Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SCLY
Basic gene info.Gene symbolSCLY
Gene nameselenocysteine lyase
SynonymsSCL|hSCL
CytomapUCSC genome browser: 2q37.3
Genomic locationchr2 :238969564-239008054
Type of geneprotein-coding
RefGenesNM_016510.5,
Ensembl idENSG00000132330
Description-
Modification date20141207
dbXrefs MIM : 611056
HGNC : HGNC
Ensembl : ENSG00000132330
HPRD : 15303
Vega : OTTHUMG00000133336
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SCLY
BioGPS: 51540
Gene Expression Atlas: ENSG00000132330
The Human Protein Atlas: ENSG00000132330
PathwayNCI Pathway Interaction Database: SCLY
KEGG: SCLY
REACTOME: SCLY
ConsensusPathDB
Pathway Commons: SCLY
MetabolismMetaCyc: SCLY
HUMANCyc: SCLY
RegulationEnsembl's Regulation: ENSG00000132330
miRBase: chr2 :238,969,564-239,008,054
TargetScan: NM_016510
cisRED: ENSG00000132330
ContextiHOP: SCLY
cancer metabolism search in PubMed: SCLY
UCL Cancer Institute: SCLY
Assigned class in ccmGDBC

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

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

Mutations for SCLY
* 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 SCLY related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA775419SCLY14142239007637239008053CHURC1-FNTB410686146541810565418383
AA813916RPL1055107X153629200153629254SCLY922412239007418239007567
BQ339693SV2A21011149878219149878321SCLY895832238991969239007008

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 # sample1         1      
GAIN (# sample)          1      
LOSS (# sample)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=3

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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=15)
Stat. for Deletions
(# total SNVs=3)
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
chr2:238976762-238976762p.K97fs*53
chr2:239003059-239003059p.?3
chr2:239003069-239003069p.F346F2
chr2:238990716-238990716p.A223T2
chr2:239006879-239006879p.F415F2
chr2:238990797-238990797p.R250C2
chr2:238990408-238990408p.L189L2
chr2:239003172-239003172p.?2
chr2:238991893-238991893p.Y269F2
chr2:238990458-238990458p.N206S2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  121 1 11 311  22 3
# mutation1  121 1 11 311  22 4
nonsynonymous SNV1  61   11 3 1  11 3
synonymous SNV   6  1     1   11 1
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
chr2:239003069p.F346F3
chr2:238990797p.Y269C2
chr2:238991893p.L189L2
chr2:238990408p.R250C2
chr2:238990470p.A91A1
chr2:239002554p.F103F1
chr2:238976752p.Y269Y1
chr2:238990708p.T104I1
chr2:238976788p.M309I1
chr2:238990731p.V119L1

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 SCLY 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 SCLY

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

AAMP,ANKZF1,ATG4B,CAPN10,COPS7B,DHX30,DIS3L2,
DTYMK,DUSP28,FBF1,ILKAP,ING5,KLHL17,NDUFA10,
PASK,POLRMT,SCLY,STK11IP,STK25,THAP4,WRAP73
EMC10,CAPN1,CCDC22,DDX41,ERCC2,FARSA,FIZ1,
GRWD1,HMG20B,LMAN2,MAEA,PPP1CA,PRPF19,RANGAP1,
RNASEH2A,RUVBL2,SCLY,SDF2L1,TRIM28,WRAP53,YIPF2

ARMC6,ATIC,BCS1L,CCT7,CIAO1,EPT1,HSPD1,
MARS2,MGC14436,PNO1,PNPT1,POLR1B,PTCD3,SCLY,
STARD7,THOP1,TMEM177,TTLL12,WDR12,WDR4,WDR43
ACOT7,APITD1,ASAH2B,RIIAD1,CARS2,CDCA3,GALK1,
GREB1L,HSD3B7,IDH2,MON1A,NMT1,P4HB,SCLY,
SEC13,SEC24D,SH3GL1,SIGMAR1,SLC25A22,TEAD4,WDR34
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 SCLY


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