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| TissGeneSummary for LIG3 |
 Gene summary |
| Basic gene information | Gene symbol | LIG3 |
| Gene name | ligase III, DNA, ATP-dependent | |
| Synonyms | LIG2 | |
| Cytomap | UCSC genome browser: 17q11.2-q12 | |
| Type of gene | protein-coding | |
| RefGenes | NM_002311.4, NM_013975.3, | |
| Description | DNA ligase 3ligase II, DNA, ATP-dependentpolydeoxyribonucleotide synthase [ATP] 3 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 600940 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000005156 | ||
| HPRD : 02966 | ||
| Vega : OTTHUMG00000128519 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LIG3 | |
| BioGPS: 3980 | ||
| Pathway | NCI Pathway Interaction Database: LIG3 | |
| KEGG: LIG3 | ||
| REACTOME: LIG3 | ||
| Pathway Commons: LIG3 | ||
| Context | iHOP: LIG3 | |
| ligand binding site mutation search in PubMed: LIG3 | ||
| UCL Cancer Institute: LIG3 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Bone marrowTestis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | LAMLTGCT | |
| Reference showing the relevant tissue of LIG3 | ||
| Description by TissGene annotations | Protective TissGene in OS Cancer gene Have significant anti-correlated miRNA TissgsLTS | |
| * Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID | GO:0033151 | V(D)J recombination | 9809069 | GO:0033151 | V(D)J recombination | 9809069 |
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| TissGeneExp for LIG3 |
| Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
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| Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
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| Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| LUSC | 0.333628506 | -0.879451887 | 1.213080392 | 1.07E-18 | 1.06E-17 |
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| TissGene-miRNA for LIG3 |
| Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
| Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
| LUAD | hsa-miR-29c-3p | MIMAT0000681 | 0.02 | -0.3 | 60 |
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| TissGeneMut for LIG3 |
| TissGeneSNV for LIG3 |
| nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
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| Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.R635* | UCEC | 2 |
| p.E376Q | BLCA | 1 |
| p.T479A | LIHC | 1 |
| p.E346K | ESCA | 1 |
| p.A432T | UCEC | 1 |
| p.R614W | PRAD | 1 |
| p.L1005P | LUAD | 1 |
| p.R445H | UCEC | 1 |
| p.G656R | SKCM | 1 |
| p.F144L | KIRP | 1 |
| p.R67H | BLCA | 1 |
| p.L822P | UCEC | 1 |
| p.P338R | BRCA | 1 |
| p.L387H | PAAD | 1 |
| p.Q199R | STAD | 1 |
| p.E238K | UCEC | 1 |
| p.S444* | LUSC | 1 |
| p.E856K | BLCA | 1 |
| p.R956G | COAD | 1 |
| p.A103V | TGCT | 1 |
| p.L321F | ESCA | 1 |
| p.D521N | HNSC | 1 |
| p.T796K | OV | 1 |
| p.E359K | CESC | 1 |
| p.L321F | BLCA | 1 |
| p.R608X | STAD | 1 |
| p.R25Q | PRAD | 1 |
| p.R30C | THYM | 1 |
| p.D399G | UCEC | 1 |
| p.V978M | STAD | 1 |
| p.D661H | LUAD | 1 |
| p.Q742R | STAD | 1 |
| p.K107T | STAD | 1 |
| p.V748M | LGG | 1 |
| p.E452X | THYM | 1 |
| p.H733Y | LUAD | 1 |
| p.A426V | STAD | 1 |
| p.S491C | SKCM | 1 |
| p.Y699C | STAD | 1 |
| p.A475S | LUAD | 1 |
| p.D323N | CESC | 1 |
| p.G731E | LUSC | 1 |
| p.D815H | LUAD | 1 |
| p.S792L | LGG | 1 |
| p.V915L | LIHC | 1 |
| p.R383W | LIHC | 1 |
| p.A215V | OV | 1 |
| p.R671W | LIHC | 1 |
| p.M747T | COAD | 1 |
| p.R957C | STAD | 1 |
| p.R267* | UCEC | 1 |
| p.S236C | BRCA | 1 |
| p.R30C | UCEC | 1 |
| p.M645L | SKCM | 1 |
| p.A458V | UCEC | 1 |
| p.T785A | COAD | 1 |
| p.Q586R | BRCA | 1 |
| p.R803* | UCEC | 1 |
| p.S424L | THYM | 1 |
| p.G859D | STAD | 1 |
| p.K54E | SKCM | 1 |
| p.E783D | STAD | 1 |
| p.S818C | CESC | 1 |
| p.R224L | LUAD | 1 |
| p.K26R | LUSC | 1 |
| p.R956K | HNSC | 1 |
| p.A584V | COAD | 1 |
| p.W673L | COAD | 1 |
| p.P823S | SKCM | 1 |
| p.S294L | HNSC | 1 |
| p.K497N | ESCA | 1 |
| p.A432T | STAD | 1 |
| p.S58L | SKCM | 1 |
| p.E834* | UCEC | 1 |
| p.P946S | COAD | 1 |
| p.S604T | LUAD | 1 |
| p.R608* | STAD | 1 |
| p.D596H | LUAD | 1 |
| p.V327M | LGG | 1 |
| p.I710V | OV | 1 |
| p.A432T | LGG | 1 |
| p.F526S | HNSC | 1 |
| p.S361I | UCEC | 1 |
| p.G706S | SKCM | 1 |
| p.S476L | LIHC | 1 |
| p.T12I | SKCM | 1 |
| p.R513* | HNSC | 1 |
| p.S363Y | UCEC | 1 |
| p.H517Q | HNSC | 1 |
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| TissGeneCNV for LIG3 |
| Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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| TissGeneFusions for LIG3 |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
| Chimerdb3.0 | ChiTaRs | NA | BF091674 | KIAA1210-LIG3 | chrX:118215027 | chr17:33324802 | |
| Chimerdb3.0 | ChiTaRs | NA | BF900318 | LIG3-FLOT1 | chr17:33310499 | chr6:2041283 | |
| Chimerdb3.0 | ChiTaRs | NA | BQ306956 | LIG3-LIG3 | chr17:33321419 | chr17:33323080 | |
| Chimerdb3.0 | FusionScan | CHOL | TCGA-W5-AA31-01A | ANKFY1-LIG3 | 5'UTR-5'UTR | chr17:4167226 | chr17:33310020 |
| Chimerdb3.0 | TopHat-Fusion | BRCA | TCGA-BH-A18R-01A | LIG3-CACNB1 | In-Frame | chr17:33326874 | chr17:37333456 |
| Chimerdb3.0 | TopHat-Fusion | BRCA | TCGA-BH-A18R-01A | LIG3-CACNB1 | In-Frame | chr17:33328421 | chr17:37333456 |
| Chimerdb3.0 | TopHat-Fusion | BRCA | TCGA-BH-A18R-01A | LIG3-CACNB1 | Out-of-Frame | chr17:33329122 | chr17:37333456 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-AR-A0TT-01A | LIG3-C19orf50 | CDS-5UTR | Chr17:33313150 | Chr19:18672846 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-E9-A1RF-01A | LIG3-ZFAT | In-frame | Chr17:33321450 | Chr8:135490964 |
| TCGAfusionPortal | PRADA | BRCA | TCGA-OL-A6VO-01A | LIG3-HAP1 | NA | Chr17:33318133 | Chr17:39874278 |
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| TissGeneNet for LIG3 |
| Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
| BRCA (tumor) | BRCA (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| COAD (tumor) | COAD (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| HNSC (tumor) | HNSC (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| KICH (tumor) | KICH (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| KIRC (tumor) | KIRC (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| KIRP (tumor) | KIRP (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| LIHC (tumor) | LIHC (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| LUAD (tumor) | LUAD (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| LUSC (tumor) | LUSC (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| PRAD (tumor) | PRAD (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| STAD (tumor) | STAD (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| THCA (tumor) | THCA (normal) |
| LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (tumor) | LIG3, XRCC5, THRA, PLCG1, SRC, PIK3R1, ABL1, THRB, CRK, XRCC1, PARP1, NCAPG, PNKP, XRCC6, APLF, TDP1, NEIL1, JTB (normal) |
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| TissGeneProg for LIG3 |
| Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
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| Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| TissGeneClin for LIG3 |
| TissGeneDrug for LIG3 |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| DB00290 | Bleomycin | Inhibitor | Small molecule | Approved |
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| TissGeneDisease for LIG3 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0242379 | Malignant neoplasm of lung | 4 | GAD |
| umls:C0006142 | Malignant neoplasm of breast | 3 | BeFree,GAD |
| umls:C0005684 | Malignant neoplasm of urinary bladder | 2 | BeFree,GAD |
| umls:C0003811 | Cardiac Arrhythmia | 1 | GAD |
| umls:C0004134 | Ataxia | 1 | BeFree |
| umls:C0004135 | Ataxia Telangiectasia | 1 | BeFree |
| umls:C0009404 | Colorectal Neoplasms | 1 | GAD |
| umls:C0014859 | Esophageal Neoplasms | 1 | GAD |
| umls:C0018133 | Graft-vs-Host Disease | 1 | GAD |
| umls:C0018671 | Head and Neck Neoplasms | 1 | GAD |
| umls:C0023055 | Laryngeal neoplasm | 1 | GAD |
| umls:C0023418 | leukemia | 1 | BeFree |
| umls:C0023452 | Leukemia, Lymphocytic, Acute, L1 | 1 | BeFree |
| umls:C0023473 | Myeloid Leukemia, Chronic | 1 | BeFree |
| umls:C0024117 | Chronic Obstructive Airway Disease | 1 | GAD |
| umls:C0024305 | Lymphoma, Non-Hodgkin | 1 | GAD |
| umls:C0026640 | Mouth Neoplasms | 1 | GAD |
| umls:C0026769 | Multiple Sclerosis | 1 | GAD |
| umls:C0027819 | Neuroblastoma | 1 | BeFree |
| umls:C0030297 | Pancreatic Neoplasm | 1 | GAD |
| umls:C0031347 | Pharyngeal Neoplasms | 1 | GAD |
| umls:C0035126 | Reperfusion Injury | 1 | RGD |
| umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
| umls:C0085298 | Sudden Cardiac Death | 1 | GAD |
| umls:C0235974 | Pancreatic carcinoma | 1 | BeFree |
| umls:C0279626 | Squamous cell carcinoma of esophagus | 1 | BeFree |
| umls:C0346647 | Malignant neoplasm of pancreas | 1 | BeFree |
| umls:C0376545 | Hematologic Neoplasms | 1 | GAD |
| umls:C0546837 | Malignant neoplasm of esophagus | 1 | GAD |
| umls:C0677886 | Epithelial ovarian cancer | 1 | GAD |
| umls:C0678222 | Breast Carcinoma | 1 | BeFree |
| umls:C0699885 | Carcinoma of bladder | 1 | BeFree |
| umls:C0700095 | Central neuroblastoma | 1 | BeFree |
| umls:C1292769 | Precursor B-cell lymphoblastic leukemia | 1 | BeFree |
| umls:C1302401 | Adenoma of large intestine | 1 | BeFree |
| umls:C1527249 | Colorectal Cancer | 1 | GAD |
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