SZGR2

Summary ?

GeneID	18
Symbol	ABAT
Synonyms	GABA-AT\|GABAT\|NPD009
Description	4-aminobutyrate aminotransferase
Reference	MIM:137150\|HGNC:HGNC:23\|Ensembl:ENSG00000183044\|HPRD:00661\|Vega:OTTHUMG00000048201
Gene type	protein-coding
Map location	16p13.2
Pascal p-value	0.211
Sherlock p-value	0.796
Fetal beta	-0.815
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).	3
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,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 5

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg01881182	16	8806531	ABAT	2.161E-4	0.523	0.036	DMG:Wockner_2014
cg08834902	16	8806690	ABAT	2.828E-4	0.439	0.039	DMG:Wockner_2014
cg08241330	16	8806663	ABAT	3.06E-4	0.532	0.04	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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AP3D1	0.95	0.95
MKL1	0.92	0.93
MEGF8	0.92	0.93
SIN3B	0.92	0.92
AP2A2	0.92	0.91
UBE2O	0.91	0.91
CACNA1B	0.91	0.93
RUSC2	0.91	0.93
ITGA3	0.90	0.92
USP35	0.90	0.91

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.75	-0.74
MT-CO2	-0.74	-0.74
AF347015.21	-0.74	-0.78
AF347015.33	-0.72	-0.69
MT-CYB	-0.71	-0.69
AC021016.1	-0.70	-0.72
HIGD1B	-0.70	-0.70
AF347015.27	-0.70	-0.71
AF347015.8	-0.70	-0.71
FXYD1	-0.69	-0.67

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003867	4-aminobutyrate transaminase activity	IDA	GABA (GO term level: 6)	15528998
GO:0047298	(S)-3-amino-2-methylpropionate transaminase activity	IEA	glutamate (GO term level: 6)	-
GO:0016740	transferase activity	IEA		-
GO:0042803	protein homodimerization activity	IPI		15528998
GO:0030170	pyridoxal phosphate binding	IDA		15650327
GO:0032145	succinate-semialdehyde dehydrogenase binding	ISS		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0009450	gamma-aminobutyric acid catabolic process	NAS	GABA, Neurotransmitter (GO term level: 11)	15528998
GO:0042135	neurotransmitter catabolic process	NAS	neuron, axon, Synap, Neurotransmitter (GO term level: 9)	15528998
GO:0007610	behavior	NAS		11918424
GO:0048148	behavioral response to cocaine	ISS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0032144	4-aminobutyrate transaminase complex	IDA	GABA (GO term level: 6)	15528998
GO:0005739	mitochondrion	ISS		-
GO:0005759	mitochondrial matrix	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	32	26	All SZGR 2.0 genes in this pathway
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION	44	26	All SZGR 2.0 genes in this pathway
KEGG BETA ALANINE METABOLISM	22	16	All SZGR 2.0 genes in this pathway
KEGG PROPANOATE METABOLISM	33	22	All SZGR 2.0 genes in this pathway
KEGG BUTANOATE METABOLISM	34	20	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE	34	30	All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION	17	16	All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE DN	84	53	All SZGR 2.0 genes in this pathway
DAVICIONI PAX FOXO1 SIGNATURE IN ARMS UP	59	38	All SZGR 2.0 genes in this pathway
FRASOR TAMOXIFEN RESPONSE DN	11	6	All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS UP	332	228	All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP	255	177	All SZGR 2.0 genes in this pathway
DAVICIONI RHABDOMYOSARCOMA PAX FOXO1 FUSION UP	64	37	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP	450	256	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP	112	72	All SZGR 2.0 genes in this pathway
RODRIGUES DCC TARGETS DN	121	84	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
ODONNELL TARGETS OF MYC AND TFRC UP	83	50	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	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
KIM WT1 TARGETS 8HR UP	164	122	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP	162	116	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	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
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
EBAUER TARGETS OF PAX3 FOXO1 FUSION DN	48	31	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL	330	215	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
LIEN BREAST CARCINOMA METAPLASTIC VS DUCTAL DN	114	58	All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 UP	36	22	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4	261	153	All SZGR 2.0 genes in this pathway
PETRETTO CARDIAC HYPERTROPHY	34	26	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER CIPROFIBRATE DN	66	43	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC TGFA DN	65	44	All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO UP	205	126	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP	240	152	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR UP	178	111	All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN	318	220	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR UP	148	96	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4	307	185	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP	282	183	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
MASSARWEH TAMOXIFEN RESISTANCE DN	258	160	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP	97	61	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP	172	109	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002	429	260	All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA	447	277	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN	366	257	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER ESR1 UP	167	99	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP	293	203	All SZGR 2.0 genes in this pathway
MCMURRAY TP53 HRAS COOPERATION RESPONSE DN	67	46	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
CHIANG LIVER CANCER SUBCLASS PROLIFERATION DN	179	97	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 9 11 TRANSLOCATION	130	87	All SZGR 2.0 genes in this pathway
STEIN ESR1 TARGETS	85	55	All SZGR 2.0 genes in this pathway
STEIN ESTROGEN RESPONSE NOT VIA ESRRA	18	12	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA DN	267	160	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR UP	55	41	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 UP	397	206	All SZGR 2.0 genes in this pathway
OHGUCHI LIVER HNF4A TARGETS DN	149	85	All SZGR 2.0 genes in this pathway
GOBERT CORE OLIGODENDROCYTE DIFFERENTIATION	40	28	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	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-369-3p	2828	2834	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	2828	2835	1A,m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-409-5p	2870	2876	1A	hsa-miR-409-5p	AGGUUACCCGAGCAACUUUGCA
miR-96	3015	3021	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: ABAT