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 CNOT7

Basic gene info.	Gene symbol	CNOT7
	Gene name	CCR4-NOT transcription complex, subunit 7
	Synonyms	CAF1\|Caf1a\|hCAF-1
	Cytomap	UCSC genome browser: 8p22-p21.3
	Genomic location	chr8 :17089021-17104387
	Type of gene	protein-coding
	RefGenes	NM_013354.5, NM_054026.2,
	Ensembl id	ENSG00000198791
	Description	BTG1 binding factor 1BTG1-binding factor 1CAF-1CCR4-NOT transcription complex subunit 7CCR4-associated factor 1carbon catabolite repressor protein (CCR4)-associative factor 1
	Modification date	20141207
dbXrefs	MIM : 604913
	HGNC : HGNC
	Ensembl : ENSG00000198791
	Vega : OTTHUMG00000096971
Protein	UniProt: Q9UIV1 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CNOT7
	BioGPS: 29883
	Gene Expression Atlas: ENSG00000198791
	The Human Protein Atlas: ENSG00000198791
Pathway	NCI Pathway Interaction Database: CNOT7
	KEGG: CNOT7
	REACTOME: CNOT7
	ConsensusPathDB
	Pathway Commons: CNOT7
Metabolism	MetaCyc: CNOT7
	HUMANCyc: CNOT7
Regulation	Ensembl's Regulation: ENSG00000198791
	miRBase: chr8 :17,089,021-17,104,387
	TargetScan: NM_013354
	cisRED: ENSG00000198791
Context	iHOP: CNOT7
	cancer metabolism search in PubMed: CNOT7
	UCL Cancer Institute: CNOT7
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of CNOT7 in cancer cell metabolism	1. Chapat C, Kolytcheff C, Le Romancer M, Auboeuf D, De La Grange P, et al. (2013) hCAF1/CNOT7 regulates interferon signalling by targeting STAT1. EMBO J 32: 688-700. doi: 10.1038/emboj.2013.11. pmid: 3594750. go to article 2. Winkler GS (2010) The mammalian anti-proliferative BTG/Tob protein family. J Cell Physiol 222: 66-72. doi: 10.1002/jcp.21919. go to article 3. Maragozidis P, Karangeli M, Labrou M, Dimoulou G, Papaspyrou K, et al. (2012) Alterations of deadenylase expression in acute leukemias: evidence for poly(a)-specific ribonuclease as a potential biomarker. Acta Haematol 128: 39-46. doi: 10.1159/000337418. go to article

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Phenotypic Information for CNOT7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CNOT7
	Familial Cancer Database: CNOT7

* 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	604913; gene.
Orphanet
Disease	KEGG Disease: CNOT7
	MedGen: CNOT7 (Human Medical Genetics with Condition)
	ClinVar: CNOT7
Phenotype	MGI: CNOT7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CNOT7

Mutations for CNOT7

* 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

* 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
breast	CNOT7	chr8	17099418	17099418	VPS37A	chr8	17122633	17122633

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 CNOT7 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
BM749134	MAT2A	14	119	2	85766291	85766396	CNOT7	116	538	8	17100571	17104270
DB368876	TUBA1B	1	131	12	49521569	49521699	CNOT7	132	523	8	17087282	17087676

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr8:17102580-17102580	p.R28C	3
chr8:17092286-17092286	p.R186Q	2
chr8:17094725-17094725	p.H157Y	2
chr8:17090016-17090016	p.E217Q	2
chr8:17094735-17094735	p.W153*	2
chr8:17094764-17094764	p.G144*	1
chr8:17102635-17102635	p.S9R	1
chr8:17090042-17090042	p.G208V	1
chr8:17094768-17094768	p.T142T	1
chr8:17102661-17102661	p.M1V	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=2

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				5								4	1				2	4	1	5
# mutation				5								6	1				2	4	1	5
nonsynonymous SNV				4								5	1				2	3	1	4
synonymous SNV				1								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
chr8:17092286	p.R28C,CNOT7	2
chr8:17102580	p.R220L,CNOT7	2
chr8:17090006	p.R186Q,CNOT7	2
chr8:17102568	p.N171N,CNOT7	1
chr8:17092325	p.N171T,CNOT7	1
chr8:17102606	p.Y164C,CNOT7	1
chr8:17092330	p.H157Y,CNOT7	1
chr8:17102653	p.W153C,CNOT7	1
chr8:17088235	p.T142T,CNOT7	1
chr8:17092331	p.Y88H,CNOT7	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 CNOT7 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 CNOT7

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


AGPAT5,CCDC25,CNOT7,ELP3,ENTPD4,ERI1,FZD3, INTS10,INTS9,KCTD9,LONRF1,MCPH1,MTMR9,PCM1, PPP2R2A,RPL23AP53,TNKS,TUSC3,VPS37A,WRN,XPO7	AASDHPPT,C5orf22,CNOT7,CSE1L,ABHD17B,FAM175B,LAMTOR3, MATR3,MTPAP,ORC4,PPP1CB,RBM18,RCHY1,RWDD4, SLC30A9,SMAD4,TADA1,TIPRL,UBQLN2,VTA1,ZNF639

AGPAT5,BIN3,CCDC25,CHMP7,CNOT7,DCTN6,ELP3, ERI1,FBXO25,GTF2E2,INTS10,INTS9,MCPH1,NEIL2, PBK,PCM1,POLR3D,PPP2R2A,R3HCC1,VPS37A,XPO7	C11orf1,FOPNL,CCNG1,CNOT7,CNOT8,CPNE3,CRLS1, DPY19L4,EBAG9,EIF2A,EIF3M,GPR160,HSDL2,METTL9, SVIP,TATDN1,TM2D2,TOMM20,TXNDC12,ZNF480,ZNF586

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 CNOT7

There's no related Drug.

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Cross referenced IDs for CNOT7

* 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