SZGR2

Summary ?

GeneID	83988
Symbol	NCALD
Synonyms	-
Description	neurocalcin delta
Reference	MIM:606722\|HGNC:HGNC:7655\|Ensembl:ENSG00000104490\|HPRD:09466\|Vega:OTTHUMG00000164876
Gene type	protein-coding
Map location	8q22.2
Pascal p-value	0.234
Sherlock p-value	0.845
Fetal beta	-1.926
DMG	1 (# studies)
eGene	Cortex Myers' cis & trans Meta
Support	INTRACELLULAR SIGNAL TRANSDUCTION

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
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).	1
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,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg03031839	8	103094119	NCALD	9.94E-5	-0.469	0.028	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs443832	chr16	83779643	NCALD	83988		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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030276	clathrin binding	IDA	Synap (GO term level: 4)	11964161
GO:0003779	actin binding	IDA		11964161
GO:0005509	calcium ion binding	IEA		-
GO:0015631	tubulin binding	IDA		11964161
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016192	vesicle-mediated transport	NAS		11964161
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	NAS		11964161
GO:0005622	intracellular	IDA		11256614
GO:0030130	clathrin coat of trans-Golgi network vesicle	NAS		11964161

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL	137	110	All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF KAINATE RECEPTORS UPON GLUTAMATE BINDING	31	23	All SZGR 2.0 genes in this pathway
REACTOME IONOTROPIC ACTIVITY OF KAINATE RECEPTORS	11	11	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS DN	384	230	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D UP	175	108	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS G UP	238	135	All SZGR 2.0 genes in this pathway
ROSS ACUTE MYELOID LEUKEMIA CBF	82	57	All SZGR 2.0 genes in this pathway
ROSS AML WITH AML1 ETO FUSION	76	55	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA UP	98	64	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3	720	440	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 UP	295	149	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K9ME3 UP	141	75	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
HOFFMANN SMALL PRE BII TO IMMATURE B LYMPHOCYTE DN	50	33	All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 13	30	20	All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G56 DN	17	9	All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS CTNNB1 DN	170	105	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION	368	247	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
KIM ALL DISORDERS DURATION CORR DN	146	90	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP	364	236	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL PROGENITOR UP	58	30	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-132/212	834	840	m8	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	834	840	m8	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-181	875	881	m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-182	1900	1907	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-182	1900	1907	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-19	909	916	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	909	916	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-204/211	322	328	1A	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	322	328	1A	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-205	2567	2573	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-27	559	565	1A	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	559	565	1A	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-30-5p	624	630	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-326	181	187	m8	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-370	538	544	m8	hsa-miR-370^brain	GCCUGCUGGGGUGGAACCUGG
miR-410	941	947	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-96	80	86	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: NCALD