Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	SPCS2
	Gene name	signal peptidase complex subunit 2 homolog (S. cerevisiae)
	Synonyms	-
	Cytomap	UCSC genome browser: 11q13.4
	Genomic location	chr11 :74660291-74690076
	Type of gene	protein-coding
	RefGenes	NM_014752.2,
	Ensembl id	ENSG00000118363
	Description	SPase 25 kDa subunitmicrosomal signal peptidase 25 kDa subunitsignal peptidase 25kDa subunitsignal peptidase complex subunit 2
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000118363
	HPRD : 15435
	Vega : OTTHUMG00000165517
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SPCS2
	BioGPS: 9789
	Gene Expression Atlas: ENSG00000118363
	The Human Protein Atlas: ENSG00000118363
Pathway	NCI Pathway Interaction Database: SPCS2
	KEGG: SPCS2
	REACTOME: SPCS2
	ConsensusPathDB
	Pathway Commons: SPCS2
Metabolism	MetaCyc: SPCS2
	HUMANCyc: SPCS2
Regulation	Ensembl's Regulation: ENSG00000118363
	miRBase: chr11 :74,660,291-74,690,076
	TargetScan: NM_014752
	cisRED: ENSG00000118363
Context	iHOP: SPCS2
	cancer metabolism search in PubMed: SPCS2
	UCL Cancer Institute: SPCS2
Assigned class in ccmGDB	C

Top

Phenotypic Information for SPCS2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SPCS2
	MedGen: SPCS2 (Human Medical Genetics with Condition)
	ClinVar: SPCS2
Phenotype	MGI: SPCS2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SPCS2 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

BI822849

XRRA1

347

74644870

74660085

SPCS2

348

867

28422276

28422819

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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

SNV 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

Somatic 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

Top 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 position	Mutation(aa)	Unique sampleID count
chr11:74676929-74676929	p.F4C	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				7								2					2	1		2
# mutation				2								2					2	1		2
nonsynonymous SNV				1								1					1			2
synonymous SNV				1								1					1	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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr11:74676928	p.F107L	5
chr11:74676882	p.S91S	2
chr11:74676930	p.F107F	2
chr11:74680701	p.I87V	1
chr11:74680729	p.V113I	1
chr11:74688037	p.I127T	1
chr11:74676868	p.M151V	1
chr11:74676946	p.S160F	1
chr11:74680630	p.P210P	1

Other 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

Copy 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

Gene 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.

Differential 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

CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting 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