Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 SPCS2
Basic gene info.Gene symbolSPCS2
Gene namesignal peptidase complex subunit 2 homolog (S. cerevisiae)
Synonyms-
CytomapUCSC genome browser: 11q13.4
Genomic locationchr11 :74660291-74690076
Type of geneprotein-coding
RefGenesNM_014752.2,
Ensembl idENSG00000118363
DescriptionSPase 25 kDa subunitmicrosomal signal peptidase 25 kDa subunitsignal peptidase 25kDa subunitsignal peptidase complex subunit 2
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000118363
HPRD : 15435
Vega : OTTHUMG00000165517
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SPCS2
BioGPS: 9789
Gene Expression Atlas: ENSG00000118363
The Human Protein Atlas: ENSG00000118363
PathwayNCI Pathway Interaction Database: SPCS2
KEGG: SPCS2
REACTOME: SPCS2
ConsensusPathDB
Pathway Commons: SPCS2
MetabolismMetaCyc: SPCS2
HUMANCyc: SPCS2
RegulationEnsembl's Regulation: ENSG00000118363
miRBase: chr11 :74,660,291-74,690,076
TargetScan: NM_014752
cisRED: ENSG00000118363
ContextiHOP: SPCS2
cancer metabolism search in PubMed: SPCS2
UCL Cancer Institute: SPCS2
Assigned class in ccmGDBC

Top
Phenotypic Information for SPCS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SPCS2
Familial Cancer Database: SPCS2
* 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: SPCS2
MedGen: SPCS2 (Human Medical Genetics with Condition)
ClinVar: SPCS2
PhenotypeMGI: SPCS2 (International Mouse Phenotyping Consortium)
PhenomicDB: SPCS2

Mutations for SPCS2
* 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 SPCS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI822849XRRA11347117464487074660085SPCS234886712842227628422819

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1    2   
GAIN (# sample)        1    2   
LOSS (# sample)                 
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)

Top
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=1

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr11:74676929-74676929p.F4C1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   7       2    21 2
# mutation   2       2    21 2
nonsynonymous SNV   1       1    1  2
synonymous SNV   1       1    11  
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])

Top
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
chr11:74676928p.F107L5
chr11:74676882p.S91S2
chr11:74676930p.F107F2
chr11:74676946p.I127T1
chr11:74680630p.M151V1
chr11:74680701p.S160F1
chr11:74680729p.P210P1
chr11:74688037p.I87V1
chr11:74676868p.V113I1

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 SPCS2 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]

Top
Gene Expression for SPCS2

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

AQP11,ARHGEF17,C11orf30,AAMDC,ZNF436-AS1,C2CD3,CAPN5,
CLNS1A,KLHL35,LIPT2,LOC653566,NDUFC2,NEU3,OMP,
POLD3,PPME1,PRKRIR,RNF169,SPCS2,UVRAG,XRRA1
C1D,TMEM243,CISD2,DPY30,FAM3C,H3F3A,IER3IP1,
LOC653566,LSM5,C7orf73,PTGES3,SEP15,SPCS1,SPCS2,
SRP9,SUMO2,TBPL1,TCEAL8,TMEM9B,TXNDC9,UBE2E1

ATP5L,BANF1,TMEM258,C11orf57,CWC15,EED,LOC653566,
MRPL48,OSTC,POLR2G,PTS,SC5D,SDHAF2,SELK,
SPCS1,SPCS2,SUMO1P3,THYN1,TMEM126A,TMEM126B,TRMT112
C19orf10,C1GALT1C1,EIF4A1,EIF5AL1,HNRNPF,ILF2,LOC653566,
LSM6,MANF,NUS1,PDIA6,PPIB,RPL22L1,RPL26L1,
RPN1,SDF2L1,SEC11C,SEC61B,SPCS2,SRGN,SSR3
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for SPCS2


There's no related Drug.
Top
Cross referenced IDs for SPCS2
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas