Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 CMAS
Basic gene info.Gene symbolCMAS
Gene namecytidine monophosphate N-acetylneuraminic acid synthetase
SynonymsCSS
CytomapUCSC genome browser: 12p12.1
Genomic locationchr12 :22199158-22218602
Type of geneprotein-coding
RefGenesNM_018686.4,
Ensembl idENSG00000111726
DescriptionCMP-N-acetylneuraminic acid synthaseCMP-N-acetylneuraminic acid synthetaseCMP-Neu5Ac synthetaseCMP-NeuNAc synthaseCMP-NeuNAc synthetaseCMP-sialic acid synthetaseN-acylneuraminate cytidylyltransferasecytidine 5'-monophosphate N-acetylneuraminic acid
Modification date20141207
dbXrefs MIM : 603316
HGNC : HGNC
Ensembl : ENSG00000111726
HPRD : 04501
Vega : OTTHUMG00000169097
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CMAS
BioGPS: 55907
Gene Expression Atlas: ENSG00000111726
The Human Protein Atlas: ENSG00000111726
PathwayNCI Pathway Interaction Database: CMAS
KEGG: CMAS
REACTOME: CMAS
ConsensusPathDB
Pathway Commons: CMAS
MetabolismMetaCyc: CMAS
HUMANCyc: CMAS
RegulationEnsembl's Regulation: ENSG00000111726
miRBase: chr12 :22,199,158-22,218,602
TargetScan: NM_018686
cisRED: ENSG00000111726
ContextiHOP: CMAS
cancer metabolism search in PubMed: CMAS
UCL Cancer Institute: CMAS
Assigned class in ccmGDBC

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Phenotypic Information for CMAS(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: CMAS
Familial Cancer Database: CMAS
* 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_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

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

Mutations for CMAS
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CMAS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA571172SH3RF111964170043326170051300CMAS193875122219946322214325
AF119840CMAS1647122221530222215952ALB641269947427000474286973
DB053027TCF121384155728316857283551CMAS385566122219917322199354
BX106129CMAS17465122221671722223561CMAS460733122221805522218328

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 # sample   1    1        
GAIN (# sample)        1        
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=2)
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
chr12:22208151-22208151p.R110Q4
chr12:22208520-22208520p.R179*2
chr12:22214246-22214246p.E274K2
chr12:22215250-22215250p.Q332H2
chr12:22199240-22199240p.M1I1
chr12:22214250-22214250p.I275R1
chr12:22208464-22208464p.M160R1
chr12:22215252-22215252p.T333M1
chr12:22213769-22213769p.G233fs*161
chr12:22218102-22218102p.G388C1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 6    11 31   25 6
# mutation11 8    11 31   25 6
nonsynonymous SNV11 7    11 31   15 5
synonymous SNV   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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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
chr12:22208151p.R110Q3
chr12:22199377p.A47V1
chr12:22213832p.K276N1
chr12:22215252p.N62S1
chr12:22199422p.V279D1
chr12:22213839p.K64R1
chr12:22215287p.H290H1
chr12:22199428p.V305L1
chr12:22213859p.D118V1
chr12:22218057p.R322M1

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 CMAS 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 CMAS

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

AEBP2,ASUN,RHNO1,CMAS,DDX47,DERA,DNM1L,
FAM60A,FGFR1OP2,GOLT1B,LDHB,MAGOHB,MED21,MRPS35,
NDUFA9,PYROXD1,RAD51AP1,STRAP,TM7SF3,TULP3,YARS2
ACP1,CCNB1IP1,CDK7,CMAS,DENR,ELF5,FANCL,
GTF2F2,HDAC2,KLF5,LRRC8D,METAP1,NIFK,NUFIP1,
PDSS1,SET,STX19,TEX10,TMSB15A,TPD52L1,YTHDF2

ARPC3,SMIM15,C6orf136,CDX2,CMAS,DBI,EPCAM,
FABP1,FAR2,HNRNPAB,LRRC19,MMAB,MVK,NDUFA12,
PDHA1,PPP1R14D,PRR13,PRSS8,SLC16A9,SNRPF,XRCC6BP1
CNOT11,MCU,CDH17,CMAS,EPCAM,ABHD17C,FUCA2,
GPD2,LIMA1,LRRFIP2,MBD2,NIPA2,PGGT1B,PIP5K1B,
PPM1B,PPP2R1B,PRSS12,RAB14,RBM47,RNF6,PTBP3
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 CMAS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB04555cytidine monophosphate N-acetylneuraminic acid synthetaseexperimentalCytidine-5'-Diphosphate


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Cross referenced IDs for CMAS
* 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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