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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CERS4 |
Basic gene info. | Gene symbol | CERS4 |
Gene name | ceramide synthase 4 | |
Synonyms | LASS4|Trh1 | |
Cytomap | UCSC genome browser: 19p13.2 | |
Genomic location | chr19 :8274216-8327304 | |
Type of gene | protein-coding | |
RefGenes | NM_024552.2, | |
Ensembl id | ENSG00000090661 | |
Description | LAG1 homolog, ceramide synthase 4LAG1 longevity assurance homolog 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 615334 | |
HGNC : HGNC | ||
Ensembl : ENSG00000090661 | ||
HPRD : 13962 | ||
Vega : OTTHUMG00000172570 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CERS4 | |
BioGPS: 79603 | ||
Gene Expression Atlas: ENSG00000090661 | ||
The Human Protein Atlas: ENSG00000090661 | ||
Pathway | NCI Pathway Interaction Database: CERS4 | |
KEGG: CERS4 | ||
REACTOME: CERS4 | ||
ConsensusPathDB | ||
Pathway Commons: CERS4 | ||
Metabolism | MetaCyc: CERS4 | |
HUMANCyc: CERS4 | ||
Regulation | Ensembl's Regulation: ENSG00000090661 | |
miRBase: chr19 :8,274,216-8,327,304 | ||
TargetScan: NM_024552 | ||
cisRED: ENSG00000090661 | ||
Context | iHOP: CERS4 | |
cancer metabolism search in PubMed: CERS4 | ||
UCL Cancer Institute: CERS4 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CERS4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CERS4 |
Familial Cancer Database: CERS4 |
* This gene is included in those cancer gene databases. |
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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_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CERS4 |
MedGen: CERS4 (Human Medical Genetics with Condition) | |
ClinVar: CERS4 | |
Phenotype | MGI: CERS4 (International Mouse Phenotyping Consortium) |
PhenomicDB: CERS4 |
Mutations for CERS4 |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | CERS4 | chr19 | 8296689 | 8296709 | CERS4 | chr19 | 8296873 | 8296893 |
ovary | CERS4 | chr19 | 8300448 | 8300468 | chr22 | 45435548 | 45435568 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CERS4 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 |
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) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) | 1 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=0) | (# total SNVs=0) |
(# 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 |
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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 |   | 5 | 2 |   | 2 |   | 2 |   |   | 4 | 2 | 3 |   | 2 | 3 | 6 |   | 4 |
# mutation |   | 1 |   | 5 | 2 |   | 2 |   | 1 |   |   | 4 | 2 | 3 |   | 2 | 3 | 6 |   | 5 |
nonsynonymous SNV |   | 1 |   | 3 | 1 |   | 1 |   |   |   |   | 3 | 2 | 1 |   | 1 | 2 | 3 |   | 3 |
synonymous SNV |   |   |   | 2 | 1 |   | 1 |   | 1 |   |   | 1 |   | 2 |   | 1 | 1 | 3 |   | 2 |
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 |
chr19:8316056 | p.V32V | 3 |
chr19:8316117 | p.T282T | 2 |
chr19:8322867 | p.R53C | 2 |
chr19:8319436 | p.R76M | 2 |
chr19:8321856 | p.C134C | 1 |
chr19:8326635 | p.R139K | 1 |
chr19:8320541 | p.Q283E | 1 |
chr19:8321862 | p.S152S | 1 |
chr19:8326716 | p.S292S | 1 |
chr19:8320582 | p.Q173K | 1 |
Other DBs for Point Mutations |
Copy Number for CERS4 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 CERS4 |
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 |
COA3,CCDC57,CHCHD5,COASY,COQ4,CYB561D2,DDRGK1, DHRS4,FAM134C,G6PC3,GAMT,HEXIM2,CERS4,LDHD, MMAB,PIGQ,RAB17,SURF1,TMEM205,TTC36,WBP1 | ABCA12,AFMID,ALDH3B2,DHCR7,EBP,GGT1,GGTLC2, GJB1,HMGCS2,HRASLS2,HSD17B7,CERS4,MVK,NSUN2, PTK6,PTPLAD1,QPRT,RASGRF1,REEP6,SPINK8,SQLE |
BCAM,ETNK2,FAM195B,FBXO17,FBXO27,GRINA,KLHDC8B, LAPTM4B,LARP6,CERS4,LDLRAD3,MYL6B,PACSIN3,PTP4A3, SLC26A11,SLC2A4RG,SLC5A6,SMO,SNTA1,TCEA2,ZNF34 | ANKRD6,BEND5,BNIP3,CA11,CDK14,CHN1,GNAI2, GNB5,KLHL22,CERS4,NKAPL,PELI3,PJA1,PLSCR3, SMARCD3,SNN,ST3GAL3,TCEA2,TNFSF12,TUBG2,USP44 |
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 CERS4 |
There's no related Drug. |
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Cross referenced IDs for CERS4 |
* 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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