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 symbolZFP36L1
Gene nameZFP36 ring finger protein-like 1
SynonymsBRF1|Berg36|ERF-1|ERF1|RNF162B|TIS11B|cMG1
CytomapUCSC genome browser: 14q22-q24
Genomic locationchr14 :69254371-69262960
Type of geneprotein-coding
RefGenesNM_001244698.1,
NM_001244701.1,NM_004926.3,
Ensembl idENSG00000185650
DescriptionEGF-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 date20141222
dbXrefs MIM : 601064
HGNC : HGNC
Ensembl : ENSG00000185650
HPRD : 03041
Vega : OTTHUMG00000171385
ProteinUniProt: Q07352
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ZFP36L1
BioGPS: 677
Gene Expression Atlas: ENSG00000185650
The Human Protein Atlas: ENSG00000185650
PathwayNCI Pathway Interaction Database: ZFP36L1
KEGG: ZFP36L1
REACTOME: ZFP36L1
ConsensusPathDB
Pathway Commons: ZFP36L1
MetabolismMetaCyc: ZFP36L1
HUMANCyc: ZFP36L1
RegulationEnsembl's Regulation: ENSG00000185650
miRBase: chr14 :69,254,371-69,262,960
TargetScan: NM_001244698
cisRED: ENSG00000185650
ContextiHOP: ZFP36L1
cancer metabolism search in PubMed: ZFP36L1
UCL Cancer Institute: ZFP36L1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ZFP36L1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 601064; gene.
Orphanet
DiseaseKEGG Disease: ZFP36L1
MedGen: ZFP36L1 (Human Medical Genetics with Condition)
ClinVar: ZFP36L1
PhenotypeMGI: ZFP36L1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryZFP36L1chr146925797069257990ZFP36L1chr146925839469258414
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ZFP36L1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA746032ZFP36L11118146926183969261956SMG61165631719683691972227
BE811922ZFP36L11185146925771669257903LARGE173349223377779833777972
CN312778TTC2612917138818525138822663ZFP36L1286681146925616169256556
AF123320CRIPT930202024684440946852137ZFP36L120212272146925531169255582
BG568132ZFP36L156196146925501469255154FGB1915434155491882155492233
BF382756ZFP36L11439146925565469256090TMED94346355177022906177023107

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr14:69256498-69256498p.E257K4
chr14:69257025-69257025p.S81fs*673
chr14:69256907-69256907p.C120*2
chr14:69259623-69259623p.F11L2
chr14:69256854-69256854p.A138E2
chr14:69256753-69256753p.R172C2
chr14:69256684-69256684p.R195C1
chr14:69257027-69257039p.P77fs*671
chr14:69256759-69256759p.G170W1
chr14:69257173-69257174p.G32fs*431

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample33141 6 12 1132135   
# mutation33241 6 12 1032135   
nonsynonymous SNV33131 2  1 63  32   
synonymous SNV  11  4 11 4 21 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr14:69259623p.Y169C,ZFP36L12
chr14:69256498p.F11L,ZFP36L12
chr14:69256761p.E257K,ZFP36L12
chr14:69256565p.T320T,ZFP36L11
chr14:69256775p.A186T,ZFP36L11
chr14:69256314p.P105S,ZFP36L11
chr14:69257020p.P319T,ZFP36L11
chr14:69256568p.R183G,ZFP36L11
chr14:69256784p.G94G,ZFP36L11
chr14:69256333p.S318F,ZFP36L11

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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