Gene Page:LHX6

Summary?
GeneID 26468
Symbol LHX6
Synonyms LHX6.1
Description LIM homeobox 6
Reference MIM:608215|HGNC:HGNC:21735|Ensembl:ENSG00000106852|HPRD:10498|Vega:OTTHUMG00000020601
Gene type protein-coding
Map location 9q33.2
Pascal p-value 0.47
Sherlock p-value 0.94
TADA p-value 0.009
Fetal beta 0.337
eGene Myers' cis & trans
Support CompositeSet

Gene in Data Sources
Gene set name Method of gene set Description Info
DNM:Fromer_2014 Whole Exome Sequencing analysis This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccur High-throughput literature-search 系统的搜索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,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
LHX6 chr9 124979560 C T NM_001242333
NM_001242334
NM_001242335
NM_014368
NM_199160		 p.146G>R
p.128G>R
.
p.157G>R
p.157G>R		 missense
missense
5-UTR
missense
missense		 Schizophrenia DNM:Fromer_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs6813178 chr4 71575238 LHX6 26468 0.13 trans
rs6856051 chr4 71600251 LHX6 26468 0.07 trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

补充说明:
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)

补充说明:
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 去的术语 Evidence Neuro keywords PubMed ID
GO:0003700 transcription factor activity IEA -
GO:0003700 transcription factor activity TAS 10393337
GO:0008270 zinc ion binding IEA -
GO:0046872 metal ion binding IEA -
GO:0043565 sequence-specific DNA binding IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0007420 brain development TAS Brain (GO term level: 7) 10393337
GO:0006355 regulation of transcription, DNA-dependent IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005634 nucleus IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
DAVICIONI MOLECULAR ARMS VS ERMS DN 182 111 All SZGR 2.0 genes in this pathway
HOOI ST7 TARGETS UP 94 57 All SZGR 2.0 genes in this pathway
LIU CMYB TARGETS UP 165 106 All SZGR 2.0 genes in this pathway
LIU VMYB TARGETS UP 127 78 All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174 695 All SZGR 2.0 genes in this pathway
MANTOVANI VIRAL GPCR SIGNALING UP 86 54 All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR UP 176 115 All SZGR 2.0 genes in this pathway
SCHAEFFER SOX9 TARGETS IN PROSTATE DEVELOPMENT UP 21 19 All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN 411 249 All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038 678 All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062 725 All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118 744 All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652 441 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 1 UP 140 85 All SZGR 2.0 genes in this pathway
佐藤在PANCREAT被甲基化IC CANCER 1 419 273 All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN 270 181 All SZGR 2.0 genes in this pathway
CHENG IMPRINTED BY ESTRADIOL 110 68 All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN 216 143 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349 234 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME2 AND H3K27ME3 59 35 All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211 131 All SZGR 2.0 genes in this pathway
LE NEURONAL DIFFERENTIATION DN 19 16 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-141/200a 418 424 m8 hsa-miR-141 UAACACUGUCUGGUAAAGAUGG
hsa-miR-200a UAACACUGUCUGGUAACGAUGU
miR-149 1048 1054 m8 hsa-miR-149brain UCUGGCUCCGUGUCUUCACUCC
miR-17-5p/20/93.mr/106/519.d 2003 2009 m8 hsa-miR-17-5p CAAAGUGCUUACAGUGCAGGUAGU
hsa-miR-20abrain UAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106a AAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZ UAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZ CAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519d CAAAGUGCCUCCCUUUAGAGUGU
miR-194 2033 2039 1A hsa-miR-194 UGUAACAGCAACUCCAUGUGGA
miR-204/211 1537 1543 1A hsa-miR-204brain UUCCCUUUGUCAUCCUAUGCCU
hsa-miR-211 UUCCCUUUGUCAUCCUUCGCCU
miR-214 108 115 1A,m8 hsa-miR-214brain ACAGCAGGCACAGACAGGCAG
miR-330 2054 2060 m8 hsa-miR-330brain GCAAAGCACACGGCCUGCAGAGA
miR-495 2031 2037 1A hsa-miR-495brain AAACAAACAUGGUGCACUUCUUU
miR-93.hd/291-3p/294/295/302/372/373/520 2002 2008 m8 hsa-miR-93brain AAAGUGCUGUUCGUGCAGGUAG
hsa-miR-302a UAAGUGCUUCCAUGUUUUGGUGA
hsa-miR-302b UAAGUGCUUCCAUGUUUUAGUAG
hsa-miR-302c UAAGUGCUUCCAUGUUUCAGUGG
hsa-miR-302d UAAGUGCUUCCAUGUUUGAGUGU
hsa-miR-372 AAAGUGCUGCGACAUUUGAGCGU
hsa-miR-373 GAAGUGCUUCGAUUUUGGGGUGU
hsa-miR-520e AAAGUGCUUCCUUUUUGAGGG
hsa-miR-520a AAAGUGCUUCCCUUUGGACUGU
hsa-miR-520b AAAGUGCUUCCUUUUAGAGGG
hsa-miR-520c AAAGUGCUUCCUUUUAGAGGGUU
hsa-miR-520d AAAGUGCUUCUCUUUGGUGGGUU