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 ZFP36L1

Basic gene info.	Gene symbol	ZFP36L1
	Gene name	ZFP36 ring finger protein-like 1
	Synonyms	BRF1\|Berg36\|ERF-1\|ERF1\|RNF162B\|TIS11B\|cMG1
	Cytomap	UCSC genome browser: 14q22-q24
	Genomic location	chr14 :69254371-69262960
	Type of gene	protein-coding
	RefGenes	NM_001244698.1, NM_001244701.1,NM_004926.3,
	Ensembl id	ENSG00000185650
	Description	EGF-response factor 1butyrate response factor 1early response factor Berg36zinc finger protein 36, C3H type-like 1zinc finger protein 36, C3H1 type-like 1zinc finger protein, C3H type, 36-like 1
	Modification date	20141222
dbXrefs	MIM : 601064
	HGNC : HGNC
	Ensembl : ENSG00000185650
	HPRD : 03041
	Vega : OTTHUMG00000171385
Protein	UniProt: Q07352 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ZFP36L1
	BioGPS: 677
	Gene Expression Atlas: ENSG00000185650
	The Human Protein Atlas: ENSG00000185650
Pathway	NCI Pathway Interaction Database: ZFP36L1
	KEGG: ZFP36L1
	REACTOME: ZFP36L1
	ConsensusPathDB
	Pathway Commons: ZFP36L1
Metabolism	MetaCyc: ZFP36L1
	HUMANCyc: ZFP36L1
Regulation	Ensembl's Regulation: ENSG00000185650
	miRBase: chr14 :69,254,371-69,262,960
	TargetScan: NM_001244698
	cisRED: ENSG00000185650
Context	iHOP: ZFP36L1
	cancer metabolism search in PubMed: ZFP36L1
	UCL Cancer Institute: ZFP36L1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ZFP36L1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ZFP36L1
	Familial Cancer Database: ZFP36L1

* 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 BLCA ⁶, BRCA ⁷,	Therapeutic Vulnerabilities in Cancer⁸

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,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
8Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	601064; gene.
Orphanet
Disease	KEGG Disease: ZFP36L1
	MedGen: ZFP36L1 (Human Medical Genetics with Condition)
	ClinVar: ZFP36L1
Phenotype	MGI: ZFP36L1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ZFP36L1

Mutations for ZFP36L1

* 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	ZFP36L1	chr14	69257970	69257990	ZFP36L1	chr14	69258394	69258414

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 ZFP36L1 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
DA746032	ZFP36L1	1	118	14	69261839	69261956	SMG6	116	563	17	1968369	1972227
BE811922	ZFP36L1	1	185	14	69257716	69257903	LARGE	173	349	22	33777798	33777972
CN312778	TTC26	1	291	7	138818525	138822663	ZFP36L1	286	681	14	69256161	69256556
AF123320	CRIPT	930	2020	2	46844409	46852137	ZFP36L1	2021	2272	14	69255311	69255582
BG568132	ZFP36L1	56	196	14	69255014	69255154	FGB	191	543	4	155491882	155492233
BF382756	ZFP36L1	1	439	14	69255654	69256090	TMED9	434	635	5	177022906	177023107

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=29)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=6)	Stat. for Insertions (# total SNVs=4)

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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
chr14:69256498-69256498	p.E257K	4
chr14:69257025-69257025	p.S81fs*67	3
chr14:69256907-69256907	p.C120*	2
chr14:69259623-69259623	p.F11L	2
chr14:69256854-69256854	p.A138E	2
chr14:69256753-69256753	p.R172C	2
chr14:69256761-69256761	p.Y169S	1
chr14:69257177-69257177	p.S30S	1
chr14:69256404-69256404	p.M288T	1
chr14:69256882-69256882	p.C129G	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	3	3	1	4	1		6		1	2		11	3	2	1	3	5
# mutation	3	3	2	4	1		6		1	2		10	3	2	1	3	5
nonsynonymous SNV	3	3	1	3	1		2			1		6	3			3	2
synonymous SNV			1	1			4		1	1		4		2	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
chr14:69259623	p.Y169C,ZFP36L1	2
chr14:69256498	p.F11L,ZFP36L1	2
chr14:69256761	p.E257K,ZFP36L1	2
chr14:69256784	p.D301V,ZFP36L1	1
chr14:69256333	p.G47G,ZFP36L1	1
chr14:69257036	p.M288T,ZFP36L1	1
chr14:69256577	p.Y169H,ZFP36L1	1
chr14:69256811	p.E15K,ZFP36L1	1
chr14:69256349	p.L278L,ZFP36L1	1
chr14:69257039	p.I164I,ZFP36L1	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 ZFP36L1 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 ZFP36L1

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 ZFP36L1

There's no related Drug.

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Cross referenced IDs for ZFP36L1

* 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