genes in this pathway
PID UPA UPAR PATHWAY	42	30	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND SERUM DEPRIVATION UP	211	136	All SZGR 2.0 genes in this pathway
CAIRO PML TARGETS BOUND BY MYC UP	23	17	All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP	584	356	All SZGR 2.0 genes in this pathway
DARWICHE SKIN TUMOR PROMOTER UP	142	96	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK LOW UP	162	104	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH UP	147	101	All SZGR 2.0 genes in this pathway
DARWICHE SQUAMOUS CELL CARCINOMA UP	146	104	All SZGR 2.0 genes in this pathway
SCHLOSSER MYC TARGETS AND SERUM RESPONSE DN	47	34	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
KIM MYC AMPLIFICATION TARGETS UP	201	127	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
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP	176	115	All SZGR 2.0 genes in this pathway
DEN INTERACT WITH LCA5	26	21	All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX	230	156	All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS	775	494	All SZGR 2.0 genes in this pathway
MENSSEN MYC TARGETS	53	35	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
COLLER MYC TARGETS UP	25	19	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
BROWN MYELOID CELL DEVELOPMENT DN	129	86	All SZGR 2.0 genes in this pathway
HESS TARGETS OF HOXA9 AND MEIS1 UP	65	44	All SZGR 2.0 genes in this pathway
MA MYELOID DIFFERENTIATION UP	39	29	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR	532	309	All SZGR 2.0 genes in this pathway
JOSEPH RESPONSE TO SODIUM BUTYRATE DN	64	45	All SZGR 2.0 genes in this pathway
ZHOU TNF SIGNALING 4HR	54	36	All SZGR 2.0 genes in this pathway
HU GENOTOXIN ACTION DIRECT VS INDIRECT 24HR	55	38	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL	311	205	All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX DN	54	43	All SZGR 2.0 genes in this pathway
BILD MYC ONCOGENIC SIGNATURE	206	117	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
RIZKI TUMOR INVASIVENESS 2D UP	69	46	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
MUELLER PLURINET	299	189	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D UP	139	95	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP	491	316	All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES	389	245	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS UP	74	45	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP	605	377	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
WONG EMBRYONIC STEM CELL CORE	335	193	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
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
IKEDA MIR1 TARGETS UP	53	39	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	90	97	1A,m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-194	57	63	m8	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-431	96	102	1A	hsa-miR-431	UGUCUUGCAGGCCGUCAUGCA

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: NCL