Summary ?
GeneID4010
SymbolLMX1B
SynonymsLMX1.2|NPS1
DescriptionLIM homeobox transcription factor 1 beta
ReferenceMIM:602575|HGNC:HGNC:6654|Ensembl:ENSG00000136944|HPRD:03986|Vega:OTTHUMG00000020692
Gene typeprotein-coding
Map location9q33.3
Pascal p-value0.063
Fetal beta-0.729
DMG2 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 2
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
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 3 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg026096929129389125LMX1B1.025E-4-0.4060.028DMG:Wockner_2014
cg146426969129386671LMX1B3.11E-11-0.0213.6E-7DMG:Jaffe_2016


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
EP4000.890.89
ZZEF10.880.87
SRCAP0.880.87
WDR810.880.88
KIAA04670.880.88
EP3000.880.88
UBR40.880.85
HERC20.870.86
ZFYVE260.870.87
HUWE10.870.86
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C1orf54-0.64-0.73
GNG11-0.61-0.69
AF347015.21-0.61-0.71
ACOT13-0.60-0.59
C5orf53-0.60-0.60
GMFG-0.60-0.67
VAMP5-0.59-0.61
SCRG1-0.59-0.62
AF347015.31-0.59-0.63
UQCRB-0.59-0.61

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityIDA10767331 
GO:0005515protein bindingIPI12792813 
GO:0008270zinc ion bindingIEA-
GO:0046872metal ion bindingIEA-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001764neuron migrationIEAneuron (GO term level: 8)-
GO:0030182neuron differentiationISSneuron (GO term level: 8)-
GO:0021954central nervous system neuron developmentIEAneuron (GO term level: 10)-
GO:0001701in utero embryonic developmentNAS12792813 
GO:0006355regulation of transcription, DNA-dependentIDA10767331 
GO:0009953dorsal/ventral pattern formationISS-
GO:0007275multicellular organismal developmentNAS9590287 |9618165 |9837817 
GO:0030199collagen fibril organizationIEA-
GO:0043010camera-type eye developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIDA10767331 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN 161105All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857456All SZGR 2.0 genes in this pathway