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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LBR |
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Phenotypic Information for LBR(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: LBR |
Familial Cancer Database: LBR |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: LBR |
MedGen: LBR (Human Medical Genetics with Condition) | |
ClinVar: LBR | |
Phenotype | MGI: LBR (International Mouse Phenotyping Consortium) |
PhenomicDB: LBR |
Mutations for LBR |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LBR related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AI630623 | SLC25A3 | 1 | 235 | 12 | 98993825 | 98995188 | LBR | 232 | 345 | 1 | 225589585 | 225589698 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=48) | (# total SNVs=16) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr1:225599097-225599097 | p.R377Q | 4 |
chr1:225607016-225607016 | p.F197V | 2 |
chr1:225598067-225598067 | p.A414T | 2 |
chr1:225600305-225600305 | p.S312C | 2 |
chr1:225607070-225607070 | p.E179* | 2 |
chr1:225607156-225607156 | p.? | 2 |
chr1:225598020-225598020 | p.L429L | 2 |
chr1:225605828-225605828 | p.M232T | 2 |
chr1:225598047-225598047 | p.M420I | 1 |
chr1:225605872-225605873 | p.L217fs*17 | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 4 | 1 | 8 | 1 |   | 1 |   | 1 | 3 |   | 5 | 4 | 2 |   | 2 | 5 | 10 |   | 8 |
# mutation | 1 | 4 | 1 | 9 | 1 |   | 1 |   | 1 | 3 |   | 5 | 4 | 2 |   | 2 | 5 | 10 |   | 9 |
nonsynonymous SNV | 1 | 3 | 1 | 7 | 1 |   | 1 |   |   | 3 |   | 4 | 2 | 1 |   | 2 | 4 | 9 |   | 8 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   | 1 |   |   | 1 | 2 | 1 |   |   | 1 | 1 |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr1:225598067 | p.L429L,LBR | 2 |
chr1:225611758 | p.A414T,LBR | 2 |
chr1:225598020 | p.A7V,LBR | 2 |
chr1:225599053 | p.P515S,LBR | 1 |
chr1:225591105 | p.V397L,LBR | 1 |
chr1:225600291 | p.N242I,LBR | 1 |
chr1:225598021 | p.A504T,LBR | 1 |
chr1:225609877 | p.G392R,LBR | 1 |
chr1:225599054 | p.K186T,LBR | 1 |
chr1:225591108 | p.F470L,LBR | 1 |
Other DBs for Point Mutations |
Copy Number for LBR in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for LBR |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
ANP32E,ASPM,B3GNT5,BUB1,CCNA2,CDCA7,CDCA8, CENPF,DBF4,DLGAP5,EXO1,FAM72B,HJURP,KIF14, LBR,LIN9,DESI2,SGOL1,SUV39H2,TTK,ZNF695 | ASAP1,ATG12,CARD8,CCDC82,CPNE8,EPS15,EXOC5, FAM160B1,FCHSD2,LBR,MTMR2,OSTM1,DESI2,RAB8B, RECQL,SNRK,SNX6,STX7,TCF4,TMX3,VAMP7 |
ABCB10,AHCTF1,BRCA2,C1orf112,CENPF,CENPJ,CKAP2, CSE1L,DARS2,DHX9,HDGF,HEATR1,KIAA1804,LBR, NUP133,RFC3,RRP15,SKA3,TARBP1,TPX2,URB2 | ANP32E,ARMCX3,C3orf58,CCP110,EIF5B,FTO,IFT81, KDELC2,LBR,LDHB,LPHN2,MBTPS2,MYEF2,NEDD1, NUCKS1,OXCT1,PRKAR1A,PSIP1,RECQL,TMEM194A,TULP3 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for LBR |
There's no related Drug. |
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Cross referenced IDs for LBR |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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