SZGR2

Summary ?

GeneID	3984
Symbol	LIMK1
Synonyms	LIMK\|LIMK-1
Description	LIM domain kinase 1
Reference	MIM:601329\|HGNC:HGNC:6613\|Ensembl:ENSG00000106683\|HPRD:03210\|Vega:OTTHUMG00000023448
Gene type	protein-coding
Map location	7q11.23
Pascal p-value	0.021
Sherlock p-value	0.432
DEG p-value	DEG:Zhao_2015:p=7.12e-06:q=0.0257
Fetal beta	-0.626

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CNV:YES	Copy number variation studies	Manual curation
CV:PGCnp	Genome-wide Association Study	GWAS
DEG:Zhao_2015	RNA Sequencing analysis	Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder.
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,schizophrenic,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 1.9241

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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		12361576 \|15220930 \|16837009
GO:0005524	ATP binding	IEA		-
GO:0004672	protein kinase activity	IEA		-
GO:0004674	protein serine/threonine kinase activity	TAS		8537403
GO:0004713	protein tyrosine kinase activity	IEA		-
GO:0016740	transferase activity	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
GO:0046982	protein heterodimerization activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0045773	positive regulation of axon extension	IEA	axon (GO term level: 15)	-
GO:0007399	nervous system development	TAS	neurite (GO term level: 5)	8689688
GO:0006468	protein amino acid phosphorylation	IEA		-
GO:0006468	protein amino acid phosphorylation	TAS		8537403
GO:0007266	Rho protein signal transduction	TAS		10436159
GO:0007165	signal transduction	TAS		10428028 \|10436159
GO:0030036	actin cytoskeleton organization	TAS		10428028
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	TAS		8537403
GO:0005925	focal adhesion	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BMPR2	BMPR-II \| BMPR3 \| BMR2 \| BRK-3 \| FLJ41585 \| FLJ76945 \| PPH1 \| T-ALK	bone morphogenetic protein receptor, type II (serine/threonine kinase)	-	HPRD,BioGRID	12963706
CDKN1C	BWCR \| BWS \| KIP2 \| WBS \| p57	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	-	HPRD,BioGRID	14530263
CFL1	CFL	cofilin 1 (non-muscle)	-	HPRD	9655398
CFL1	CFL	cofilin 1 (non-muscle)	Biochemical Activity	BioGRID	10436159 \|12963706
LATS1	WARTS \| wts	LATS, large tumor suppressor, homolog 1 (Drosophila)	LATS1 interacts with LIMK1.	BIND	15220930
LIMK1	LIMK	LIM domain kinase 1	-	HPRD,BioGRID	8980133
LIMK2	-	LIM domain kinase 2	-	HPRD,BioGRID	8980133
NRG1	ARIA \| GGF \| GGF2 \| HGL \| HRG \| HRG1 \| HRGA \| NDF \| SMDF	neuregulin 1	-	HPRD,BioGRID	9685409
PAK1	MGC130000 \| MGC130001 \| PAKalpha	p21 protein (Cdc42/Rac)-activated kinase 1	-	HPRD,BioGRID	10559936
PAK4	-	p21 protein (Cdc42/Rac)-activated kinase 4	PAK4 interacts with and phosphorylates LIMK1.	BIND	15660133
PAK4	-	p21 protein (Cdc42/Rac)-activated kinase 4	-	HPRD,BioGRID	11413130
PXN	FLJ16691	paxillin	-	HPRD	15023529
RNF12	MGC15161 \| NY-REN-43 \| RLIM	ring finger protein 12	-	HPRD	10431247
ROCK1	MGC131603 \| MGC43611 \| P160ROCK \| PRO0435	Rho-associated, coiled-coil containing protein kinase 1	-	HPRD	10436159
SSH1	FLJ38102 \| KIAA1298 \| SSH-1	slingshot homolog 1 (Drosophila)	SSH-1S interacts with LIMK1.	BIND	15660133
SSH1	FLJ38102 \| KIAA1298 \| SSH-1	slingshot homolog 1 (Drosophila)	SSH-1L interacts with and dephosphorylates LIMK1.	BIND	15660133
SSH2	KIAA1725 \| MGC78588 \| SSH-2	slingshot homolog 2 (Drosophila)	The shorter isoform, SSH-2S, interacts with LIMK1.	BIND	15660133
SSH3	FLJ10928 \| FLJ20515 \| SSH-3	slingshot homolog 3 (Drosophila)	SSH-3S interacts with LIMK1.	BIND	15660133
YWHAZ	KCIP-1 \| MGC111427 \| MGC126532 \| MGC138156	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	-	HPRD,BioGRID	12323073

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG AXON GUIDANCE	129	103	All SZGR 2.0 genes in this pathway
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS	97	71	All SZGR 2.0 genes in this pathway
KEGG REGULATION OF ACTIN CYTOSKELETON	216	144	All SZGR 2.0 genes in this pathway
BIOCARTA CCR3 PATHWAY	23	21	All SZGR 2.0 genes in this pathway
BIOCARTA RAC1 PATHWAY	23	16	All SZGR 2.0 genes in this pathway
BIOCARTA RHO PATHWAY	32	23	All SZGR 2.0 genes in this pathway
BIOCARTA MAL PATHWAY	19	17	All SZGR 2.0 genes in this pathway
SIG CHEMOTAXIS	45	37	All SZGR 2.0 genes in this pathway
SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	35	25	All SZGR 2.0 genes in this pathway
PID RHOA PATHWAY	45	33	All SZGR 2.0 genes in this pathway
PID CDC42 PATHWAY	70	51	All SZGR 2.0 genes in this pathway
PID CXCR4 PATHWAY	102	78	All SZGR 2.0 genes in this pathway
PID CASPASE PATHWAY	52	39	All SZGR 2.0 genes in this pathway
PID RAC1 PATHWAY	54	37	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE	251	188	All SZGR 2.0 genes in this pathway
REACTOME SEMA3A PAK DEPENDENT AXON REPULSION	15	14	All SZGR 2.0 genes in this pathway
REACTOME SEMA4D IN SEMAPHORIN SIGNALING	32	22	All SZGR 2.0 genes in this pathway
REACTOME SEMAPHORIN INTERACTIONS	68	53	All SZGR 2.0 genes in this pathway
REACTOME SEMA4D INDUCED CELL MIGRATION AND GROWTH CONE COLLAPSE	27	21	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	All SZGR 2.0 genes in this pathway
RODRIGUES NTN1 TARGETS DN	158	102	All SZGR 2.0 genes in this pathway
CASTELLANO NRAS TARGETS DN	14	14	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	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
NUYTTEN NIPP1 TARGETS UP	769	437	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 2	72	52	All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP	89	59	All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE UP	95	64	All SZGR 2.0 genes in this pathway
HILLION HMGA1 TARGETS	90	71	All SZGR 2.0 genes in this pathway
HILLION HMGA1B TARGETS	92	68	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS DN	120	81	All SZGR 2.0 genes in this pathway
BHATI G2M ARREST BY 2METHOXYESTRADIOL UP	125	68	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP	259	185	All SZGR 2.0 genes in this pathway
FIRESTEIN PROLIFERATION	175	125	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
SCHRAETS MLL TARGETS DN	33	24	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
IVANOVSKA MIR106B TARGETS	90	56	All SZGR 2.0 genes in this pathway
LINSLEY MIR16 TARGETS	206	127	All SZGR 2.0 genes in this pathway
WANG TNF TARGETS	24	17	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN	882	538	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP	107	72	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-128	1057	1063	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	1057	1063	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-138	801	808	1A,m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-143	824	831	1A,m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-17-5p/20/93.mr/106/519.d	1076	1082	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
				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-27	1057	1064	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	1057	1064	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-369-3p	932	938	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU

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: LIMK1