Gene Page: LIG3

Summary ?
GeneID3980
SymbolLIG3
SynonymsLIG2
Descriptionligase III, DNA, ATP-dependent
ReferenceMIM:600940|HGNC:HGNC:6600|Ensembl:ENSG00000005156|HPRD:02966|Vega:OTTHUMG00000128519
Gene typeprotein-coding
Map location17q11.2-q12
Pascal p-value0.104
Sherlock p-value0.009
Fetal beta0.423
eGeneCaudate basal ganglia
Cerebellar Hemisphere
Cerebellum
Cortex
Frontal Cortex BA9
Hippocampus
Hypothalamus
Nucleus accumbens basal ganglia
Putamen basal ganglia
Meta
SupportAscano FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs129454281733307586LIG3ENSG00000005156.71.82E-6073gtex_brain_putamen_basal
rs31359671733313729LIG3ENSG00000005156.72.62E-706216gtex_brain_putamen_basal
rs20745181733324382LIG3ENSG00000005156.73.165E-7016869gtex_brain_putamen_basal
rs10525361733331575LIG3ENSG00000005156.73.165E-7024062gtex_brain_putamen_basal
rs10039181733332177LIG3ENSG00000005156.75.073E-7024664gtex_brain_putamen_basal
rs129483621733332629LIG3ENSG00000005156.73.165E-7025116gtex_brain_putamen_basal
rs108531741733351917LIG3ENSG00000005156.73.165E-7044404gtex_brain_putamen_basal
rs16348021733360374LIG3ENSG00000005156.72.007E-7052861gtex_brain_putamen_basal
rs8100421733382205LIG3ENSG00000005156.73.163E-7074692gtex_brain_putamen_basal
rs23391231733382734LIG3ENSG00000005156.73.163E-7075221gtex_brain_putamen_basal
rs23391221733382801LIG3ENSG00000005156.73.163E-7075288gtex_brain_putamen_basal
rs16348001733383030LIG3ENSG00000005156.73.163E-7075517gtex_brain_putamen_basal
rs10884501733399745LIG3ENSG00000005156.76.986E-8092232gtex_brain_putamen_basal
rs7979901733412739LIG3ENSG00000005156.71.463E-70105226gtex_brain_putamen_basal
rs7979891733414758LIG3ENSG00000005156.71.084E-70107245gtex_brain_putamen_basal

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
ITGB50.720.69
APCDD10.700.66
SLC12A40.700.61
LMCD10.700.76
GIMAP10.700.67
LSR0.690.68
FZD60.690.61
A2ML10.670.60
BCAN0.660.62
TMEM510.660.69
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
GPR22-0.42-0.41
C6orf115-0.40-0.39
GPR21-0.40-0.41
RLBP1L1-0.40-0.36
C18orf8-0.40-0.38
NELL2-0.39-0.38
NEUROD6-0.39-0.38
TIAM2-0.39-0.39
WASF1-0.39-0.34
NFIL3-0.39-0.37

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG BASE EXCISION REPAIR 3522All SZGR 2.0 genes in this pathway
REACTOME BASE EXCISION REPAIR 1913All SZGR 2.0 genes in this pathway
REACTOME DNA REPAIR 11259All SZGR 2.0 genes in this pathway
REACTOME RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 127All SZGR 2.0 genes in this pathway
UDAYAKUMAR MED1 TARGETS UP 13582All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP 329196All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552347All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142669All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN 17811082All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN 770415All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS A UP 191128All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 UP 15093All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423265All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPLICATION GENES 14787All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
PEART HDAC PROLIFERATION CLUSTER DN 7657All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 DN 163115All SZGR 2.0 genes in this pathway
JAIN NFKB SIGNALING 7544All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS DN 234137All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS EARLY PROGENITOR 532309All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
CHIBA RESPONSE TO TSA DN 2314All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS 217138All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS DN 543317All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN 593372All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN 591366All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER UP 2014All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN 353226All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6 469239All SZGR 2.0 genes in this pathway
VANASSE BCL2 TARGETS DN 7450All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 14888All SZGR 2.0 genes in this pathway