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 SPTLC2

Basic gene info.	Gene symbol	SPTLC2
	Gene name	serine palmitoyltransferase, long chain base subunit 2
	Synonyms	HSN1C\|LCB2\|LCB2A\|NSAN1C\|SPT2\|hLCB2a
	Cytomap	UCSC genome browser: 14q24.3
	Genomic location	chr14 :77972339-78083110
	Type of gene	protein-coding
	RefGenes	NM_004863.3,
	Ensembl id	ENSG00000100596
	Description	LCB 2SPT 2long chain base biosynthesis protein 2aserine palmitoyltransferase 2serine palmitoyltransferase, subunit IIserine-palmitoyl-CoA transferase 2
	Modification date	20141207
dbXrefs	MIM : 605713
	HGNC : HGNC
	Ensembl : ENSG00000100596
	HPRD : 05755
	Vega : OTTHUMG00000171540
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SPTLC2
	BioGPS: 9517
	Gene Expression Atlas: ENSG00000100596
	The Human Protein Atlas: ENSG00000100596
Pathway	NCI Pathway Interaction Database: SPTLC2
	KEGG: SPTLC2
	REACTOME: SPTLC2
	ConsensusPathDB
	Pathway Commons: SPTLC2
Metabolism	MetaCyc: SPTLC2
	HUMANCyc: SPTLC2
Regulation	Ensembl's Regulation: ENSG00000100596
	miRBase: chr14 :77,972,339-78,083,110
	TargetScan: NM_004863
	cisRED: ENSG00000100596
Context	iHOP: SPTLC2
	cancer metabolism search in PubMed: SPTLC2
	UCL Cancer Institute: SPTLC2
Assigned class in ccmGDB	C

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Phenotypic Information for SPTLC2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SPTLC2
	Familial Cancer Database: SPTLC2

* 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: SPTLC2
	MedGen: SPTLC2 (Human Medical Genetics with Condition)
	ClinVar: SPTLC2
Phenotype	MGI: SPTLC2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SPTLC2

Mutations for SPTLC2

* 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
ovary	SPTLC2	chr14	78021370	78021390	SPTLC2	chr14	78008114	78008134

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 SPTLC2 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
N98751	SURF4	6	229	9	136228340	136228561	SPTLC2	230	402	14	77972559	77972728
AW376098	SPTLC2	1	257	14	77978692	77987860	SPTLC2	254	320	14	77978648	77978714
AW376106	SPTLC2	5	274	14	77978692	77987873	SPTLC2	271	337	14	77978648	77978714
AW803684	SPTLC2	14	107	14	77972428	77972521	ACTB	92	182	7	5567258	5567348

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

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)

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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=44)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr14:77987880-77987880	p.R450R	3
chr14:78018519-78018519	p.A408D	2
chr14:78045431-78045431	p.D117Y	2
chr14:78063594-78063594	p.R88*	2
chr14:77978689-77978689	p.R543W	2
chr14:77987898-77987898	p.E444K	2
chr14:77978747-77978747	p.?	2
chr14:78021720-78021720	p.P367S	2
chr14:77984470-77984470	p.V494I	2
chr14:78021755-78021755	p.T355I	2

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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=4

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	3	2	1	10			2		1	1	1	5	3	1			5	4		4
# mutation	4	2	1	9			2		1	1	1	5	3	1			5	4		5
nonsynonymous SNV	3	2	1	6			2			1	1	4	3				4	3		4
synonymous SNV	1			3					1			1		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])

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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
chr14:77987880	p.R450G	3
chr14:77978688	p.R543Q	2
chr14:78063612	p.T82S	2
chr14:78028787	p.D366H	1
chr14:78063576	p.W94R	1
chr14:78018487	p.R541S	1
chr14:78028820	p.A351S	1
chr14:77978695	p.L87I	1
chr14:78063597	p.E519Q	1
chr14:78018495	p.L341L	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 SPTLC2 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 SPTLC2

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


ALDH6A1,ALKBH1,AR,BTBD7,GPATCH2L,DCAF5,GTF2A1, IDE,KIAA1244,CIPC,MPP5,NUMB,PPP2R5E,PSEN1, RPS6KA5,SEL1L,SLC39A9,SPTLC2,TC2N,TRIP11,YLPM1	ANAPC1,AQR,CEP128,C9orf41,CDK12,CLCN3,CPD, DPY19L3,FAM73A,GPR107,HDX,HFE,IPMK,SCYL2, SPG11,SPTLC2,TMEM181,TMTC2,XYLB,ZDHHC20,ZFYVE16

ALDH6A1,BTBD7,CDC42BPB,DOCK5,DYNC1H1,HEATR5A,AREL1, KIAA0586,MPP5,MUC4,NUMB,PPP2R5E,RCOR1,SEL1L, SHROOM3,SMEK1,SPTLC2,TC2N,TMED10,TRIP11,YLPM1	AIM1,ARFGEF2,ARHGAP32,PRR14L,CLTC,CNOT1,DCAF7, DNAJC16,FAM120A,FNBP1L,KDM4A,LARP4B,MAML2,MLEC, OSBP,RALGAPA2,SPG11,SPTLC2,SYNE2,ZBED4,ZBTB10

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 SPTLC2

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 2	nutraceutical	Pyridoxal Phosphate
DB00133	serine palmitoyltransferase, long chain base subunit 2	approved; nutraceutical	L-Serine

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Cross referenced IDs for SPTLC2

* 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