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 SAT1

Basic gene info.	Gene symbol	SAT1
	Gene name	spermidine/spermine N1-acetyltransferase 1
	Synonyms	DC21\|KFSD\|KFSDX\|SAT\|SSAT\|SSAT-1
	Cytomap	UCSC genome browser: Xp22.1
	Genomic location	chrX :23801274-23804327
	Type of gene	protein-coding
	RefGenes	NM_002970.3, NR_027783.2,
	Ensembl id	ENSG00000130066
	Description	diamine N-acetyltransferase 1diamine acetyltransferase 1polyamine N-acetyltransferase 1putrescine acetyltransferasespermidine/spermine N1-acetyltransferase alpha
	Modification date	20141222
dbXrefs	MIM : 313020
	HGNC : HGNC
	Ensembl : ENSG00000130066
	HPRD : 02431
	Vega : OTTHUMG00000021256
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SAT1
	BioGPS: 6303
	Gene Expression Atlas: ENSG00000130066
	The Human Protein Atlas: ENSG00000130066
Pathway	NCI Pathway Interaction Database: SAT1
	KEGG: SAT1
	REACTOME: SAT1
	ConsensusPathDB
	Pathway Commons: SAT1
Metabolism	MetaCyc: SAT1
	HUMANCyc: SAT1
Regulation	Ensembl's Regulation: ENSG00000130066
	miRBase: chrX :23,801,274-23,804,327
	TargetScan: NM_002970
	cisRED: ENSG00000130066
Context	iHOP: SAT1
	cancer metabolism search in PubMed: SAT1
	UCL Cancer Institute: SAT1
Assigned class in ccmGDB	C

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Phenotypic Information for SAT1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SAT1
	Familial Cancer Database: SAT1

* 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_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES

Others
OMIM
Orphanet
Disease	KEGG Disease: SAT1
	MedGen: SAT1 (Human Medical Genetics with Condition)
	ClinVar: SAT1
Phenotype	MGI: SAT1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SAT1

Mutations for SAT1

* 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 SAT1 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
BM263653	MPHOSPH8	17	178	13	20224144	20224305	SAT1	173	560	X	23803938	23804325
CA848235	SAT1	14	403	X	23803938	23804327	MPHOSPH8	398	555	13	20224148	20224305
H56980	FYCO1	1	136	3	46000973	46003790	SAT1	130	426	X	23803976	23804269
BQ023122	SAT1	20	258	X	23804087	23804325	FNDC3B	257	444	3	172117517	172117705
BM263362	SAT1	22	403	X	23803938	23804319	MPHOSPH8	398	558	13	20224145	20224305
BE765420	SAT1	17	280	X	23804055	23804318	SERPINE1	277	445	7	100781379	100781547
BE180881	SAT1	9	102	X	23803088	23803181	SAT1	98	273	X	23802946	23803121
AW582417	SAT1	8	171	X	23803948	23804110	SAT1	165	267	X	23803841	23803943
W39276	SAT1	1	111	X	23803945	23804055	SAT1	109	341	X	23804095	23804326
W31613	SAT1	1	232	X	23804095	23804326	SAT1	230	304	X	23803945	23804019
AW361033	SAT1	12	270	X	23802021	23802281	ANKH	265	565	5	14710193	14710493
BU674743	SAT1	17	96	X	23804248	23804327	SAT1	92	253	X	23803954	23804115

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=14)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr23:23803528-23803528	p.V96M	2
chr23:23801821-23801821	p.D40fs*3	1
chr23:23801932-23801932	p.G45D	1
chr23:23803544-23803544	p.R101T	1
chr23:23801942-23801942	p.E48D	1
chr23:23803813-23803813	p.R119K	1
chr23:23801955-23801955	p.H53Y	1
chr23:23803814-23803814	p.R119R	1
chr23:23801965-23801965	p.V56A	1
chr23:23803819-23803819	p.R121H	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		1			2		1			3			1					7
# mutation		2		1			2		2			3			1					7
nonsynonymous SNV		2		1			2		1			2			1					6
synonymous SNV									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
chrX:23803528	p.V96M	2
chrX:23801949	p.V56A	1
chrX:23803891	p.P60L	1
chrX:23801955	p.P60P	1
chrX:23803899	p.H69R	1
chrX:23801965	p.P83L	1
chrX:23803921	p.R119K	1
chrX:23801977	p.R119R	1
chrX:23803928	p.R121H	1
chrX:23801978	p.A145V	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 SAT1 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 SAT1

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


ACOT9,ACTB,APOO,AVEN,B3GNT3,BRI3,SMCO4, CLDN2,FUT3,LPXN,MALL,NXT1,PLAUR,PRDX4, PRR18,S100A10,SAT1,SLC35C1,TAAR6,UGT2B7,VNN2	ADAP2,AIF1,CD86,GMFG,HCK,HLA-DMA,HLA-DMB, IRF8,LAPTM5,LILRB4,LOC541471,NPL,OSTF1,PLEK, RAB32,RAP2B,SAMSN1,SAT1,SLC11A1,SRGN,TMSB4XP8

ACOT9,ANKRD37,ANXA2,APOO,CIB1,COQ10B,GTF2A2, ISG20,KIAA0895,MAFF,OBFC1,RAB11A,RAB9A,RND1, S100A13,SAT1,SEC61B,SERTAD3,TMSB10,TRIM15,ZFYVE19	LINC00483,NMRK1,CCNDBP1,CLRN3,DERA,DNAJC17,DNAJC22, GRAMD1C,HTATIP2,NDFIP2,NIT1,OCIAD2,PRSS3,RAB20, SAT1,SEPHS2,SLC25A20,SLC25A5,SLC35D2,TRAF4,ZFAND2B

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 SAT1

There's no related Drug.

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Cross referenced IDs for SAT1

* 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