SZGR2

Summary ?

GeneID	4739
Symbol	NEDD9
Synonyms	CAS-L\|CAS2\|CASL\|CASS2\|HEF1
Description	neural precursor cell expressed, developmentally down-regulated 9
Reference	MIM:602265\|HGNC:HGNC:7733\|Ensembl:ENSG00000111859\|HPRD:11888\|Vega:OTTHUMG00000014255
Gene type	protein-coding
Map location	6p24.2
Pascal p-value	0.183
Fetal beta	2.44
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).	2
GSMA_I	Genome scan meta-analysis	Psr: 0.0159
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
cg15972264	6	11279680	NEDD9	4.64E-6	0.999	0.01	DMG:Wockner_2014
cg16955407	6	11279656	NEDD9	6.31E-5	0.415	0.023	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:0005515	protein binding	IPI		11827972
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001558	regulation of cell growth	IEA		-
GO:0007155	cell adhesion	NAS		9584194
GO:0007229	integrin-mediated signaling pathway	NAS		11827972
GO:0007010	cytoskeleton organization	NAS		11827972
GO:0007165	signal transduction	TAS		8668148
GO:0007049	cell cycle	IEA		-
GO:0007067	mitosis	IEA		-
GO:0051017	actin filament bundle formation	NAS		11827972
GO:0051301	cell division	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0042995	cell projection	IEA	axon (GO term level: 4)	-
GO:0005794	Golgi apparatus	IEA		-
GO:0005819	spindle	TAS		9584194
GO:0005856	cytoskeleton	IEA		-
GO:0005634	nucleus	TAS		8668148
GO:0005737	cytoplasm	TAS		9584194
GO:0030054	cell junction	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ABL1	ABL \| JTK7 \| bcr/abl \| c-ABL \| p150 \| v-abl	c-abl oncogene 1, receptor tyrosine kinase	-	HPRD,BioGRID	8668148 \|8879209
BCAR1	CAS \| CAS1 \| CASS1 \| CRKAS \| P130Cas	breast cancer anti-estrogen resistance 1	-	HPRD	8668148 \|9366405
BCAR1	CAS \| CAS1 \| CASS1 \| CRKAS \| P130Cas	breast cancer anti-estrogen resistance 1	Affinity Capture-Western	BioGRID	10502414
BCAR3	KIAA0554 \| NSP2 \| SH2D3B	breast cancer anti-estrogen resistance 3	-	HPRD,BioGRID	12517963
CDH1	Arc-1 \| CD324 \| CDHE \| ECAD \| LCAM \| UVO	cadherin 1, type 1, E-cadherin (epithelial)	-	HPRD,BioGRID	15144564
CHAT	CMS1A \| CMS1A2	choline acetyltransferase	-	HPRD	10692442
CRK	CRKII	v-crk sarcoma virus CT10 oncogene homolog (avian)	-	HPRD	8879209 \|9366405 \|9497377
CRK	CRKII	v-crk sarcoma virus CT10 oncogene homolog (avian)	Affinity Capture-Western Reconstituted Complex	BioGRID	8879209 \|9497377
CRKL	-	v-crk sarcoma virus CT10 oncogene homolog (avian)-like	-	HPRD	9020138 \|9405482 \|9498705
CRKL	-	v-crk sarcoma virus CT10 oncogene homolog (avian)-like	Affinity Capture-Western Reconstituted Complex	BioGRID	9020138 \|9162067 \|9498705 \|9820532
DIMT1L	DIMT1 \| HSA9761	DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)	-	HPRD	9584194
ELSPBP1	E12 \| HE12	epididymal sperm binding protein 1	-	HPRD,BioGRID	10502414
FYN	MGC45350 \| SLK \| SYN	FYN oncogene related to SRC, FGR, YES	-	HPRD,BioGRID	9360983
FZR1	CDC20C \| CDH1 \| FZR \| FZR2 \| HCDH \| HCDH1 \| KIAA1242	fizzy/cell division cycle 20 related 1 (Drosophila)	CDH1 interacts with HEF1.	BIND	15144564
ID2	GIG8 \| ID2A \| ID2H \| MGC26389 \| bHLHb26	inhibitor of DNA binding 2, dominant negative helix-loop-helix protein	-	HPRD,BioGRID	10502414
ITCH	AIF4 \| AIP4 \| NAPP1 \| dJ468O1.1	itchy E3 ubiquitin protein ligase homolog (mouse)	-	HPRD,BioGRID	15051726
LCK	YT16 \| p56lck \| pp58lck	lymphocyte-specific protein tyrosine kinase	-	HPRD,BioGRID	8879209
LYN	FLJ26625 \| JTK8	v-yes-1 Yamaguchi sarcoma viral related oncogene homolog	-	HPRD,BioGRID	9020138
MICAL1	DKFZp434B1517 \| FLJ11937 \| FLJ21739 \| MICAL \| MICAL-1 \| NICAL	microtubule associated monoxygenase, calponin and LIM domain containing 1	-	HPRD,BioGRID	11827972
NCK1	MGC12668 \| NCK \| NCKalpha	NCK adaptor protein 1	-	HPRD,BioGRID	8879209
NCK1	MGC12668 \| NCK \| NCKalpha	NCK adaptor protein 1	-	HPRD	10808124
NEDD9	CAS-L \| CAS2 \| CASL \| CASS2 \| HEF1 \| dJ49G10.2 \| dJ761I2.1	neural precursor cell expressed, developmentally down-regulated 9	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	8668148 \|10502414
PTK2	FADK \| FAK \| FAK1 \| pp125FAK	PTK2 protein tyrosine kinase 2	-	HPRD,BioGRID	8668148 \|8879209 \|10455189
PTK2B	CADTK \| CAKB \| FADK2 \| FAK2 \| FRNK \| PKB \| PTK \| PYK2 \| RAFTK	PTK2B protein tyrosine kinase 2 beta	-	HPRD,BioGRID	9020138
PTPN11	BPTP3 \| CFC \| MGC14433 \| NS1 \| PTP-1D \| PTP2C \| SH-PTP2 \| SH-PTP3 \| SHP2	protein tyrosine phosphatase, non-receptor type 11	-	HPRD	8879209
PTPN12	PTP-PEST \| PTPG1	protein tyrosine phosphatase, non-receptor type 12	-	HPRD,BioGRID	9748319
PXN	FLJ16691	paxillin	-	HPRD,BioGRID	10455189
RAPGEF1	C3G \| DKFZp781P1719 \| GRF2	Rap guanine nucleotide exchange factor (GEF) 1	Affinity Capture-Western	BioGRID	9498705
SH2D3C	CHAT \| FLJ39664 \| NSP3 \| PRO34088	SH2 domain containing 3C	Affinity Capture-Western	BioGRID	10692442
SMAD1	BSP1 \| JV4-1 \| JV41 \| MADH1 \| MADR1	SMAD family member 1	-	HPRD,BioGRID	11118211
SMAD2	JV18 \| JV18-1 \| MADH2 \| MADR2 \| MGC22139 \| MGC34440 \| hMAD-2 \| hSMAD2	SMAD family member 2	-	HPRD,BioGRID	11118211
SMAD3	DKFZp586N0721 \| DKFZp686J10186 \| HSPC193 \| HsT17436 \| JV15-2 \| MADH3 \| MGC60396	SMAD family member 3	Smad3 interacts with HEF1.	BIND	15144564
SMAD3	DKFZp586N0721 \| DKFZp686J10186 \| HSPC193 \| HsT17436 \| JV15-2 \| MADH3 \| MGC60396	SMAD family member 3	-	HPRD,BioGRID	11118211 \|15051726 \|15144564
TCF3	E2A \| ITF1 \| MGC129647 \| MGC129648 \| bHLHb21	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)	-	HPRD	10502414
TRIP6	MGC10556 \| MGC10558 \| MGC29959 \| MGC3837 \| MGC4423 \| OIP1 \| ZRP-1	thyroid hormone receptor interactor 6	-	HPRD,BioGRID	11782456
ZYX	ESP-2 \| HED-2	zyxin	-	HPRD,BioGRID	11782456

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
ONKEN UVEAL MELANOMA DN	526	357	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC UP	185	126	All SZGR 2.0 genes in this pathway
SCIBETTA KDM5B TARGETS DN	81	55	All SZGR 2.0 genes in this pathway
NAGASHIMA NRG1 SIGNALING UP	176	123	All SZGR 2.0 genes in this pathway
NAGASHIMA EGF SIGNALING UP	58	40	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR DN	209	122	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 DN	378	231	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP	329	196	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
GAUSSMANN MLL AF4 FUSION TARGETS C UP	170	114	All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER DN	37	22	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
MAHADEVAN GIST MORPHOLOGICAL SWITCH	15	11	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1	229	137	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 DN	156	106	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 AND HIF1A UP	142	104	All SZGR 2.0 genes in this pathway
SCIAN CELL CYCLE TARGETS OF TP53 AND TP73 UP	9	7	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
WU CELL MIGRATION	184	114	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE DN	165	104	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA	164	118	All SZGR 2.0 genes in this pathway
AMIT SERUM RESPONSE 120 MCF10A	65	44	All SZGR 2.0 genes in this pathway
JI METASTASIS REPRESSED BY STK11	27	17	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC TGFA UP	61	40	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 9	92	59	All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A UP	81	52	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED	1022	619	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
JI CARCINOGENESIS BY KRAS AND STK11 DN	17	12	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP	317	208	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN	216	143	All SZGR 2.0 genes in this pathway
CHEN HOXA5 TARGETS 9HR UP	223	132	All SZGR 2.0 genes in this pathway
JIANG TIP30 TARGETS UP	46	28	All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM DN	40	31	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 DN	315	201	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF DN	235	144	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP	408	276	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4	196	124	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN	442	275	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
UZONYI RESPONSE TO LEUKOTRIENE AND THROMBIN	37	26	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
PANGAS TUMOR SUPPRESSION BY SMAD1 AND SMAD5 UP	134	85	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
ISSAEVA MLL2 TARGETS	62	35	All SZGR 2.0 genes in this pathway
DURAND STROMA NS UP	162	103	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	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-103/107	360	367	1A,m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	360	367	1A,m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-125/351	153	159	1A	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	153	159	1A	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-145	47	54	1A,m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-18	338	345	1A,m8	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	338	345	1A,m8	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-24	436	442	m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG

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: NEDD9