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 RORA
Basic gene info.Gene symbolRORA
Gene nameRAR-related orphan receptor A
SynonymsNR1F1|ROR1|ROR2|ROR3|RZR-ALPHA|RZRA
CytomapUCSC genome browser: 15q22.2
Genomic locationchr15 :60780482-60884707
Type of geneprotein-coding
RefGenesNM_002943.3,
NM_134260.2,NM_134261.2,NM_134262.2,
Ensembl idENSG00000069667
DescriptionROR-alphanuclear receptor ROR-alphanuclear receptor RZR-alphanuclear receptor subfamily 1 group F member 1retinoic acid receptor-related orphan receptor alpharetinoid-related orphan receptor alphathyroid hormone nuclear receptor alpha variant 4tran
Modification date20141222
dbXrefs MIM : 600825
HGNC : HGNC
Ensembl : ENSG00000069667
HPRD : 02896
Vega : OTTHUMG00000132769
ProteinUniProt: P35398
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RORA
BioGPS: 6095
Gene Expression Atlas: ENSG00000069667
The Human Protein Atlas: ENSG00000069667
PathwayNCI Pathway Interaction Database: RORA
KEGG: RORA
REACTOME: RORA
ConsensusPathDB
Pathway Commons: RORA
MetabolismMetaCyc: RORA
HUMANCyc: RORA
RegulationEnsembl's Regulation: ENSG00000069667
miRBase: chr15 :60,780,482-60,884,707
TargetScan: NM_002943
cisRED: ENSG00000069667
ContextiHOP: RORA
cancer metabolism search in PubMed: RORA
UCL Cancer Institute: RORA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 600825; gene.
Orphanet
DiseaseKEGG Disease: RORA
MedGen: RORA (Human Medical Genetics with Condition)
ClinVar: RORA
PhenotypeMGI: RORA (International Mouse Phenotyping Consortium)
PhenomicDB: RORA

Mutations for RORA
* 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
haematopoietic_and_lymphoid_tissueRORAchr156080833560808335chr176806001768060017
ovaryRORAchr156083560760835627chr152010198120102001
ovaryRORAchr156084634260846362chr158961040289610422
ovaryRORAchr156085213160852151RORAchr156085361660853636
pancreasRORAchr156083077360830793RORAchr156083167060831690
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 RORA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF858891RORA14363156137165761372006KLK3353447195136368051363778
BF091671MRO15241184832174248321967RORA229472156147394561474188
CV392982RORA10310156134340261343701BAI330553566935280869353038

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2         2  1   
GAIN (# sample)1         1  1   
LOSS (# sample)1         1      
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=1)

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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
chr15:60795033-60795033p.R403H3
chr15:60919533-60919533p.E14G2
chr15:60919479-60919479p.R32I2
chr15:60803679-60803679p.S222L2
chr15:60919495-60919495p.R27*2
chr15:60803461-60803461p.G295S2
chr15:60919521-60919521p.P18L2
chr15:60795067-60795067p.?1
chr15:60850430-60850430p.G71G1
chr15:60803546-60803546p.G266G1

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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
# sample11 6  1 21 832  45 12
# mutation11 5  1 21 932  35 14
nonsynonymous SNV 1 4  1 11 632  24 11
synonymous SNV1  1    1  3    11 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
chr15:60919533p.E14G,RORA2
chr15:60970872p.T60T2
chr15:60919479p.R32T,RORA2
chr15:60919521p.P18L,RORA2
chr15:60803725p.R312K,RORA1
chr15:60850430p.R64Q,RORA1
chr15:60795042p.L300I,RORA1
chr15:60803735p.T51S,RORA1
chr15:60789657p.G4E,RORA1
chr15:60907114p.Q223R,RORA1

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 RORA 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 RORA

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

ABCA6,AKAP13,CREBRF,DENND4A,DPP8,ELK3,FEM1B,
FOXN3,KCTD12,LRCH1,MYO9A,PCNX,PIAS1,RAB8B,
RORA,PEAK1,TBC1D2B,TCF4,VPS13C,ZEB1,ZEB2
AHCYL2,CEP85L,CUL5,DENND2C,DPP8,CCSER2,HECTD1,
HERC1,IBTK,KIAA2018,LOC729082,MEF2A,NEDD4,OTUD4,
PPTC7,PYGO1,RORA,SOS2,TNKS2,USP15,WDR47

A2M,AKAP2,AMOTL1,ARHGEF6,ATP8B2,DAAM2,FILIP1L,
IL6ST,ITPR1,LBH,MAF,NR3C1,PLCL1,PTPLAD2,
PTPRM,RORA,SLC9A9,SYT11,TCF4,WIPF1,ZIK1
ABCA3,EFS,ENO2,FGFR1,HSPA12A,KCNIP3,KCTD7,
KLC1,LIX1L,NCAM1,NFIA,POU6F1,RIC3,RORA,
SLC12A4,SLC45A1,SLC4A3,SYT11,TCF7L1,TMEM43,TRO
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 RORA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P35398; -.
ChemistryChEMBL CHEMBL5868; -.
ChemistryGuidetoPHARMACOLOGY 598; -.
Organism-specific databasesPharmGKB PA34630; -.
Organism-specific databasesCTD 6095; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00709RAR-related orphan receptor Aapproved; investigationalLamivudine


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Cross referenced IDs for RORA
* 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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