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 ELAVL1
Basic gene info.Gene symbolELAVL1
Gene nameELAV like RNA binding protein 1
SynonymsELAV1|HUR|Hua|MelG
CytomapUCSC genome browser: 19p13.2
Genomic locationchr19 :8023456-8070529
Type of geneprotein-coding
RefGenesNM_001419.2,
Ensembl idENSG00000066044
DescriptionELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)ELAV-like protein 1Hu antigen Rembryonic lethal, abnormal vision, drosophila, homolog-like 1hu-antigen R
Modification date20141222
dbXrefs MIM : 603466
HGNC : HGNC
Ensembl : ENSG00000066044
HPRD : 16025
Vega : OTTHUMG00000182470
ProteinUniProt: Q15717
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ELAVL1
BioGPS: 1994
Gene Expression Atlas: ENSG00000066044
The Human Protein Atlas: ENSG00000066044
PathwayNCI Pathway Interaction Database: ELAVL1
KEGG: ELAVL1
REACTOME: ELAVL1
ConsensusPathDB
Pathway Commons: ELAVL1
MetabolismMetaCyc: ELAVL1
HUMANCyc: ELAVL1
RegulationEnsembl's Regulation: ENSG00000066044
miRBase: chr19 :8,023,456-8,070,529
TargetScan: NM_001419
cisRED: ENSG00000066044
ContextiHOP: ELAVL1
cancer metabolism search in PubMed: ELAVL1
UCL Cancer Institute: ELAVL1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ELAVL1 in cancer cell metabolism1. Chou SD, Murshid A, Eguchi T, Gong J, Calderwood SK (2015) HSF1 regulation of beta-catenin in mammary cancer cells through control of HuR/elavL1 expression. Oncogene 34: 2178-2188. doi: 10.1038/onc.2014.177. pmid: 4275421. go to article
2. Degese MS, Tanos T, Naipauer J, Gingerich T, Chiappe D, et al. (2015) An interplay between the p38 MAPK pathway and AUBPs regulates c-fos mRNA stability during mitogenic stimulation. Biochem J 467: 77-90. doi: 10.1042/BJ20141100. go to article

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Phenotypic Information for ELAVL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ELAVL1
Familial Cancer Database: ELAVL1
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 603466; gene.
Orphanet
DiseaseKEGG Disease: ELAVL1
MedGen: ELAVL1 (Human Medical Genetics with Condition)
ClinVar: ELAVL1
PhenotypeMGI: ELAVL1 (International Mouse Phenotyping Consortium)
PhenomicDB: ELAVL1

Mutations for ELAVL1
* 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
ovaryELAVL1chr1980460138046033ELAVL1chr1980415508041570
ovaryELAVL1chr1980512848051304ZNF562chr1997739279773947
prostateELAVL1chr1980338628035862ALDH7A1chr5125921404125923404
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 ELAVL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=34)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr19:8028639-8028639p.P237S2
chr19:8028528-8028528p.K274E2
chr19:8046044-8046044p.N67H2
chr19:8045966-8045966p.?2
chr19:8032655-8032655p.A150A2
chr19:8046013-8046013p.A77V2
chr19:8056590-8056590p.R37Q2
chr19:8056617-8056617p.P28L1
chr19:8032481-8032481p.G208G1
chr19:8028474-8028474p.M292V1

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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
# sample23 91 1 1  61   1816
# mutation23 81 1 1  71   1816
nonsynonymous SNV12 51 1 1  6    17 4
synonymous SNV11 3       11    112
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
chr19:8046013p.N272S2
chr19:8028533p.G18W2
chr19:8056648p.A77V2
chr19:8028686p.M292V1
chr19:8038675p.E177E1
chr19:8028472p.T20M1
chr19:8056617p.R277L1
chr19:8032455p.R157W1
chr19:8038737p.R19K1
chr19:8028474p.D155H1

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 ELAVL1 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 ELAVL1

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

AURKB,AUNIP,CDC25A,CDCA3,CDCA8,CENPA,ELAVL1,
HJURP,KHSRP,NDC80,NOP58,PDSS1,RAD54L,RAVER1,
RNASEH2A,SKA1,SKA3,SNRPD1,STMN1,TIMM44,TTK
ATXN10,RHNO1,CNOT11,CKS2,COPZ1,EBPL,ELAVL1,
ENOPH1,H3F3A,HDAC2,HMGN1,HNRNPA1,HPRT1,MYCBP,
OSTC,PERP,PEX11B,PPA2,PPIL1,PRMT6,SNRPE

C19orf43,CARM1,CHERP,CLPP,DAZAP1,DOHH,ELAVL1,
FARSA,HDGFRP2,HNRNPL,MBD3,PPAN,PTBP1,RAD23A,
RAVER1,RNASEH2A,SF3A2,SGTA,SNRPA,TMEM161A,TOMM40
BMS1,DHX9,DOHH,EIF3B,EIF4G1,ELAVL1,GSPT1,
HNRNPM,HNRNPU,KHSRP,NOC2L,RANGAP1,RBM14,SAFB,
SF3B3,SFPQ,SLC7A1,SRRT,SYNCRIP,TMEM201,VARS
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 ELAVL1


There's no related Drug.
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Cross referenced IDs for ELAVL1
* 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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