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 SPCS1
Basic gene info.Gene symbolSPCS1
Gene namesignal peptidase complex subunit 1 homolog (S. cerevisiae)
SynonymsSPC1|SPC12|YJR010C-A
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :52739856-52742197
Type of geneprotein-coding
RefGenesNM_014041.3,
Ensembl idENSG00000114902
DescriptionSPase 12 kDa subunitmicrosomal signal peptidase 12 kDa subunitsignal peptidase 12kDasignal peptidase complex subunit 1
Modification date20141207
dbXrefs MIM : 610358
HGNC : HGNC
Ensembl : ENSG00000114902
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SPCS1
BioGPS: 28972
Gene Expression Atlas: ENSG00000114902
The Human Protein Atlas: ENSG00000114902
PathwayNCI Pathway Interaction Database: SPCS1
KEGG: SPCS1
REACTOME: SPCS1
ConsensusPathDB
Pathway Commons: SPCS1
MetabolismMetaCyc: SPCS1
HUMANCyc: SPCS1
RegulationEnsembl's Regulation: ENSG00000114902
miRBase: chr3 :52,739,856-52,742,197
TargetScan: NM_014041
cisRED: ENSG00000114902
ContextiHOP: SPCS1
cancer metabolism search in PubMed: SPCS1
UCL Cancer Institute: SPCS1
Assigned class in ccmGDBC

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Phenotypic Information for SPCS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SPCS1
Familial Cancer Database: SPCS1
* 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_INTEGRATION_OF_ENERGY_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SPCS1
MedGen: SPCS1 (Human Medical Genetics with Condition)
ClinVar: SPCS1
PhenotypeMGI: SPCS1 (International Mouse Phenotyping Consortium)
PhenomicDB: SPCS1

Mutations for SPCS1
* 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
pancreasSPCS1chr35274172752741747chr35274296152742981
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 SPCS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ680964SPCS1261335274067752742184EBNA1BP260362414367660043676621
BI335113CIB11162159077353690773698SPCS116372435274015352741972
BU932269SPCS1312135274013552740253RPL4115652156679377266795784
AI221915SPCS1212135274206552742184NTM12032811131404621131404829

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=6)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr3:52740861-52740861p.Y50C2
chr3:52741807-52741807p.K96K2
chr3:52740708-52740709p.S31fs*131
chr3:52740855-52740855p.T48I1
chr3:52740858-52740858p.V49G1
chr3:52741704-52741704p.L62R1
chr3:52741730-52741730p.R71C1
chr3:52741771-52741772p.T85fs*111
chr3:52741784-52741784p.K89fs*>141
chr3:52740293-52740293p.Q11K1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample        2  1 1  11 1
# mutation        2  1 1  11 1
nonsynonymous SNV        2  1 1   1 1
synonymous SNV                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
chr3:52740858p.D154H1
chr3:52741704p.K163K1
chr3:52741778p.C61S1
chr3:52741807p.Q78K1
chr3:52740242p.T115I1
chr3:52740293p.V116G1
chr3:52740855p.L129R1

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 SPCS1 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 SPCS1

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

ABHD14A,ABHD14B,APEH,ELP6,CCDC51,CMC1,COPZ1,
CYB561D2,GLT8D1,KIF9,NDUFAF3,NPRL2,PDHB,PSMD6,
RFT1,SELK,SLC25A38,SPCS1,TEX264,TMEM115,TUSC2
C14orf119,C8orf59,CETN2,CISD2,COX16,DPY30,DYNLT1,
ERH,HMGN2,LSM12,MYL12B,PPA2,PSMG1,SF3B14,
SPCS1,SS18L2,SUMO2,TMCO1,TMEM59,TMEM60,TMEM9B

ARPC4,ATP5J2,TMEM258,ELP6,TMA7,CMC1,COX7A2,
HIGD1A,HSBP1,JAGN1,KIF9,LOC440957,LSM3,NDUFAB1,
NDUFB5,SELK,SNRPG,SPCS1,THOC7,TIMM8B,TUSC2
ATG3,ATP5J2,ATP5S,C14orf2,CHCHD1,CKLF,COX7A2,
DGUOK,FAM96A,GTF2B,HINT1,MRPS36,PDCD6,PGK1,
PPCS,SEC11C,SERP1,SPCS1,TMEM106C,UQCR10,VPS25
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 SPCS1


There's no related Drug.
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Cross referenced IDs for SPCS1
* 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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