SZGR2

Summary ?

GeneID	19
Symbol	ABCA1
Synonyms	ABC-1\|ABC1\|CERP\|HDLDT1\|TGD
Description	ATP binding cassette subfamily A member 1
Reference	MIM:600046\|HGNC:HGNC:29\|Ensembl:ENSG00000165029\|HPRD:02501\|Vega:OTTHUMG00000020417
Gene type	protein-coding
Map location	9q31.1
Pascal p-value	0.243
Sherlock p-value	0.383
DEG p-value	DEG:Maycox_2009:CC_BA10_fold_change=1.14:CC_BA10_disease_P=0.0337:HBB_BA9_fold_change=1.28:HBB_BA9_disease_P=0.0220
Fetal beta	1.893
DMG	1 (# studies)

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DEG:Maycox_2009	Microarray to determine the expression of over 30000 mRNA transcripts in post-mortem tissue	We included 51 genes whose expression changes are common between two schizophrenia cohorts.
DMG:vanEijk_2014	Genome-wide DNA methylation analysis	This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250).	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
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0323

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg13160888	9	107526516	ABCA1	0.016	-7.686		DMG:vanEijk_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
DHX15	0.94	0.91
SF3B1	0.93	0.92
ZNF22	0.93	0.90
ELP2	0.93	0.91
CDKAL1	0.93	0.89
METAP2	0.92	0.92
C2orf67	0.92	0.91
DHX9	0.92	0.88
DDX5	0.92	0.91
UHRF2	0.92	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.27	-0.70	-0.81
MT-CO2	-0.69	-0.82
AF347015.31	-0.69	-0.82
IFI27	-0.67	-0.82
AF347015.33	-0.67	-0.78
HLA-F	-0.67	-0.72
AF347015.8	-0.67	-0.81
MT-CYB	-0.67	-0.80
AIFM3	-0.66	-0.72
PTH1R	-0.66	-0.73

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0005543	phospholipid binding	IC		16702602
GO:0005548	phospholipid transporter activity	IDA		16702602
GO:0005515	protein binding	IPI		16192269
GO:0005524	ATP binding	IEA		-
GO:0008509	anion transmembrane transporter activity	IEA		-
GO:0017127	cholesterol transporter activity	IDA		12084722
GO:0016887	ATPase activity	IEA		-
GO:0015485	cholesterol binding	IC		12084722
GO:0031267	small GTPase binding	IPI		16443932
GO:0030349	syntaxin-13 binding	IPI		15469992
GO:0034188	apolipoprotein A-I receptor activity	IDA		16443932
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0060155	platelet dense granule organization	IMP	serotonin (GO term level: 7)	15163665
GO:0002790	peptide secretion	IEA		-
GO:0007186	G-protein coupled receptor protein signaling pathway	IMP		16443932
GO:0006497	protein amino acid lipidation	IEA		-
GO:0008202	steroid metabolic process	IEA		-
GO:0008203	cholesterol metabolic process	IEA		-
GO:0006810	transport	IEA		-
GO:0007040	lysosome organization	IDA		15163665
GO:0006629	lipid metabolic process	IEA		-
GO:0006911	phagocytosis, engulfment	IEA		-
GO:0016197	endosome transport	IDA		14747463
GO:0033344	cholesterol efflux	IEA		-
GO:0032367	intracellular cholesterol transport	IMP		10431236
GO:0030819	positive regulation of cAMP biosynthetic process	IMP		14701824
GO:0032488	Cdc42 protein signal transduction	IMP		16443932
GO:0033700	phospholipid efflux	IDA		10431236 \|11162594
GO:0033700	phospholipid efflux	IMP		16702602
GO:0042632	cholesterol homeostasis	IDA		10431236
GO:0045332	phospholipid translocation	IEA		-
GO:0050702	interleukin-1 beta secretion	IMP		11855831
GO:0043691	reverse cholesterol transport	IEA		-
GO:0055091	phospholipid homeostasis	IMP		16702602
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005794	Golgi apparatus	IEA		-
GO:0005624	membrane fraction	IDA		10525055
GO:0005886	plasma membrane	IEA		-
GO:0005887	integral to plasma membrane	IEA		-
GO:0045335	phagocytic vesicle	IDA		15469992
GO:0045121	membrane raft	IDA		15469992

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ABC TRANSPORTERS	44	29	All SZGR 2.0 genes in this pathway
PID RXR VDR PATHWAY	26	24	All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION	104	72	All SZGR 2.0 genes in this pathway
REACTOME HDL MEDIATED LIPID TRANSPORT	15	12	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS	478	302	All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM	168	115	All SZGR 2.0 genes in this pathway
REACTOME LIPID DIGESTION MOBILIZATION AND TRANSPORT	46	37	All SZGR 2.0 genes in this pathway
REACTOME LIPOPROTEIN METABOLISM	28	24	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
SAMOLS TARGETS OF KHSV MIRNAS DN	62	35	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP	177	110	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL DN	60	39	All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP	306	188	All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP	158	103	All SZGR 2.0 genes in this pathway
HOEBEKE LYMPHOID STEM CELL UP	95	64	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY UP	78	41	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN	329	219	All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF UP	215	137	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP	97	60	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	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
XU HGF TARGETS REPRESSED BY AKT1 DN	95	58	All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS UP	49	35	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 UP	811	508	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP	283	177	All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE UP	90	62	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL AND BRAIN QTL TRANS	185	114	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
YU MYC TARGETS DN	55	38	All SZGR 2.0 genes in this pathway
GERY CEBP TARGETS	126	90	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF UP	12	10	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 3	101	64	All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF TROGLITAZONE UP	17	11	All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN	245	144	All SZGR 2.0 genes in this pathway
SARTIPY NORMAL AT INSULIN RESISTANCE DN	21	11	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP	280	183	All SZGR 2.0 genes in this pathway
HAN JNK SINGALING DN	39	27	All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP	253	147	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 6	189	112	All SZGR 2.0 genes in this pathway
BILD HRAS ONCOGENIC SIGNATURE	261	166	All SZGR 2.0 genes in this pathway
JEPSEN SMRT TARGETS	33	23	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP	578	341	All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS	425	261	All SZGR 2.0 genes in this pathway
MATZUK POST-IMPLANTATION AND POST-PARTUM	14	13	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN	546	362	All SZGR 2.0 genes in this pathway
BREDEMEYER RAG SIGNALING NOT VIA ATM DN	57	34	All SZGR 2.0 genes in this pathway
BEIER GLIOMA STEM CELL UP	39	17	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE DN	72	47	All SZGR 2.0 genes in this pathway
MCMURRAY TP53 HRAS COOPERATION RESPONSE DN	67	46	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 0	76	54	All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS EARLY UP	66	44	All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS LATE UP	104	67	All SZGR 2.0 genes in this pathway
HIRSCH CELLULAR TRANSFORMATION SIGNATURE UP	242	159	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
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 UP	344	215	All SZGR 2.0 genes in this pathway
GOBERT CORE OLIGODENDROCYTE DIFFERENTIATION	40	28	All SZGR 2.0 genes in this pathway
SCHMIDT POR TARGETS IN LIMB BUD DN	8	7	All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP	364	236	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM A	182	108	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-101	2687	2693	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124/506	185	191	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	185	191	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-128	2593	2599	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	2593	2599	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-130/301	3111	3117	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-142-5p	3223	3230	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-144	2687	2693	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-145	3115	3121	1A	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-145	3115	3121	1A	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-148/152	3112	3118	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-17-5p/20/93.mr/106/519.d	3079	3086	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
miR-183	1367	1373	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-19	3110	3116	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	3110	3116	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-199	3114	3120	1A	hsa-miR-199a	CCCAGUGUUCAGACUACCUGUUC
miR-199	3114	3120	1A	hsa-miR-199b	CCCAGUGUUUAGACUAUCUGUUC
miR-23	255	261	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	255	261	1A	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-26	227	233	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	227	233	1A	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-27	2593	2600	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	2593	2600	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-324-3p	181	187	m8	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-33	150	157	1A,m8	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
				hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
				hsa-miR-33	GUGCAUUGUAGUUGCAUUG
				hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
				hsa-miR-33	GUGCAUUGUAGUUGCAUUG
				hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-376c	3252	3258	m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-381	2808	2814	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	2808	2814	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-9	2833	2839	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-93.hd/291-3p/294/295/302/372/373/520	3078	3084	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
miR-96	499	505	m8	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: ABCA1