SZGR2

Summary ?

GeneID	27253
Symbol	PCDH17
Synonyms	PCDH68\|PCH68
Description	protocadherin 17
Reference	MIM:611760\|HGNC:HGNC:14267\|Ensembl:ENSG00000118946\|Vega:OTTHUMG00000016992
Gene type	protein-coding
Map location	13q21.1
Pascal p-value	0.378
Sherlock p-value	0.555
Fetal beta	0.513
DMG	1 (# studies)

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

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg26444528	13	58207859	PCDH17	2.969E-4	-0.529	0.039	DMG:Wockner_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.

No co-expressed genes in brain regions

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:0007155	cell adhesion	IEA		-
GO:0007156	homophilic cell adhesion	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP	255	177	All SZGR 2.0 genes in this pathway
ROY WOUND BLOOD VESSEL UP	50	30	All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP	306	188	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS GREY DN	74	44	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 6HR UP	85	54	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION UP	60	45	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA UP	98	64	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS 30MIN	29	21	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING	510	309	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN	216	143	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS UP	163	100	All SZGR 2.0 genes in this pathway
CADWELL ATG16L1 TARGETS UP	93	56	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE DN	204	114	All SZGR 2.0 genes in this pathway
WINNEPENNINCKX MELANOMA METASTASIS UP	162	86	All SZGR 2.0 genes in this pathway
HOELZEL NF1 TARGETS UP	139	93	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
KUMAR PATHOGEN LOAD BY MACROPHAGES	275	155	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	589	596	1A,m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-124/506	2016	2022	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	2016	2022	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-141/200a	2752	2758	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	2752	2758	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-15/16/195/424/497	105	111	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-182	2939	2945	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-203.1	545	551	m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-217	499	505	1A	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-217	499	505	1A	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-219	309	315	m8	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU
miR-224	388	394	1A	hsa-miR-224	CAAGUCACUAGUGGUUCCGUUUA
miR-24	1049	1055	1A	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-29	1940	1946	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
				hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-30-3p	1323	1329	m8	hsa-miR-30a-3p	CUUUCAGUCGGAUGUUUGCAGC
miR-30-3p	1323	1329	m8	hsa-miR-30e-3p	CUUUCAGUCGGAUGUUUACAGC
miR-30-5p	998	1005	1A,m8	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
				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-339	84	90	1A	hsa-miR-339	UCCCUGUCCUCCAGGAGCUCA
miR-376	1174	1180	m8	hsa-miR-376a	AUCAUAGAGGAAAAUCCACGU
miR-376	1174	1180	m8	hsa-miR-376b	AUCAUAGAGGAAAAUCCAUGUU
miR-378	922	928	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU
miR-378	922	928	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU
miR-378*	505	511	1A	hsa-miR-422b	CUGGACUUGGAGUCAGAAGGCC
miR-378*	505	511	1A	hsa-miR-422a	CUGGACUUAGGGUCAGAAGGCC
miR-379	1261	1268	1A,m8	hsa-miR-379^brain	UGGUAGACUAUGGAACGUA
miR-383	352	359	1A,m8	hsa-miR-383^brain	AGAUCAGAAGGUGAUUGUGGCU
miR-495	3606	3613	1A,m8	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-496	673	679	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-504	423	430	1A,m8	hsa-miR-504	AGACCCUGGUCUGCACUCUAU
miR-542-3p	2733	2739	m8	hsa-miR-542-3p	UGUGACAGAUUGAUAACUGAAA
miR-96	2939	2945	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC
miR-96	2939	2945	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: PCDH17