SZGR2

Summary ?

GeneID	5155
Symbol	PDGFB
Synonyms	IBGC5\|PDGF-2\|PDGF2\|SIS\|SSV\|c-sis
Description	platelet derived growth factor subunit B
Reference	MIM:190040\|HGNC:HGNC:8800\|Ensembl:ENSG00000100311\|HPRD:01815\|Vega:OTTHUMG00000151029
Gene type	protein-coding
Map location	22q13.1
Pascal p-value	0.153
Sherlock p-value	0.008
Fetal beta	0.208
eGene	Meta

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,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

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
DUSP7	0.77	0.74
DUSP8	0.76	0.75
SPEG	0.74	0.71
DENND1A	0.73	0.75
BAI2	0.73	0.73
C11orf81	0.72	0.76
KIAA0664	0.72	0.73
RHOBTB2	0.71	0.69
MGAT5B	0.71	0.71
PIP5K1C	0.71	0.70

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
SYCP3	-0.52	-0.54
RPS27L	-0.51	-0.52
C1orf54	-0.49	-0.49
GNG11	-0.48	-0.48
CLEC2B	-0.47	-0.44
DBI	-0.47	-0.48
C8orf59	-0.47	-0.48
MTCP1NB	-0.46	-0.48
S100A13	-0.45	-0.38
AF347015.21	-0.45	-0.43

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005161	platelet-derived growth factor receptor binding	NAS		1661670
GO:0005515	protein binding	IPI		17981115
GO:0008083	growth factor activity	IEA		-
GO:0048407	platelet-derived growth factor binding	IPI		7073684
GO:0042803	protein homodimerization activity	IDA		2836953
GO:0043498	cell surface binding	IDA		291037 \|2538439 \|2836953
GO:0046982	protein heterodimerization activity	IPI		7073684
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030031	cell projection biogenesis	IEA	axon (GO term level: 8)	-
GO:0001938	positive regulation of endothelial cell proliferation	IEA		-
GO:0010544	negative regulation of platelet activation	IDA		2538439
GO:0010512	negative regulation of phosphatidylinositol biosynthetic process	IDA		2538439
GO:0008283	cell proliferation	IEA		-
GO:0009611	response to wounding	NAS		1661670
GO:0048008	platelet-derived growth factor receptor signaling pathway	IDA		2439522 \|2536956 \|2836953
GO:0006929	substrate-bound cell migration	IEA		-
GO:0030036	actin cytoskeleton organization	IEA		-
GO:0014911	positive regulation of smooth muscle cell migration	IDA		9409235
GO:0050921	positive regulation of chemotaxis	IDA		9409235
GO:0030336	negative regulation of cell migration	IEA		-
GO:0043406	positive regulation of MAP kinase activity	IDA		9685360
GO:0045740	positive regulation of DNA replication	IDA		2439522 \|2836953
GO:0048146	positive regulation of fibroblast proliferation	IDA		2439522
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	IEA		-
GO:0043536	positive regulation of blood vessel endothelial cell migration	IDA		9685360
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	EXP		287022
GO:0005576	extracellular region	NAS		1661670
GO:0016020	membrane	IEA		-
GO:0009986	cell surface	IDA		291037 \|2836953 \|9685360
GO:0031089	platelet dense granule lumen	EXP		287022

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
A2M	CPAMD5 \| DKFZp779B086 \| FWP007 \| S863-7	alpha-2-macroglobulin	-	HPRD	10681572
ART1	ART2 \| CD296 \| MGC133217 \| RT6	ADP-ribosyltransferase 1	-	HPRD	11498506
COL1A1	OI4	collagen, type I, alpha 1	-	HPRD	10446987
HNRNPC	C1 \| C2 \| HNRNP \| HNRPC \| MGC104306 \| MGC105117 \| MGC117353 \| MGC131677 \| SNRPC	heterogeneous nuclear ribonucleoprotein C (C1/C2)	-	HPRD	10409733
HRAS	C-BAS/HAS \| C-H-RAS \| C-HA-RAS1 \| CTLO \| H-RASIDX \| HAMSV \| HRAS1 \| K-RAS \| N-RAS \| RASH1	v-Ha-ras Harvey rat sarcoma viral oncogene homolog	-	HPRD	10485711
HSPG2	PLC \| PRCAN \| SJA \| SJS \| SJS1	heparan sulfate proteoglycan 2	-	HPRD,BioGRID	9692901
LRP1	A2MR \| APOER \| APR \| CD91 \| FLJ16451 \| IGFBP3R \| LRP \| MGC88725 \| TGFBR5	low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)	-	HPRD,BioGRID	11854294
PDAP1	HASPP28 \| PAP \| PAP1	PDGFA associated protein 1	-	HPRD,BioGRID	8780057
PDGFB	FLJ12858 \| PDGF2 \| SIS \| SSV \| c-sis	platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)	-	HPRD,BioGRID	1396586
PDGFRA	CD140A \| MGC74795 \| PDGFR2 \| Rhe-PDGFRA	platelet-derived growth factor receptor, alpha polypeptide	-	HPRD,BioGRID	2544881
PDGFRB	CD140B \| JTK12 \| PDGF-R-beta \| PDGFR \| PDGFR1	platelet-derived growth factor receptor, beta polypeptide	-	HPRD	11903042
SPARC	ON	secreted protein, acidic, cysteine-rich (osteonectin)	Reconstituted Complex	BioGRID	1311092
THBS1	THBS \| TSP \| TSP1	thrombospondin 1	-	HPRD,BioGRID	9334164

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MAPK SIGNALING PATHWAY	267	205	All SZGR 2.0 genes in this pathway
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION	267	161	All SZGR 2.0 genes in this pathway
KEGG FOCAL ADHESION	201	138	All SZGR 2.0 genes in this pathway
KEGG GAP JUNCTION	90	68	All SZGR 2.0 genes in this pathway
KEGG REGULATION OF ACTIN CYTOSKELETON	216	144	All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER	328	259	All SZGR 2.0 genes in this pathway
KEGG RENAL CELL CARCINOMA	70	60	All SZGR 2.0 genes in this pathway
KEGG GLIOMA	65	56	All SZGR 2.0 genes in this pathway
KEGG PROSTATE CANCER	89	75	All SZGR 2.0 genes in this pathway
KEGG MELANOMA	71	57	All SZGR 2.0 genes in this pathway
PID PTP1B PATHWAY	52	40	All SZGR 2.0 genes in this pathway
PID INTEGRIN3 PATHWAY	43	25	All SZGR 2.0 genes in this pathway
PID S1P S1P3 PATHWAY	29	24	All SZGR 2.0 genes in this pathway
PID NECTIN PATHWAY	30	20	All SZGR 2.0 genes in this pathway
PID TCPTP PATHWAY	43	33	All SZGR 2.0 genes in this pathway
PID SHP2 PATHWAY	58	46	All SZGR 2.0 genes in this pathway
PID S1P S1P1 PATHWAY	21	18	All SZGR 2.0 genes in this pathway
PID PDGFRB PATHWAY	129	103	All SZGR 2.0 genes in this pathway
REACTOME RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2	89	56	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF	122	93	All SZGR 2.0 genes in this pathway
REACTOME DOWNSTREAM SIGNAL TRANSDUCTION	95	76	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION	208	138	All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING DN	46	29	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	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
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA UP	171	112	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A TARGETS DN	91	58	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A AND HIF2A TARGETS DN	104	72	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP	1142	669	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP	612	367	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS F UP	185	119	All SZGR 2.0 genes in this pathway
STREICHER LSM1 TARGETS UP	44	34	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 3	48	31	All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 22	13	9	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
TAGHAVI NEOPLASTIC TRANSFORMATION	12	10	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN	357	212	All SZGR 2.0 genes in this pathway
TENEDINI MEGAKARYOCYTE MARKERS	66	48	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
GALINDO IMMUNE RESPONSE TO ENTEROTOXIN	85	67	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP	89	61	All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI UP	412	249	All SZGR 2.0 genes in this pathway
MOREAUX B LYMPHOCYTE MATURATION BY TACI UP	92	58	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER HEREDITARY VS SPORADIC	50	32	All SZGR 2.0 genes in this pathway
HARRIS HYPOXIA	81	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
LEONARD HYPOXIA	47	35	All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER BRCA1 VS BRCA2	163	113	All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN	271	175	All SZGR 2.0 genes in this pathway
CLASPER LYMPHATIC VESSELS DURING METASTASIS UP	20	12	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
SAGIV CD24 TARGETS DN	46	26	All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS UP	112	71	All SZGR 2.0 genes in this pathway
LABBE TGFB1 TARGETS UP	102	64	All SZGR 2.0 genes in this pathway
LABBE TARGETS OF TGFB1 AND WNT3A UP	111	70	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP	259	185	All SZGR 2.0 genes in this pathway
WINTER HYPOXIA METAGENE	242	168	All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP	323	240	All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS UP	165	118	All SZGR 2.0 genes in this pathway
MIZUKAMI HYPOXIA DN	6	5	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN	238	145	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3	349	234	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
DANG MYC TARGETS DN	31	25	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3	341	243	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS UP	169	105	All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS DN	72	52	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR UP	199	143	All SZGR 2.0 genes in this pathway
NABA SECRETED FACTORS	344	197	All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED	753	411	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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
let-7/98	796	802	m8	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-29	132	138	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-496	1593	1599	1A	hsa-miR-496	AUUACAUGGCCAAUCUC

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: PDGFB