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 WDR77
Basic gene info.Gene symbolWDR77
Gene nameWD repeat domain 77
SynonymsMEP-50|MEP50|Nbla10071|p44|p44/Mep50
CytomapUCSC genome browser: 1p13.2
Genomic locationchr1 :111982511-111991830
Type of geneprotein-coding
RefGenesNM_024102.2,
Ensembl idENSG00000116455
DescriptionWD repeat-containing protein 77androgen receptor cofactor p44methylosome protein 50
Modification date20141207
dbXrefs MIM : 611734
HGNC : HGNC
Ensembl : ENSG00000116455
HPRD : 14387
Vega : OTTHUMG00000011748
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_WDR77
BioGPS: 79084
Gene Expression Atlas: ENSG00000116455
The Human Protein Atlas: ENSG00000116455
PathwayNCI Pathway Interaction Database: WDR77
KEGG: WDR77
REACTOME: WDR77
ConsensusPathDB
Pathway Commons: WDR77
MetabolismMetaCyc: WDR77
HUMANCyc: WDR77
RegulationEnsembl's Regulation: ENSG00000116455
miRBase: chr1 :111,982,511-111,991,830
TargetScan: NM_024102
cisRED: ENSG00000116455
ContextiHOP: WDR77
cancer metabolism search in PubMed: WDR77
UCL Cancer Institute: WDR77
Assigned class in ccmGDBC

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Phenotypic Information for WDR77(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: WDR77
Familial Cancer Database: WDR77
* 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_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: WDR77
MedGen: WDR77 (Human Medical Genetics with Condition)
ClinVar: WDR77
PhenotypeMGI: WDR77 (International Mouse Phenotyping Consortium)
PhenomicDB: WDR77

Mutations for WDR77
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows WDR77 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA428438WDR7711261111985296111985982WDR771214061111983302111984662
BE312794WDR7714781111983976111990072HERPUD1478735165697610956977254

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=12)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr1:111984672-111984672p.V282M2
chr1:111983962-111983962p.P307S1
chr1:111990200-111990200p.?1
chr1:111991257-111991257p.L95L1
chr1:111985955-111985955p.V227V1
chr1:111991285-111991285p.L86P1
chr1:111983882-111983882p.P333P1
chr1:111985985-111985985p.S217S1
chr1:111991297-111991297p.G82E1
chr1:111983884-111983884p.P333S1

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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
# sample2  1  3 2  4   12  6
# mutation2  1  3 2  4   12  6
nonsynonymous SNV1     2 1  3   12  3
synonymous SNV1  1  1 1  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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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
chr1:111985333p.R164Q1
chr1:111991351p.L154R1
chr1:111985355p.K150K1
chr1:111991375p.P333P1
chr1:111985955p.G137S1
chr1:111991770p.V327V1
chr1:111983882p.V116V1
chr1:111985985p.V326I1
chr1:111983900p.L86P1
chr1:111986535p.Q321K1

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 WDR77 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 WDR77

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

ATP5F1,CDC20,CDCA3,CDCA8,CENPA,ECE2,FAM136A,
LSM2,LYAR,MAGOH,NDUFAF4,NOP58,PDSS1,PSMA5,
PSMB2,PSMG1,PSRC1,SERBP1,SNRPC,UQCRH,WDR77
AIMP2,ATP5G3,PRADC1,TIMMDC1,COX5A,FH,HIGD2A,
LACTB,LSM10,MRPS16,NDUFA4,NDUFA9,NDUFAB1,NDUFB2,
NDUFB3,PGK1,UQCR10,UQCR11,UQCRFS1,WDR77,WSB2

ACOT8,C20orf24,CASP6,CSE1L,DNAJA3,EIF2B3,GPSM2,
GSS,HSD17B10,LRRC8D,MAGOH,MAPKAPK5,MTCH2,PDHA1,
POU5F1B,PSMA7,RPIA,RPP40,TINAG,TSPAN6,WDR77
ABCE1,BRIX1,CCT2,DKC1,FARSB,GART,KIAA0020,
METTL1,MRPL3,MRTO4,NOC3L,NOP56,NOP58,PUS7,
RRP9,SRFBP1,SRPRB,SUV39H2,TFDP1,UTP6,WDR77
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 WDR77


There's no related Drug.
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Cross referenced IDs for WDR77
* 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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