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 SQRDL
Basic gene info.Gene symbolSQRDL
Gene namesulfide quinone reductase-like (yeast)
SynonymsPRO1975|SQOR
CytomapUCSC genome browser: 15q15
Genomic locationchr15 :45927255-45983479
Type of geneprotein-coding
RefGenesNM_001271213.1,
NM_021199.3,
Ensembl idENSG00000260170
Descriptionsulfide dehydrogenase likesulfide:quinone oxidoreductase, mitochondrial
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000137767
HPRD : 18102
Vega : OTTHUMG00000131476
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SQRDL
BioGPS: 58472
Gene Expression Atlas: ENSG00000260170
The Human Protein Atlas: ENSG00000260170
PathwayNCI Pathway Interaction Database: SQRDL
KEGG: SQRDL
REACTOME: SQRDL
ConsensusPathDB
Pathway Commons: SQRDL
MetabolismMetaCyc: SQRDL
HUMANCyc: SQRDL
RegulationEnsembl's Regulation: ENSG00000260170
miRBase: chr15 :45,927,255-45,983,479
TargetScan: NM_001271213
cisRED: ENSG00000260170
ContextiHOP: SQRDL
cancer metabolism search in PubMed: SQRDL
UCL Cancer Institute: SQRDL
Assigned class in ccmGDBC

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

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

Mutations for SQRDL
* 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
There's no inter-chromosomal structural variation.
- 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
ovarySQRDLchr154596343945963459SQRDLchr154596390645963926
ovarySQRDLchr154597583645975856chr154600214446002164
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 SQRDL related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU581446NID142991236143879236148727SQRDL300495154598135445983304
BU075210SQRDL41401154598135445983469NID14025831236143879236145017

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 # sample        1        
GAIN (# sample)                 
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr15:45965849-45965849p.S168S4
chr15:45951155-45951155p.R12fs*512
chr15:45965918-45965918p.I191M2
chr15:45968449-45968449p.D269N2
chr15:45968487-45968487p.P281P2
chr15:45981249-45981249p.T377A2
chr15:45968423-45968423p.K260R1
chr15:45981265-45981265p.V382G1
chr15:45962137-45962137p.R139R1
chr15:45968435-45968435p.I264T1

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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
# sample 2 2  3 2  6 1 1111 6
# mutation 2 2  3 2  7 1 1111 6
nonsynonymous SNV 2 2  2 1  6 1  61 3
synonymous SNV      1 1  1   15  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
chr15:45965849p.S168S,SQRDL3
chr15:45981368p.P195L,SQRDL1
chr15:45951232p.L416L,SQRDL1
chr15:45968356p.S37R,SQRDL1
chr15:45981393p.V199L,SQRDL1
chr15:45951281p.L425L,SQRDL1
chr15:45965852p.G54S,SQRDL1
chr15:45968358p.K221T,SQRDL1
chr15:45983189p.P438P,SQRDL1
chr15:45954156p.H80Y,SQRDL1

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 SQRDL 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 SQRDL

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

B2M,EMC7,RHOV___CHP1,CYB561D2,CYB5A,DNAJC17,FAH,
RMDN3,FTH1,GCHFR,NDUFAF1,PPP1R7,RARRES3,SQRDL,
TMEM62,TPST2,TSPAN15,UQCRQ,VPS18,YIPF1,ZFYVE19
ARHGDIB,ARPC3,BCAS4,BRE,CAPZB,CLIC1,GSTO1,
JTB,MFSD5,MIF4GD,N6AMT2,NPC2,PRR13,PSMA4,
PSMA5,RHOG,RNF181,S100A11,SDHAF2,SQRDL,TM2D2

ACADS,BCL10,GSKIP,C15orf48,CCL28,CIB1,ETFA,
ETHE1,F2RL1,FAM118B,GPA33,LDHD,LGALS3,MPDU1,
PIGR,RILP,SCO2,SQRDL,TMEM54,TNFSF13,TSPO
ATP5B,MCU,CCL28,CD24,CSTF2,GNG5,HCCS,
HDAC1,HPSE,IL18,MAP2K6,MMAA,MYCBP,OSTF1,
PSMD3,RAB11A,RTN4IP1,SCO1,SQRDL,TMEM54,TPM3
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 SQRDL


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