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 ZFP36

Basic gene info.	Gene symbol	ZFP36
	Gene name	ZFP36 ring finger protein
	Synonyms	G0S24\|GOS24\|NUP475\|RNF162A\|TIS11\|TTP\|zfp-36
	Cytomap	UCSC genome browser: 19q13.1
	Genomic location	chr19 :39897486-39900045
	Type of gene	protein-coding
	RefGenes	NM_003407.3,
	Ensembl id	ENSG00000128016
	Description	G0/G1 switch regulatory protein 24growth factor-inducible nuclear protein NUP475tristetraprolintristetraprolinezinc finger protein 36 homologzinc finger protein 36, C3H type, homologzinc finger protein, C3H type, 36 homolog
	Modification date	20141207
dbXrefs	MIM : 190700
	HGNC : HGNC
	Ensembl : ENSG00000128016
	HPRD : 01835
	Vega : OTTHUMG00000182970
Protein	UniProt: P26651 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ZFP36
	BioGPS: 7538
	Gene Expression Atlas: ENSG00000128016
	The Human Protein Atlas: ENSG00000128016
Pathway	NCI Pathway Interaction Database: ZFP36
	KEGG: ZFP36
	REACTOME: ZFP36
	ConsensusPathDB
	Pathway Commons: ZFP36
Metabolism	MetaCyc: ZFP36
	HUMANCyc: ZFP36
Regulation	Ensembl's Regulation: ENSG00000128016
	miRBase: chr19 :39,897,486-39,900,045
	TargetScan: NM_003407
	cisRED: ENSG00000128016
Context	iHOP: ZFP36
	cancer metabolism search in PubMed: ZFP36
	UCL Cancer Institute: ZFP36
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ZFP36(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ZFP36
	Familial Cancer Database: ZFP36

* 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	190700; gene.
Orphanet
Disease	KEGG Disease: ZFP36
	MedGen: ZFP36 (Human Medical Genetics with Condition)
	ClinVar: ZFP36
Phenotype	MGI: ZFP36 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ZFP36

Mutations for ZFP36

* 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
ovary	ZFP36	chr19	39898319	39898339	ZFP36	chr19	39898378	39898398
pancreas	ZFP36	chr19	39899401	39899421		chr19	39901891	39901911

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 ZFP36 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
AI927524	FUT5	1	116	19	5894691	5894806	ZFP36	113	357	19	39898797	39899042
BF930057	ZFP36	24	332	19	39899509	39899819	YY1AP1	329	549	1	155629534	155629754
AM287184	MYC	1	1432	8	128749879	128751310	ZFP36	1431	1646	19	39898260	39898475
BF853292	ATP1A1	1	102	1	116943296	116943397	ZFP36	99	202	19	39898812	39898915
BF511918	PAK4	18	68	19	39669996	39670046	ZFP36	62	197	19	39898643	39898778
BF094229	SLC12A8	23	184	3	124990872	124991033	ZFP36	175	356	19	39899528	39899709
BM990034	PSMB7	18	224	9	127115749	127115955	ZFP36	222	621	19	39899603	39900002

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=23)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr19:39899054-39899054	p.F232L	1
chr19:39899332-39899332	p.S325Y	1
chr19:39898393-39898393	p.S12*	1
chr19:39898789-39898789	p.T144R	1
chr19:39899071-39899071	p.L240fs*>87	1
chr19:39899333-39899333	p.S325S	1
chr19:39898403-39898403	p.P15P	1
chr19:39898869-39898869	p.D171Y	1
chr19:39899088-39899088	p.D244Y	1
chr19:39899334-39899334	p.E326K	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			4			1		5	1	1	1		1	1	1	1
# mutation	1		1	1			4			1		5	1	1	1		1	1	1	2
nonsynonymous SNV	1		1	1			3					3		1			1	1	1	1
synonymous SNV							1			1		2	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
chr19:39898488	p.S27Y	1
chr19:39898933	p.P287T	1
chr19:39898530	p.S41L	1
chr19:39899054	p.E332K	1
chr19:39898586	p.D50Y	1
chr19:39899162	p.S64T	1
chr19:39898592	p.F82F	1
chr19:39899199	p.P84P	1
chr19:39898698	p.E120K	1
chr19:39899334	p.R144H	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 ZFP36 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 ZFP36

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


CYR61,EGR1,EVC,GAS7,GEM,GLI2,GPR124, ITPRIP,JUN,LRP1,MFAP4,PEAR1,PHLDB1,PODN, RHOJ,TGFB3,TSHZ3,YAP1,ZFP36,ZFP36L1,ZFP36L2	ATF3,BCL10,CHIC2,CXCL2,DUSP1,DUSP5,EGR1, FOS,ID2,LPAR6,NFKBIZ,NR4A2,PTGS2,RAB2B, SERTAD2,TBPL1,TMEM170A,TNFSF10,TUBD1,TUBE1,ZFP36L1

ATXN1,BICC1,BMPR2,ELK3,FAM26E,FILIP1L,GEM, HIVEP2,ISLR,PPP1R18,KLF7,LCA5,LRRC32,LTBP1, MFRP,RUNX1,SULF1,TSHZ3,ZFP36L1,ZNF362,ZNF532	CHST3,DLG2,DZIP1,EFS,HSPA12A,IPW,MPPED2, NCAM1,NLGN2,NLGN3,NPR2,PEG3,PLXNB3,PRIMA1, SCN2B,SLC4A3,TCF7L1,TRO,WASF1,WHAMMP2,ZFP36L1

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 ZFP36

There's no related Drug.

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Cross referenced IDs for ZFP36

* 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