Gene Page: LIMS1

Summary ?
GeneID3987
SymbolLIMS1
SynonymsPINCH|PINCH-1|PINCH1
DescriptionLIM zinc finger domain containing 1
ReferenceMIM:602567|HGNC:HGNC:6616|Ensembl:ENSG00000169756|HPRD:03978|Vega:OTTHUMG00000130983
Gene typeprotein-coding
Map location2q12.3
Pascal p-value0.086
Fetal beta-0.453
DMG1 (# studies)
eGeneCerebellar Hemisphere
Cerebellum
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 2
GSMA_IGenome scan meta-analysisPsr: 0.0004 
GSMA_IIAGenome scan meta-analysis (All samples)Psr: 0.00755 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg213857482109203905LIMS13.52E-50.3290.02DMG:Wockner_2014
cg146639732109252890LIMS15.099E-4-0.4320.047DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
snp_a-20909420LIMS139870.14trans
rs17014165chr1206856485LIMS139870.14trans
rs7595584chr2175652187LIMS139870.01trans
rs1831517chr92513405LIMS139870.12trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
ARFGEF20.920.92
DPP80.910.92
ZFP1060.910.91
DMXL10.910.91
ADAM220.900.92
VPS13D0.900.91
ROCK20.900.89
EEA10.890.88
CPD0.890.86
ATG2B0.890.89
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AC006276.2-0.42-0.43
C1orf61-0.41-0.58
NUDT8-0.40-0.45
RPL35-0.40-0.47
DBI-0.39-0.49
PFDN5-0.39-0.40
RHOC-0.38-0.48
ST20-0.38-0.43
RPL36-0.38-0.43
TBC1D10A-0.38-0.31

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0008270zinc ion bindingIEA-
GO:0046872metal ion bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007569cell agingTAS7517666 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005886plasma membraneIEA-
GO:0030054cell junctionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID ILK PATHWAY 4532All SZGR 2.0 genes in this pathway
REACTOME CELL CELL COMMUNICATION 12077All SZGR 2.0 genes in this pathway
REACTOME CELL EXTRACELLULAR MATRIX INTERACTIONS 1410All SZGR 2.0 genes in this pathway
REACTOME CELL JUNCTION ORGANIZATION 7843All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP 285181All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP 408247All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP 276165All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP 13983All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 UP 341197All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION MONOCYTE UP 204140All SZGR 2.0 genes in this pathway
PASTURAL RIZ1 TARGETS UP 115All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 DN 229142All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
SILIGAN TARGETS OF EWS FLI1 FUSION UP 1512All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215 893528All SZGR 2.0 genes in this pathway
SAKAI TUMOR INFILTRATING MONOCYTES UP 2719All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE UP 5335All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309206All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP 207145All SZGR 2.0 genes in this pathway
ABBUD LIF SIGNALING 1 DN 2617All SZGR 2.0 genes in this pathway
IGLESIAS E2F TARGETS UP 151103All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION 405264All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS MATURE CELL 293160All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP 198132All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 11 5740All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280183All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS 217138All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY 4NQO OR GAMMA RADIATION 1513All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN 195135All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP 12589All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP 673430All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS UP 602364All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS UP 601369All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR DN 185116All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518299All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN 253192All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D 658397All SZGR 2.0 genes in this pathway