Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 CMAS

Basic gene info.	Gene symbol	CMAS
	Gene name	cytidine monophosphate N-acetylneuraminic acid synthetase
	Synonyms	CSS
	Cytomap	UCSC genome browser: 12p12.1
	Genomic location	chr12 :22199158-22218602
	Type of gene	protein-coding
	RefGenes	NM_018686.4,
	Ensembl id	ENSG00000111726
	Description	CMP-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 date	20141207
dbXrefs	MIM : 603316
	HGNC : HGNC
	Ensembl : ENSG00000111726
	HPRD : 04501
	Vega : OTTHUMG00000169097
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CMAS
	BioGPS: 55907
	Gene Expression Atlas: ENSG00000111726
	The Human Protein Atlas: ENSG00000111726
Pathway	NCI Pathway Interaction Database: CMAS
	KEGG: CMAS
	REACTOME: CMAS
	ConsensusPathDB
	Pathway Commons: CMAS
Metabolism	MetaCyc: CMAS
	HUMANCyc: CMAS
Regulation	Ensembl's Regulation: ENSG00000111726
	miRBase: chr12 :22,199,158-22,218,602
	TargetScan: NM_018686
	cisRED: ENSG00000111726
Context	iHOP: CMAS
	cancer metabolism search in PubMed: CMAS
	UCL Cancer Institute: CMAS
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: CMAS
	MedGen: CMAS (Human Medical Genetics with Condition)
	ClinVar: CMAS
Phenotype	MGI: CMAS (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CMAS 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
DA571172	SH3RF1	1	196	4	170043326	170051300	CMAS	193	875	12	22199463	22214325
AF119840	CMAS	1	647	12	22215302	22215952	ALB	641	2699	4	74270004	74286973
DB053027	TCF12	1	384	15	57283168	57283551	CMAS	385	566	12	22199173	22199354
BX106129	CMAS	17	465	12	22216717	22223561	CMAS	460	733	12	22218055	22218328

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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Somatic 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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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
chr12:22208151-22208151	p.R110Q	4
chr12:22214246-22214246	p.E274K	2
chr12:22215250-22215250	p.Q332H	2
chr12:22208520-22208520	p.R179*	2
chr12:22208175-22208175	p.D118V	1
chr12:22215219-22215219	p.R322M	1
chr12:22208545-22208545	p.?	1
chr12:22218082-22218082	p.L381S	1
chr12:22214234-22214234	p.E270K	1
chr12:22208418-22208418	p.T145A	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		6					1	1		3	1				2	5		6
# mutation	1	1		8					1	1		3	1				2	5		6
nonsynonymous SNV	1	1		7					1	1		3	1				1	5		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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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
chr12:22208151	p.R110Q	3
chr12:22208521	p.R263G	1
chr12:22214339	p.E270K	1
chr12:22211515	p.E274K	1
chr12:22215219	p.A47V	1
chr12:22211542	p.K276N	1
chr12:22215238	p.N62S	1
chr12:22199377	p.V279D	1
chr12:22213832	p.K64R	1
chr12:22215252	p.H290H	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB04555	cytidine monophosphate N-acetylneuraminic acid synthetase	experimental	Cytidine-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