Summary ?
GeneID8994
SymbolLIMD1
Synonyms-
DescriptionLIM domains containing 1
ReferenceMIM:604543|HGNC:HGNC:6612|HPRD:05177|
Gene typeprotein-coding
Map location3p21.3
Pascal p-value0.953
Fetal beta1.583
eGeneCortex
Frontal Cortex BA9
Nucleus accumbens basal ganglia
Myers' cis & trans
Meta
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
LIMD1chr345637495CGNM_014240p.375T>RmissenseSchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs2494067chr1108245614LIMD189940.17trans

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
WDR45L0.800.74
IKZF50.800.80
KIAA17370.790.78
KIAA01960.790.75
BCL2L130.790.75
HIATL10.790.74
RFT10.780.73
ADIPOR10.780.69
KIAA06520.780.76
SLC35A50.780.75
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.65-0.50
AF347015.18-0.64-0.52
IL32-0.60-0.48
AC098691.2-0.60-0.50
AF347015.8-0.58-0.46
MT-CO2-0.57-0.46
MT-ATP8-0.54-0.46
AC100783.1-0.53-0.43
AC010300.1-0.53-0.49
AF347015.26-0.52-0.40

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN 463290All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN 805505All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
LIU COMMON CANCER GENES 7947All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 720440All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS UP 221135All SZGR 2.0 genes in this pathway
SENGUPTA EBNA1 ANTICORRELATED 17385All SZGR 2.0 genes in this pathway
KYNG RESPONSE TO H2O2 VIA ERCC6 UP 4030All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN 315215All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway