Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for DEGS1
Basic gene info.Gene symbolDEGS1
Gene namedelta(4)-desaturase, sphingolipid 1
SynonymsDEGS|DEGS-1|DES1|Des-1|FADS7|MLD
CytomapUCSC genome browser: 1q42.11
Genomic locationchr1 :224370909-224381142
Type of geneprotein-coding
RefGenesNM_144780.1,
NM_003676.3,
Ensembl idENSG00000143753
Descriptioncell migration-inducing gene 15 proteindegenerative spermatocyte homolog 1, lipid desaturasedegenerative spermatocyte homolog, lipid desaturasedihydroceramide desaturase 1membrane fatty acid (lipid) desaturasemembrane lipid desaturasemigration-induc
Modification date20141207
dbXrefs MIM : 615843
HGNC : HGNC
Ensembl : ENSG00000143753
HPRD : 13133
Vega : OTTHUMG00000037496
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DEGS1
BioGPS: 8560
Gene Expression Atlas: ENSG00000143753
The Human Protein Atlas: ENSG00000143753
PathwayNCI Pathway Interaction Database: DEGS1
KEGG: DEGS1
REACTOME: DEGS1
ConsensusPathDB
Pathway Commons: DEGS1
MetabolismMetaCyc: DEGS1
HUMANCyc: DEGS1
RegulationEnsembl's Regulation: ENSG00000143753
miRBase: chr1 :224,370,909-224,381,142
TargetScan: NM_144780
cisRED: ENSG00000143753
ContextiHOP: DEGS1
cancer metabolism search in PubMed: DEGS1
UCL Cancer Institute: DEGS1
Assigned class in ccmGDBC

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Phenotypic Information for DEGS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DEGS1
Familial Cancer Database: DEGS1
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_SPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DEGS1
MedGen: DEGS1 (Human Medical Genetics with Condition)
ClinVar: DEGS1
PhenotypeMGI: DEGS1 (International Mouse Phenotyping Consortium)
PhenomicDB: DEGS1

Mutations for DEGS1
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DEGS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF944194DEGS1242431224377512224377733DMPK243402194628336946283522
BG249152DEGS11601224377865224377924SERINC1587536122765667122767951
AI167570DEGS111811224379907224380087CDC731784781193189506193189807
AL079576DEGS1411081224377681224377748DEGS11043311224377728224377955

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:224371065-224371065p.D9E2
chr1:224377819-224377819p.S208Y2
chr1:224377699-224377699p.L168H1
chr1:224377904-224377904p.F236L1
chr1:224377500-224377500p.A102T1
chr1:224377714-224377714p.R173Q1
chr1:224377954-224377954p.F254fs*231
chr1:224377539-224377539p.P115S1
chr1:224377724-224377724p.F176F1
chr1:224377282-224377282p.K29R1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 3 2  1 3  31   12 4
# mutation 3 2  1 3  31   12 6
nonsynonymous SNV 3 2  1 3  31   12 4
synonymous SNV                   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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:224377867p.I164V1
chr1:224377623p.R173Q1
chr1:224378005p.T183T1
chr1:224371065p.D9E1
chr1:224377643p.V191M1
chr1:224380110p.K29R1
chr1:224377282p.I200V1
chr1:224377672p.M37I1
chr1:224380147p.S208Y1
chr1:224377307p.P39H1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for DEGS1 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 DEGS1

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

ABCC6P2,CALCR,CNIH4,DEGS1,ENAH,EPHX1,FBXO28,
GGPS1,GHITM,GRIP1,MSLNL,NVL,NXPH2,OMG,
OR2AT4,PAX7,SLC12A8,SRP9,ST6GAL1,TMEM159,WDR26
ANXA1,ARF4,ARL2BP,ATP6AP2,DTD2,TPGS2,C1orf198,
CALM2,CCNY,CMPK1,DEGS1,ETF1,MAPRE1,PPA1,
PPP2CB,PWP1,RAB1A,RAB9A,RAP1B,SLC25A43,UBE2E2

AIDA,MSANTD3,CALU,CHST15,COPZ2,DEGS1,DYRK3,
EHD2,EMP3,GPX8,IKBIP,JAZF1,KLHL5,LGALS1,
MSN,PEA15,PRKCDBP,PTRF,SELM,SRGAP2,TIMP1
ARL4D,CLMP,BAG2,CALU,CCDC69,CFL2,DEGS1,
DTNA,GUCY1B3,KCNJ8,PEA15,PLEKHO1,RAB31,RAB34,
RAMP1,RASSF8,RPS6KC1,SCRG1,SELM,TEAD2,TMEM55A
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for DEGS1


There's no related Drug.
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Cross referenced IDs for DEGS1
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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