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 ELAVL1

Basic gene info.	Gene symbol	ELAVL1
	Gene name	ELAV like RNA binding protein 1
	Synonyms	ELAV1\|HUR\|Hua\|MelG
	Cytomap	UCSC genome browser: 19p13.2
	Genomic location	chr19 :8023456-8070529
	Type of gene	protein-coding
	RefGenes	NM_001419.2,
	Ensembl id	ENSG00000066044
	Description	ELAV (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 date	20141222
dbXrefs	MIM : 603466
	HGNC : HGNC
	Ensembl : ENSG00000066044
	HPRD : 16025
	Vega : OTTHUMG00000182470
Protein	UniProt: Q15717 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ELAVL1
	BioGPS: 1994
	Gene Expression Atlas: ENSG00000066044
	The Human Protein Atlas: ENSG00000066044
Pathway	NCI Pathway Interaction Database: ELAVL1
	KEGG: ELAVL1
	REACTOME: ELAVL1
	ConsensusPathDB
	Pathway Commons: ELAVL1
Metabolism	MetaCyc: ELAVL1
	HUMANCyc: ELAVL1
Regulation	Ensembl's Regulation: ENSG00000066044
	miRBase: chr19 :8,023,456-8,070,529
	TargetScan: NM_001419
	cisRED: ENSG00000066044
Context	iHOP: ELAVL1
	cancer metabolism search in PubMed: ELAVL1
	UCL Cancer Institute: ELAVL1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ELAVL1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	603466; gene.
Orphanet
Disease	KEGG Disease: ELAVL1
	MedGen: ELAVL1 (Human Medical Genetics with Condition)
	ClinVar: ELAVL1
Phenotype	MGI: ELAVL1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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	ELAVL1	chr19	8046013	8046033	ELAVL1	chr19	8041550	8041570
ovary	ELAVL1	chr19	8051284	8051304	ZNF562	chr19	9773927	9773947
prostate	ELAVL1	chr19	8033862	8035862	ALDH7A1	chr5	125921404	125923404

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 ELAVL1 related fusion information.

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

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=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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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
chr19:8028528-8028528	p.K274E	2
chr19:8046044-8046044	p.N67H	2
chr19:8045966-8045966	p.?	2
chr19:8032655-8032655	p.A150A	2
chr19:8046013-8046013	p.A77V	2
chr19:8056590-8056590	p.R37Q	2
chr19:8028639-8028639	p.P237S	2
chr19:8038746-8038746	p.P98L	1
chr19:8028518-8028518	p.R277H	1
chr19:8046039-8046039	p.Y68Y	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	2	3		9	1		1		1			6	1				1	8	1	6
# mutation	2	3		8	1		1		1			7	1				1	8	1	6
nonsynonymous SNV	1	2		5	1		1		1			6					1	7		4
synonymous SNV	1	1		3								1	1					1	1	2

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
chr19:8046013	p.A77V	2
chr19:8056648	p.G18W	2
chr19:8028533	p.N272S	2
chr19:8056644	p.A150A	1
chr19:8028518	p.E11K	1
chr19:8032470	p.G268D	1
chr19:8032481	p.V122L	1
chr19:8046018	p.D256D	1
chr19:8056669	p.E101G	1
chr19:8028545	p.A255A	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 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

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


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

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 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