SZGR2

Summary ?

GeneID	56134
Symbol	PCDHAC2
Synonyms	PCDH-ALPHA-C2
Description	protocadherin alpha subfamily C, 2
Reference	MIM:606321\|HGNC:HGNC:8677\|Ensembl:ENSG00000243232\|HPRD:07331\|Vega:OTTHUMG00000129607
Gene type	protein-coding
Map location	5q31
Pascal p-value	4.115E-5
TADA p-value	0.003
Fetal beta	-0.467
Support	CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GSMA_I	Genome scan meta-analysis	Psr: 0.0032
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
PCDHAC2	chr5	140346499	G	T	NM_018898 NM_018899 NM_018900 NM_018901 NM_018902 NM_018903 NM_018904 NM_018905 NM_018906 NM_018907 NM_018908 NM_018909 NM_018910 NM_018911 NM_031411 NM_031849 NM_031857 NM_031860 NM_031883	. p.50E>* . . . . . . . . . . . . . . . . p.50E>*	intronic nonsense intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic intronic nonsense			Schizophrenia	DNM:Fromer_2014

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
SNX10	0.91	0.90
GLRB	0.90	0.84
ATP6V1C1	0.89	0.86
GHITM	0.89	0.87
IDH3A	0.89	0.88
ENPP5	0.89	0.89
MAPK10	0.88	0.89
KRT222P	0.88	0.85
GOT1	0.88	0.90
NIPAL2	0.88	0.85

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
BCL7C	-0.53	-0.58
SH3BP2	-0.52	-0.55
FADS2	-0.52	-0.45
SEMA4B	-0.51	-0.45
NME4	-0.51	-0.62
PDE9A	-0.51	-0.49
KIAA1949	-0.51	-0.38
SH2D2A	-0.50	-0.53
TRAF4	-0.50	-0.51
TUBB2B	-0.50	-0.49

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007399	nervous system development	TAS	neurite (GO term level: 5)	10380929
GO:0007155	cell adhesion	TAS		10380929
GO:0007156	homophilic cell adhesion	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	TAS		10380929

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
LEE METASTASIS AND ALTERNATIVE SPLICING DN	45	31	All SZGR 2.0 genes in this pathway
BONCI TARGETS OF MIR15A AND MIR16 1	91	75	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	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-124/506	2194	2200	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	2194	2200	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-15/16/195/424/497	1015	1022	1A,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-153	841	847	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	1189	1195	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
				hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-181	1523	1530	1A,m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-185	204	211	1A,m8	hsa-miR-185^brain	UGGAGAGAAAGGCAGUUC
miR-185	204	211	1A,m8	hsa-miR-185^brain	UGGAGAGAAAGGCAGUUC
miR-186	791	797	m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-19	796	803	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	796	803	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-218	1791	1798	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	60	67	1A,m8	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	60	67	1A,m8	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-23	2125	2131	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
				hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-29	2355	2362	1A,m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-320	1083	1090	1A,m8	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
				hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
				hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-329	2071	2078	1A,m8	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-330	1833	1840	1A,m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-362	2320	2326	1A	hsa-miR-362	AAUCCUUGGAACCUAGGUGUGAGU
miR-369-3p	1057	1064	1A,m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-448	841	847	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-495	883	889	m8	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-503	1016	1022	1A	hsa-miR-503	UAGCAGCGGGAACAGUUCUGCAG
miR-505	1520	1526	1A	hsa-miR-505	GUCAACACUUGCUGGUUUCCUC
miR-539	1257	1263	1A	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-93.hd/291-3p/294/295/302/372/373/520	2258	2264	m8	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: PCDHAC2