Gene Page: LHX1

Summary ?
GeneID3975
SymbolLHX1
SynonymsLIM-1|LIM1
DescriptionLIM homeobox 1
ReferenceMIM:601999|HGNC:HGNC:6593|Ensembl:ENSG00000273706|HPRD:09067|Vega:OTTHUMG00000188456
Gene typeprotein-coding
Map location17q12
Pascal p-value0.18
Fetal beta0.635
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CNV:YESCopy number variation studiesManual curation
CV:PGCnpGenome-wide Association StudyGWAS
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

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6687849chr1175904808LHX139750.18trans
rs2502827chr1176044216LHX139750.02trans
rs17572651chr1218943612LHX139751.642E-4trans
rs6734526chr25616370LHX139750.02trans
rs6753473chr226526418LHX139750.12trans
rs17028363chr241913161LHX139750.18trans
rs16829545chr2151977407LHX139756.31E-36trans
rs16841750chr2158288461LHX139752.792E-4trans
rs3845734chr2171125572LHX139750.02trans
rs7584986chr2184111432LHX139752.139E-11trans
rs6741060chr2217169088LHX139750trans
rs9810143chr35060209LHX139753.73E-4trans
rs6797307chr38601563LHX139750.03trans
rs7692715chr4125335209LHX139750.15trans
rs2183142chr4159232695LHX139750.03trans
rs170776chr4173276735LHX139750.02trans
rs1396222chr4173279496LHX139750.01trans
rs335993chr4173321789LHX139750.03trans
rs335980chr4173329784LHX139750.01trans
rs335982chr4173330945LHX139750.03trans
rs336016chr4173366576LHX139750.14trans
rs337984chr4173411662LHX139750.03trans
rs17762315chr576807576LHX139750.02trans
rs10491487chr580323367LHX139750.03trans
rs10474151chr584286402LHX139750.02trans
rs133604960LHX139750.11trans
rs13191953chr624151042LHX139750.04trans
rs12196880chr624313746LHX139750.04trans
rs10806988chr624341768LHX139750.11trans
rs16890367chr638078448LHX139750.01trans
rs12706918chr780266147LHX139750.16trans
rs7787830chr798797019LHX139750.18trans
rs6996695chr877540580LHX139750.01trans
rs3118341chr925185518LHX139750.02trans
rs9406868chr925223372LHX139750.03trans
rs11139334chr984209393LHX139750trans
rs2393316chr1059333070LHX139750.01trans
rs11061703chr121436977LHX139750.07trans
rs7337967chr1353519044LHX139750.1trans
rs16955618chr1529937543LHX139751.572E-45trans
rs2077735chr1558479024LHX139750.08trans
rs11873184chr181584081LHX139750.01trans
rs12458173chr1831430166LHX139750.07trans
rs17681878chr1834767223LHX139750.05trans
rs749043chr2046995700LHX139750.19trans
rs1041786chr2122617710LHX139751.039E-5trans
rs16986332chrX10958354LHX139750.13trans
rs16990575chrX32691327LHX139750.03trans

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
ARAP10.830.83
LTBP30.800.81
LZTS20.770.77
PLXNB10.760.75
RNPEPL10.760.75
DNM20.750.72
SLC38A100.750.72
TLN10.740.74
PLOD30.730.76
TMEM1040.730.71
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C18orf32-0.39-0.47
LY96-0.38-0.26
GLMN-0.37-0.39
CLEC2B-0.37-0.19
SYCP3-0.37-0.25
NOX1-0.37-0.29
AC087071.1-0.37-0.21
CAPZA2-0.36-0.40
TMEM126A-0.36-0.38
AL050337.1-0.36-0.25

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003700transcription factor activityNAS9212161 
GO:0003702RNA polymerase II transcription factor activityTAS9212161 
GO:0008270zinc ion bindingIEA-
GO:0046872metal ion bindingIEA-
GO:0043565sequence-specific DNA bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0021702cerebellar Purkinje cell differentiationIEAneuron, GABA, Brain (GO term level: 15)-
GO:0021549cerebellum developmentIEABrain (GO term level: 10)-
GO:0007399nervous system developmentTASneurite (GO term level: 5)9212161 
GO:0001706endoderm formationIEA-
GO:0006355regulation of transcription, DNA-dependentIEA-
GO:0009887organ morphogenesisTAS7700351 
GO:0009791post-embryonic developmentIEA-
GO:0030154cell differentiationIEA-
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
TANAKA METHYLATED IN ESOPHAGEAL CARCINOMA 10358All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN 5142All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN 200112All SZGR 2.0 genes in this pathway
SHEPARD BMYB TARGETS 7441All SZGR 2.0 genes in this pathway
SHEPARD CRUSH AND BURN MUTANT DN 185111All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 2 5034All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
LEIN CEREBELLUM MARKERS 8547All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425261All SZGR 2.0 genes in this pathway
MATZUK IMPLANTATION AND UTERINE 2215All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K27ME3 269159All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 DN 448282All SZGR 2.0 genes in this pathway