SZGR2

Summary ?

GeneID	8878
Symbol	SQSTM1
Synonyms	A170\|FTDALS3\|OSIL\|PDB3\|ZIP3\|p60\|p62\|p62B
Description	sequestosome 1
Reference	MIM:601530\|HGNC:HGNC:11280\|Ensembl:ENSG00000161011\|HPRD:03319\|Vega:OTTHUMG00000150643
Gene type	protein-coding
Map location	5q35
Pascal p-value	0.086
Sherlock p-value	0.928
Fetal beta	-1.559
DMG	1 (# studies)
eGene	Myers' cis & trans Meta

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	1
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.0276
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0685

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg24421668	5	179244452	SQSTM1	1.72E-8	-0.023	6.24E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs2450484	chr5	179259841	SQSTM1	8878	0.02	cis
rs10277	chr5	179264730	SQSTM1	8878	0	cis
rs1065154	chr5	179264914	SQSTM1	8878	0.04	cis
rs748197	chr5	179273819	SQSTM1	8878	0.19	cis
rs11249661	chr5	179277873	SQSTM1	8878	0.09	cis
rs16827324	chr1	40927958	SQSTM1	8878	0	trans
rs10277	chr5	179264730	SQSTM1	8878	0.2	trans
rs1889151	chr9	137160636	SQSTM1	8878	0.12	trans
rs7917302	chr10	15474549	SQSTM1	8878	0.03	trans
rs10842557		0	SQSTM1	8878	0.04	trans
rs11161196	chr15	25859201	SQSTM1	8878	0.13	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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
PINK1	0.89	0.89
PRRT3	0.88	0.90
CEND1	0.87	0.90
TOM1	0.87	0.87
DLGAP3	0.87	0.91
TUBG2	0.87	0.91
LENG3	0.86	0.86
PPAPDC3	0.86	0.86
ZFYVE28	0.85	0.89
VGF	0.85	0.91

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TUBB2B	-0.57	-0.56
RBMX2	-0.57	-0.64
CARHSP1	-0.56	-0.60
TIGD1	-0.56	-0.47
KIAA1949	-0.56	-0.45
ZNF300	-0.56	-0.39
C9orf46	-0.56	-0.62
IGF2BP3	-0.56	-0.52
TRAF4	-0.56	-0.60
EXOSC8	-0.56	-0.57

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		14676191
GO:0005515	protein binding	ISS		-
GO:0008270	zinc ion binding	IEA		-
GO:0042169	SH2 domain binding	IDA		8650207
GO:0042169	SH2 domain binding	ISS		-
GO:0030971	receptor tyrosine kinase binding	TAS		8650207
GO:0019901	protein kinase binding	IDA		8650207
GO:0019901	protein kinase binding	ISS		-
GO:0043130	ubiquitin binding	IDA		12857745
GO:0043130	ubiquitin binding	ISS		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006511	ubiquitin-dependent protein catabolic process	TAS		8702753
GO:0007242	intracellular signaling cascade	TAS		8650207
GO:0006950	response to stress	TAS		12857745
GO:0008104	protein localization	TAS		8650207
GO:0006955	immune response	IEA		-
GO:0006915	apoptosis	IEA		-
GO:0016197	endosome transport	TAS		12857745
GO:0030154	cell differentiation	IEA		-
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	IMP		12857745
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	ISS		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	TAS		12857745
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	NAS		-
GO:0005829	cytosol	TAS		8650207
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	IEA		-
GO:0005770	late endosome	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
C14orf139	FLJ21276	chromosome 14 open reading frame 139	Two-hybrid	BioGRID	16169070
ERCC2	COFS2 \| EM9 \| MGC102762 \| MGC126218 \| MGC126219 \| TTD \| XPD	excision repair cross-complementing rodent repair deficiency, complementation group 2	-	HPRD	8652557
GABARAPL1	APG8-LIKE \| APG8L \| ATG8 \| ATG8L \| GEC1	GABA(A) receptor-associated protein like 1	Two-hybrid	BioGRID	16189514
GABARAPL2	ATG8 \| GATE-16 \| GATE16 \| GEF-2 \| GEF2	GABA(A) receptor-associated protein-like 2	Two-hybrid	BioGRID	16189514
IRAK1	IRAK \| pelle	interleukin-1 receptor-associated kinase 1	-	HPRD	12034707
IRAK1	IRAK \| pelle	interleukin-1 receptor-associated kinase 1	Affinity Capture-Western	BioGRID	10747026
LCK	YT16 \| p56lck \| pp58lck	lymphocyte-specific protein tyrosine kinase	-	HPRD,BioGRID	8650207
MAP1LC3B	LC3B \| MAP1A/1BLC3	microtubule-associated protein 1 light chain 3 beta	Two-hybrid	BioGRID	16169070
MAP2K5	HsT17454 \| MAPKK5 \| MEK5 \| PRKMK5	mitogen-activated protein kinase kinase 5	MEK5 interacts with p62. This interaction was modelled on a demonstrated interaction between mouse MEK5 and human p62.	BIND	12813044
NR2F2	ARP1 \| COUP-TFII \| COUPTFB \| MGC117452 \| SVP40 \| TFCOUP2	nuclear receptor subfamily 2, group F, member 2	-	HPRD	8910285
NTRK1	DKFZp781I14186 \| MTC \| TRK \| TRK1 \| TRKA \| p140-TrkA	neurotrophic tyrosine kinase, receptor, type 1	Affinity Capture-Western	BioGRID	11244088 \|12471037
NTRK2	GP145-TrkB \| TRKB	neurotrophic tyrosine kinase, receptor, type 2	-	HPRD,BioGRID	12471037
NTRK3	TRKC \| gp145(trkC)	neurotrophic tyrosine kinase, receptor, type 3	-	HPRD,BioGRID	12471037
PRKCI	DXS1179E \| MGC26534 \| PKCI \| nPKC-iota	protein kinase C, iota	-	HPRD,BioGRID	9566925
PRKCI	DXS1179E \| MGC26534 \| PKCI \| nPKC-iota	protein kinase C, iota	lamdaPKC interacts with p62. This interaction was modelled on a demonstrated interaction between mouse lamdaPKC and human p62.	BIND	12813044
PRKCZ	PKC-ZETA \| PKC2	protein kinase C, zeta	zetaPKC interacts with p62. This interaction was modelled on a demonstrated interaction between rat zetaPKC and human p62.	BIND	12813044
PRKCZ	PKC-ZETA \| PKC2	protein kinase C, zeta	-	HPRD	9566925 \|10356400
PRKCZ	PKC-ZETA \| PKC2	protein kinase C, zeta	Affinity Capture-Western	BioGRID	10747026
PTPRJ	CD148 \| DEP1 \| HPTPeta \| R-PTP-ETA \| SCC1	protein tyrosine phosphatase, receptor type, J	-	HPRD	9115287
RAD23A	HHR23A \| MGC111083	RAD23 homolog A (S. cerevisiae)	Affinity Capture-Western Two-hybrid	BioGRID	16189514
RIPK1	FLJ39204 \| RIP \| RIP1	receptor (TNFRSF)-interacting serine-threonine kinase 1	-	HPRD,BioGRID	10356400
SNCA	MGC110988 \| NACP \| PARK1 \| PARK4 \| PD1	synuclein, alpha (non A4 component of amyloid precursor)	-	HPRD	11447312
SQSTM1	A170 \| OSIL \| PDB3 \| ZIP3 \| p60 \| p62 \| p62B	sequestosome 1	p62 forms a dimer.	BIND	12813044
SQSTM1	A170 \| OSIL \| PDB3 \| ZIP3 \| p60 \| p62 \| p62B	sequestosome 1	Two-hybrid	BioGRID	16169070
TRAF6	MGC:3310 \| RNF85	TNF receptor-associated factor 6	-	HPRD,BioGRID	10747026 \|11244088
TTN	CMD1G \| CMH9 \| CMPD4 \| CONNECTIN \| DKFZp451N061 \| EOMFC \| FLJ26020 \| FLJ26409 \| FLJ32040 \| FLJ34413 \| FLJ39564 \| FLJ43066 \| HMERF \| LGMD2J \| TMD	titin	Titin interacts with p62. This interaction was modelled on a demonstrated interaction between human Titin and rat p62.	BIND	15802564

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID IL1 PATHWAY	34	28	All SZGR 2.0 genes in this pathway
PID TNF PATHWAY	46	33	All SZGR 2.0 genes in this pathway
PID P75 NTR PATHWAY	69	51	All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY	62	48	All SZGR 2.0 genes in this pathway
REACTOME SIGNALLING BY NGF	217	167	All SZGR 2.0 genes in this pathway
REACTOME P75NTR RECRUITS SIGNALLING COMPLEXES	12	8	All SZGR 2.0 genes in this pathway
REACTOME P75NTR SIGNALS VIA NFKB	14	10	All SZGR 2.0 genes in this pathway
REACTOME NRIF SIGNALS CELL DEATH FROM THE NUCLEUS	15	10	All SZGR 2.0 genes in this pathway
REACTOME NFKB IS ACTIVATED AND SIGNALS SURVIVAL	11	8	All SZGR 2.0 genes in this pathway
REACTOME CELL DEATH SIGNALLING VIA NRAGE NRIF AND NADE	60	43	All SZGR 2.0 genes in this pathway
REACTOME P75 NTR RECEPTOR MEDIATED SIGNALLING	81	61	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY ILS	107	86	All SZGR 2.0 genes in this pathway
REACTOME IL1 SIGNALING	39	30	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM	270	204	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP	473	314	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN	244	147	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS TURQUOISE UP	79	50	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP	457	269	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
HUMMEL BURKITTS LYMPHOMA DN	15	10	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN	214	133	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA REVERSIBLY UP	8	6	All SZGR 2.0 genes in this pathway
MARKEY RB1 CHRONIC LOF DN	118	78	All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN UP	239	157	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION UP	126	78	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 2	127	92	All SZGR 2.0 genes in this pathway
HERNANDEZ MITOTIC ARREST BY DOCETAXEL 2 UP	64	45	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP	309	199	All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE LATE UP	57	41	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP	414	287	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE DN	98	59	All SZGR 2.0 genes in this pathway
NAKAYAMA FRA2 TARGETS	43	27	All SZGR 2.0 genes in this pathway
SUH COEXPRESSED WITH ID1 AND ID2 UP	19	14	All SZGR 2.0 genes in this pathway
COLIN PILOCYTIC ASTROCYTOMA VS GLIOBLASTOMA DN	28	21	All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX	230	156	All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS	775	494	All SZGR 2.0 genes in this pathway
ZHANG RESPONSE TO IKK INHIBITOR AND TNF UP	223	140	All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK	169	111	All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO UP	205	126	All SZGR 2.0 genes in this pathway
GOLUB ALL VS AML DN	24	14	All SZGR 2.0 genes in this pathway
GALINDO IMMUNE RESPONSE TO ENTEROTOXIN	85	67	All SZGR 2.0 genes in this pathway
ASTIER INTEGRIN SIGNALING	59	44	All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS UP	88	64	All SZGR 2.0 genes in this pathway
BRUNO HEMATOPOIESIS	66	48	All SZGR 2.0 genes in this pathway
CHIBA RESPONSE TO TSA	50	31	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C0	107	72	All SZGR 2.0 genes in this pathway
GERHOLD ADIPOGENESIS UP	49	40	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS DN	314	188	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP	783	442	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
WONG PROTEASOME GENE MODULE	49	35	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K9ME3 DN	120	71	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER ERBB2 UP	147	83	All SZGR 2.0 genes in this pathway
PODAR RESPONSE TO ADAPHOSTIN UP	147	98	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB UP	245	159	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP	338	225	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP	418	282	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
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
HSIAO HOUSEKEEPING GENES	389	245	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
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION	456	287	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS UP	217	131	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS GROUP2	60	38	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B	549	316	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
KOHOUTEK CCNT1 TARGETS	50	26	All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS UP	149	96	All SZGR 2.0 genes in this pathway
DELACROIX RARG BOUND MEF	367	231	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 PARTIAL	160	106	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-17-5p/20/93.mr/106/519.d	649	656	1A,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

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: SQSTM1