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 SPTLC1

Basic gene info.	Gene symbol	SPTLC1
	Gene name	serine palmitoyltransferase, long chain base subunit 1
	Synonyms	HSAN1\|HSN1\|LBC1\|LCB1\|SPT1\|SPTI
	Cytomap	UCSC genome browser: 9q22.2
	Genomic location	chr9 :94841345-94877690
	Type of gene	protein-coding
	RefGenes	NM_001281303.1, NM_006415.3,NM_178324.2,
	Ensembl id	ENSG00000090054
	Description	LCB 1SPT 1long chain base biosynthesis protein 1serine C-palmitoyltransferaseserine palmitoyltransferase 1serine-palmitoyl-CoA transferase 1
	Modification date	20141219
dbXrefs	MIM : 605712
	HGNC : HGNC
	Ensembl : ENSG00000090054
	HPRD : 05754
	Vega : OTTHUMG00000021047
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SPTLC1
	BioGPS: 10558
	Gene Expression Atlas: ENSG00000090054
	The Human Protein Atlas: ENSG00000090054
Pathway	NCI Pathway Interaction Database: SPTLC1
	KEGG: SPTLC1
	REACTOME: SPTLC1
	ConsensusPathDB
	Pathway Commons: SPTLC1
Metabolism	MetaCyc: SPTLC1
	HUMANCyc: SPTLC1
Regulation	Ensembl's Regulation: ENSG00000090054
	miRBase: chr9 :94,841,345-94,877,690
	TargetScan: NM_001281303
	cisRED: ENSG00000090054
Context	iHOP: SPTLC1
	cancer metabolism search in PubMed: SPTLC1
	UCL Cancer Institute: SPTLC1
Assigned class in ccmGDB	C

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Phenotypic Information for SPTLC1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SPTLC1
	Familial Cancer Database: SPTLC1

* 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
KEGG_SPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SPTLC1
	MedGen: SPTLC1 (Human Medical Genetics with Condition)
	ClinVar: SPTLC1
Phenotype	MGI: SPTLC1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SPTLC1

Mutations for SPTLC1

* 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 SPTLC1 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
AK309775	MRPL51	1	337	12	6601611	6602426	SPTLC1	334	1311	9	94794734	94830350
DA774691	MRPL51	1	337	12	6601611	6602426	SPTLC1	334	555	9	94821472	94830350
AI065091	ITIH3	1	74	3	52839263	52839336	SPTLC1	75	716	9	94809464	94830379
BG951421	ACSS1	4	220	20	24987624	24987843	SPTLC1	202	439	9	94794795	94800648
BF803026	SPTLC1	1	80	9	94821117	94821587	SPTLC1	76	132	9	94842298	94842354
BF832583	PLD5	414	439	1	242655244	242655281	SPTLC1	430	489	9	94802700	94802759

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr9:94842338-94842338	p.G129G	3
chr9:94821591-94821591	p.?	2
chr9:94809461-94809461	p.E358D	2
chr9:94843163-94843164	p.P115S	2
chr9:94843197-94843197	p.F103F	2
chr9:94877644-94877644	p.T3T	2
chr9:94821582-94821582	p.A190V	1
chr9:94800620-94800620	p.E388D	1
chr9:94874764-94874764	p.L46F	1
chr9:94809924-94809924	p.C319G	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=2

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	3		7					1	1		4		1			3	2		6
# mutation	2	3		8					1	1		4		1			3	2		6
nonsynonymous SNV	2	2		8					1			3		1			2			5
synonymous SNV		1								1		1					1	2		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
chr9:94809461	p.E358D,SPTLC1	2
chr9:94809515	p.V9V,SPTLC1	1
chr9:94821582	p.C255F,SPTLC1	1
chr9:94877644	p.T3T,SPTLC1	1
chr9:94809914	p.K230N,SPTLC1	1
chr9:94842318	p.D228N,SPTLC1	1
chr9:94809915	p.A477T	1
chr9:94842338	p.E227K,SPTLC1	1
chr9:94794708	p.V451L	1
chr9:94809924	p.K222N,SPTLC1	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 SPTLC1 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 SPTLC1

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


C9orf41,TMEM245,INIP,FAM120A,FKTN,FUBP3,HIATL1, IARS,ISCA1,KIAA0368,NAA35,NOL8,RAB14,RAD23B, RNF20,SPIN1,SPTLC1,TSTD2,UBQLN1,ZBTB6,ZNF510	BET1,CGGBP1,HIAT1,MIER1,PLEKHA3,RAB14,RAB18, SLC25A24,SLC30A5,SPTLC1,SSR1,TAF9B,TCEA1,TM9SF3, TMED7,TMX1,TRAM1,TROVE2,TWF1,YIPF5,ZMPSTE24

ATP6V1G1,C3orf38,FAM206A,INIP,CRIPT,ISCA1,ISCA1P1, LOC441089,MOB4,MRPL50,NIPSNAP3A,PCNP,PDCD10,POLE3, PPP6C,RAB14,RFK,RMI1,SELT,SPTLC1,UBQLN1	ABI1,ARFIP1,SMIM15,CDC42SE2,CMPK1,FAM105A,GMFB, MAL2,NDFIP2,NRAS,PEX13,RAB11A,SFT2D1,SLC35A3, SLC35F5,SPTLC1,STAMBP,TMEM9B,TWF1,VTA1,ZNRF2

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 SPTLC1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00114	serine palmitoyltransferase, long chain base subunit 1	nutraceutical	Pyridoxal Phosphate
DB00133	serine palmitoyltransferase, long chain base subunit 1	approved; nutraceutical	L-Serine

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Cross referenced IDs for SPTLC1

* 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