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 CNOT8

Basic gene info.	Gene symbol	CNOT8
	Gene name	CCR4-NOT transcription complex, subunit 8
	Synonyms	CAF1\|CALIF\|Caf1b\|POP2\|hCAF1
	Cytomap	UCSC genome browser: 5q31-q33
	Genomic location	chr5 :154238197-154256352
	Type of gene	protein-coding
	RefGenes	NM_001301073.1, NM_001301074.1,NM_001301075.1,NM_001301077.1,NM_001301080.1, NM_001301082.1,NM_001301083.1,NM_001301086.1,NM_004779.5,
	Ensembl id	ENSG00000155508
	Description	CAF1-like proteinCAF2CALIFpCCR4-NOT transcription complex subunit 8CCR4-associated factor 8PGK promoter directed over production
	Modification date	20141207
dbXrefs	MIM : 603731
	HGNC : HGNC
	Ensembl : ENSG00000155508
	HPRD : 07225
	Vega : OTTHUMG00000130192
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CNOT8
	BioGPS: 9337
	Gene Expression Atlas: ENSG00000155508
	The Human Protein Atlas: ENSG00000155508
Pathway	NCI Pathway Interaction Database: CNOT8
	KEGG: CNOT8
	REACTOME: CNOT8
	ConsensusPathDB
	Pathway Commons: CNOT8
Metabolism	MetaCyc: CNOT8
	HUMANCyc: CNOT8
Regulation	Ensembl's Regulation: ENSG00000155508
	miRBase: chr5 :154,238,197-154,256,352
	TargetScan: NM_001301073
	cisRED: ENSG00000155508
Context	iHOP: CNOT8
	cancer metabolism search in PubMed: CNOT8
	UCL Cancer Institute: CNOT8
Assigned class in ccmGDB	C

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Phenotypic Information for CNOT8(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CNOT8
	Familial Cancer Database: CNOT8

* 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: CNOT8
	MedGen: CNOT8 (Human Medical Genetics with Condition)
	ClinVar: CNOT8
Phenotype	MGI: CNOT8 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CNOT8

Mutations for CNOT8

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CNOT8 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
BE720800	MALAT1	10	110	11	65268014	65268112	CNOT8	93	295	5	154242795	154244793
AW015591	JUND	1	142	19	18390987	18391128	CNOT8	137	296	5	154238456	154238615
BG979616	PLEKHA6	13	190	1	204210536	204210919	CNOT8	185	311	5	154240133	154240259
BF901254	CNOT8	11	369	5	154244520	154244876	GOLGB1	361	465	3	121411199	121411303
BF063953	JUND	1	144	19	18390986	18391128	CNOT8	139	397	5	154238357	154238615

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr5:154254952-154254952	p.Q278*	2
chr5:154250219-154250219	p.?	1
chr5:154252121-154252121	p.A213A	1
chr5:154250221-154250221	p.T104T	1
chr5:154252129-154252129	p.L216*	1
chr5:154250226-154250226	p.D106G	1
chr5:154252171-154252172	p.D230fs*11	1
chr5:154242857-154242857	p.E7K	1
chr5:154250228-154250228	p.M107V	1
chr5:154252176-154252176	p.L232fs*2	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	1	1		1	1		2					1						1		3
# mutation	1	1		1	1		2					1						1		3
nonsynonymous SNV	1	1		1	1		2											1		3
synonymous SNV												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
chr5:154250226	p.D106G	2
chr5:154252115	p.E84K	1
chr5:154254903	p.M107V	1
chr5:154254920	p.A117V	1
chr5:154244884	p.N118I	1
chr5:154250228	p.G144E	1
chr5:154250259	p.R173H	1
chr5:154250262	p.F188L	1
chr5:154250340	p.E211D	1
chr5:154251334	p.G261G	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 CNOT8 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 CNOT8

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


C5orf15,CEP120,CNOT8,CSNK1A1,CSNK1G3,DCTN4,FAM114A2, FBXL17,FBXO38,GIN1,KDM3B,MATR3,MFAP3,PGGT1B, PJA2,PWWP2A,RBM22,RBM27,SLU7,SMAD5,ZCCHC10	ATG5,BET1,CMPK1,CNOT8,DTWD1,EXOC1,GOLPH3, NUP54,NXT2,PAPD4,PDCD10,SMAD2,SPTLC1,SSR1, TCEA1,TMEM128,TMEM167B,TMEM50A,UFM1,VPS26A,YIPF5

C5orf24,TRAPPC13,CNOT8,CRBN,FBXO38,HINT1,MAT2B, MATR3,MED7,RBM22,RNF14,RPS14,SREK1IP1,SKP1, SLU7,SRP9,TAF7,TTC1,UBE2B,ZCCHC10,ZNF627	ASF1A,DHRS4-AS1,METTL23,C6orf57,TRIQK,CLNS1A,CNOT8, CRLS1,DUSP11,EBAG9,FAM60A,ISCA2,LIAS,NXT2, PEX11B,RCHY1,SLC35A1,TBPL1,TGDS,TMEM69,TXNDC12

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 CNOT8

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
DB01033	CCR4-NOT transcription complex, subunit 8	approved	Mercaptopurine
DB00563	CCR4-NOT transcription complex, subunit 8	approved	Methotrexate

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Cross referenced IDs for CNOT8

* 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