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 CNOT2

Basic gene info.	Gene symbol	CNOT2
	Gene name	CCR4-NOT transcription complex, subunit 2
	Synonyms	CDC36\|NOT2\|NOT2H
	Cytomap	UCSC genome browser: 12q15
	Genomic location	chr12 :70637493-70748773
	Type of gene	protein-coding
	RefGenes	NM_001199302.1, NM_001199303.1,NM_014515.5,NR_037615.1,
	Ensembl id	ENSG00000111596
	Description	CCR4-NOT transcription complex subunit 2CCR4-associated factor 2negative regulator of transcription 2
	Modification date	20141207
dbXrefs	MIM : 604909
	HGNC : HGNC
	Ensembl : ENSG00000111596
	HPRD : 05367
	Vega : OTTHUMG00000169481
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CNOT2
	BioGPS: 4848
	Gene Expression Atlas: ENSG00000111596
	The Human Protein Atlas: ENSG00000111596
Pathway	NCI Pathway Interaction Database: CNOT2
	KEGG: CNOT2
	REACTOME: CNOT2
	ConsensusPathDB
	Pathway Commons: CNOT2
Metabolism	MetaCyc: CNOT2
	HUMANCyc: CNOT2
Regulation	Ensembl's Regulation: ENSG00000111596
	miRBase: chr12 :70,637,493-70,748,773
	TargetScan: NM_001199302
	cisRED: ENSG00000111596
Context	iHOP: CNOT2
	cancer metabolism search in PubMed: CNOT2
	UCL Cancer Institute: CNOT2
Assigned class in ccmGDB	C

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Phenotypic Information for CNOT2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CNOT2
	Familial Cancer Database: CNOT2

* 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
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: CNOT2
	MedGen: CNOT2 (Human Medical Genetics with Condition)
	ClinVar: CNOT2
Phenotype	MGI: CNOT2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CNOT2

Mutations for CNOT2

* 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

* 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	CNOT2	chr12	70650450	70650470		chr15	27825113	27825133
ovary	CNOT2	chr12	70659511	70659531	CNOT2	chr12	70659270	70659290
ovary	CNOT2	chr12	70681821	70681841	CNOT2	chr12	70681953	70681973

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 CNOT2 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
AA071465	FAU	22	74	11	64888102	64888154	CNOT2	66	491	12	70747715	70748140
AF130057	CNOT2	1	2594	12	70715461	70718054	AHSG	2584	2860	3	186338832	186339107
BC008476	PCDH9	1	1019	13	67748432	67749456	CNOT2	1018	1205	12	70677266	70677455

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=54)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr12:70723257-70723257	p.R98H	4
chr12:70724190-70724190	p.S170S	3
chr12:70747693-70747693	p.*541K	3
chr12:70739968-70739968	p.R467H	2
chr12:70704760-70704760	p.S45N	2
chr12:70723292-70723292	p.V110I	2
chr12:70723313-70723313	p.P117T	2
chr12:70672044-70672044	p.R13I	2
chr12:70723334-70723334	p.P124S	2
chr12:70735907-70735907	p.A400V	2

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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		2		5	1				1	1		5	4	1			3	4	1	10
# mutation		2		6	2				1	1		6	4	1			3	4	1	10
nonsynonymous SNV		2		4	2				1			4	3	1			2	4		7
synonymous SNV				2						1		2	1				1		1	3

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
chr12:70724190	p.S170S,CNOT2	3
chr12:70672044	p.R13I,CNOT2	2
chr12:70735907	p.V110I,CNOT2	2
chr12:70704760	p.A400V,CNOT2	2
chr12:70723292	p.S45N,CNOT2	2
chr12:70732321	p.R98C,CNOT2	1
chr12:70704789	p.K333K,CNOT2	1
chr12:70724100	p.G103S,CNOT2	1
chr12:70732322	p.G334W,CNOT2	1
chr12:70713103	p.G103D,CNOT2	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 CNOT2 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 CNOT2

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


CAND1,CCT2,CNOT2,CPSF6,DEFB128,FRS2,LEMD3, MDM1,MDM2,NUP107,RAB21,RAB3IP,RAP1B,SLC35E3, TBC1D15,TBK1,THAP2,TMBIM4,TMEM19,YEATS4,ZFC3H1	CAND1,CCDC60,CNOT2,DCAF10,DQX1,ELAVL3,FRS2, GRIP1,HELB,ITFG1,LOC653544,MDM2,MS4A8,NUP107, OR4F17,RAB3IP,SLC35E3,VPS35,YEATS4,ZFC3H1,ZMYM2

ACTR6,ATXN7L3B,BRAP,CAND1,CNOT2,CPSF6,DENR, FBXO21,FRS2,KIAA1033,KRR1,METAP2,PLEKHA5,PRDM4, RAB3IP,RNF34,SCYL2,SCAF11,TDG,VEZT,ZNF664	ACTR2,CNOT11,CMAS,CNOT2,CXorf56,EXOC1,GDAP2, GPBP1,IFT74,C2CD5,LACTB,MTF2,NLK,NSUN3, PGGT1B,PPP2R5A,PWWP2A,RAB14,RFFL,SLC38A9,TBL1XR1

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 CNOT2

There's no related Drug.

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Cross referenced IDs for CNOT2

* 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