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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	SPCS1
	Gene name	signal peptidase complex subunit 1 homolog (S. cerevisiae)
	Synonyms	SPC1\|SPC12\|YJR010C-A
	Cytomap	UCSC genome browser: 3p21.1
	Genomic location	chr3 :52739856-52742197
	Type of gene	protein-coding
	RefGenes	NM_014041.3,
	Ensembl id	ENSG00000114902
	Description	SPase 12 kDa subunitmicrosomal signal peptidase 12 kDa subunitsignal peptidase 12kDasignal peptidase complex subunit 1
	Modification date	20141207
dbXrefs	MIM : 610358
	HGNC : HGNC
	Ensembl : ENSG00000114902
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SPCS1
	BioGPS: 28972
	Gene Expression Atlas: ENSG00000114902
	The Human Protein Atlas: ENSG00000114902
Pathway	NCI Pathway Interaction Database: SPCS1
	KEGG: SPCS1
	REACTOME: SPCS1
	ConsensusPathDB
	Pathway Commons: SPCS1
Metabolism	MetaCyc: SPCS1
	HUMANCyc: SPCS1
Regulation	Ensembl's Regulation: ENSG00000114902
	miRBase: chr3 :52,739,856-52,742,197
	TargetScan: NM_014041
	cisRED: ENSG00000114902
Context	iHOP: SPCS1
	cancer metabolism search in PubMed: SPCS1
	UCL Cancer Institute: SPCS1
Assigned class in ccmGDB	C

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Phenotypic Information for SPCS1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SPCS1
	MedGen: SPCS1 (Human Medical Genetics with Condition)
	ClinVar: SPCS1
Phenotype	MGI: SPCS1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SPCS1	chr3	52741727	52741747		chr3	52742961	52742981

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SPCS1 related fusion information.

ID	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
BQ680964	SPCS1	2	613	3	52740677	52742184	EBNA1BP2	603	624	1	43676600	43676621
BI335113	CIB1	1	162	15	90773536	90773698	SPCS1	163	724	3	52740153	52741972
BU932269	SPCS1	3	121	3	52740135	52740253	RPL4	115	652	15	66793772	66795784
AI221915	SPCS1	2	121	3	52742065	52742184	NTM	120	328	11	131404621	131404829

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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=2

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Somatic 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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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
chr3:52740861-52740861	p.Y50C	2
chr3:52741807-52741807	p.K96K	2
chr3:52740666-52740666	p.K15*	1
chr3:52740706-52740706	p.I28T	1
chr3:52740708-52740709	p.S31fs*13	1
chr3:52740855-52740855	p.T48I	1
chr3:52740858-52740858	p.V49G	1
chr3:52741704-52741704	p.L62R	1
chr3:52741730-52741730	p.R71C	1
chr3:52741771-52741772	p.T85fs*11	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample									2			1		1			1	1		1
# mutation									2			1		1			1	1		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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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
chr3:52740293	p.Q78K	1
chr3:52740855	p.T115I	1
chr3:52740858	p.V116G	1
chr3:52741704	p.L129R	1
chr3:52741778	p.D154H	1
chr3:52741807	p.K163K	1
chr3:52740242	p.C61S	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 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

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))

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CNV 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

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


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

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

: Open all plots for all cancer types

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Interacting 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