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| TissGeneSummary for LFNG |
 Gene summary |
| Basic gene information | Gene symbol | LFNG |
| Gene name | LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase | |
| Synonyms | SCDO3 | |
| Cytomap | UCSC genome browser: 7p22.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001040167.1, NM_001040168.1,NM_001166355.1,NM_002304.2, | |
| Description | beta-1,3-N-acetylglucosaminyltransferase lunatic fringe | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 602576 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000106003 | ||
| Vega : OTTHUMG00000152043 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LFNG | |
| BioGPS: 3955 | ||
| Pathway | NCI Pathway Interaction Database: LFNG | |
| KEGG: LFNG | ||
| REACTOME: LFNG | ||
| Pathway Commons: LFNG | ||
| Context | iHOP: LFNG | |
| ligand binding site mutation search in PubMed: LFNG | ||
| UCL Cancer Institute: LFNG | ||
| 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) | KidneyPancreas | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHPAAD | |
| Reference showing the relevant tissue of LFNG | ||
| Description by TissGene annotations | ||
| * 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 |
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| TissGeneExp for LFNG |
| 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 |
| KICH | -2.586132979 | -0.761596979 | -1.824536 | 2.68E-09 | 1.55E-08 |
| PRAD | 1.816280791 | 0.661646175 | 1.154634615 | 2.09E-06 | 1.38E-05 |
| STAD | 1.688996896 | 0.335284396 | 1.3537125 | 6.60E-05 | 0.000545713 |
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| TissGene-miRNA for LFNG |
| 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 |
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| TissGeneMut for LFNG |
| TissGeneSNV for LFNG |
| 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.E56G | LIHC | 2 |
| p.T46I | ESCA | 1 |
| p.R29M | KIRC | 1 |
| p.Q235P | COAD | 1 |
| p.R208P | SKCM | 1 |
| p.H198Q | ESCA | 1 |
| p.W45* | SKCM | 1 |
| p.H219L | SKCM | 1 |
| p.H277R | LUAD | 1 |
| p.N162K | BLCA | 1 |
| p.R239W | PRAD | 1 |
| p.H159Y | LIHC | 1 |
| p.T46I | LIHC | 1 |
| p.D355N | HNSC | 1 |
| p.A171S | CESC | 1 |
| p.K180E | THYM | 1 |
| p.G256S | THYM | 1 |
| p.R174C | COAD | 1 |
| p.E56G | KIRC | 1 |
| p.R307H | LGG | 1 |
| p.V240D | LIHC | 1 |
| p.A182V | COAD | 1 |
| p.A176E | KIRP | 1 |
| p.R212W | THYM | 1 |
| p.D55G | KIRC | 1 |
| p.A171T | SKCM | 1 |
| p.G48R | ESCA | 1 |
| p.F311L | BLCA | 1 |
| p.P371S | SKCM | 1 |
| p.V297M | HNSC | 1 |
| p.R187H | STAD | 1 |
| p.R375S | UCEC | 1 |
| p.K142R | LUAD | 1 |
| p.K123R | LGG | 1 |
| p.A107T | PAAD | 1 |
| p.S24G | LIHC | 1 |
| p.N203Y | LUAD | 1 |
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| TissGeneCNV for LFNG |
| 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 LFNG |
| 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 | BF373191 | PRPSAP2-LFNG | chr17:18768839 | chr7:2565187 | |
| Chimerdb3.0 | ChiTaRs | NA | BE772582 | PRPSAP2-LFNG | chr17:18768832 | chr7:2565187 |
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| TissGeneNet for LFNG |
| 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) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| COAD (tumor) | COAD (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| KICH (tumor) | KICH (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| STAD (tumor) | STAD (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| THCA (tumor) | THCA (normal) |
| LFNG, NOTCH1, NOTCH2 (tumor) | LFNG, NOTCH1, NOTCH2 (normal) |
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| TissGeneProg for LFNG |
| 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 LFNG |
| TissGeneDrug for LFNG |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for LFNG |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0013393 | Dysostoses | 1 | LHGDN |
| umls:C0338831 | Manic | 1 | BeFree |
| umls:C1458155 | Mammary Neoplasms | 1 | BeFree |
| umls:C1853296 | SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE 3 | 1 | CLINVAR,CTD_human,UNIPROT |
| umls:C0265343 | Jarcho-Levin syndrome | 0 | ORPHANET |
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