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 TPI1

Basic gene info.	Gene symbol	TPI1
	Gene name	triosephosphate isomerase 1
	Synonyms	HEL-S-49\|TIM\|TPI\|TPID
	Cytomap	UCSC genome browser: 12p13
	Genomic location	chr12 :6977277-6980110
	Type of gene	protein-coding
	RefGenes	NM_000365.5, NM_001159287.1,NM_001258026.1,
	Ensembl id	ENSG00000268548
	Description	epididymis secretory protein Li 49triose-phosphate isomerasetriosephosphate isomerase
	Modification date	20141207
dbXrefs	MIM : 190450
	HGNC : HGNC
	Ensembl : ENSG00000111669
	HPRD : 01833
	Vega : OTTHUMG00000133767
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TPI1
	BioGPS: 7167
	Gene Expression Atlas: ENSG00000268548
	The Human Protein Atlas: ENSG00000268548
Pathway	NCI Pathway Interaction Database: TPI1
	KEGG: TPI1
	REACTOME: TPI1
	ConsensusPathDB
	Pathway Commons: TPI1
Metabolism	MetaCyc: TPI1
	HUMANCyc: TPI1
Regulation	Ensembl's Regulation: ENSG00000268548
	miRBase: chr12 :6,977,277-6,980,110
	TargetScan: NM_000365
	cisRED: ENSG00000268548
Context	iHOP: TPI1
	cancer metabolism search in PubMed: TPI1
	UCL Cancer Institute: TPI1
Assigned class in ccmGDB	C

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Phenotypic Information for TPI1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TPI1
	Familial Cancer Database: TPI1

* 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_GLYCOLYSIS_GLUCONEOGENESIS KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM KEGG_INOSITOL_PHOSPHATE_METABOLISM BIOCARTA_GLYCOLYSIS_PATHWAY REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: TPI1
	MedGen: TPI1 (Human Medical Genetics with Condition)
	ClinVar: TPI1
Phenotype	MGI: TPI1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TPI1

Mutations for TPI1

* 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 TPI1 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
BC054482	TPI1	5	102	12	6976695	6976792	TOP2B	95	559	3	25656965	25661417
DW413329	CHD2	17	143	15	93467720	93470537	TPI1	144	320	12	6979751	6979927
CA431273	TPI1	19	189	12	6979822	6979992	ILF3	187	774	19	10801474	10802067
BQ000670	SERPINH1	18	298	11	75283546	75283826	TPI1	294	683	12	6979538	6979927
BG751641	CAPNS1	4	536	19	36636905	36641020	TPI1	529	633	12	6979864	6979968
AI652202	TPI1	18	72	12	6979938	6979992	MAPK14	69	205	6	36076697	36076833
AF086180	TPI1	1	88	12	6979877	6979964	PFKL	83	322	21	45747008	45747247
BC004230	RPL28	44	532	19	55897311	55899744	TPI1	529	1753	12	6976702	6979993
BC009885	RPL28	44	532	19	55897311	55899744	TPI1	529	1753	12	6976702	6979993

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=27)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr12:6978532-6978532	p.F145F	2
chr12:6978338-6978338	p.E105D	2
chr12:6978930-6978930	p.P179L	1
chr12:6976808-6976808	p.I26I	1
chr12:6979542-6979542	p.Q249K	1
chr12:6978433-6978433	p.Q112H	1
chr12:6979213-6979213	p.A182S	1
chr12:6976815-6976815	p.L29V	1
chr12:6978441-6978441	p.A115V	1
chr12:6979227-6979227	p.H186H	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=3

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		1		3			2		3			8	4					3		5
# mutation		1		3			2		3			9	5					3		5
nonsynonymous SNV		1		3			2		3			7	4					2		4
synonymous SNV												2	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
chr12:6976727	p.S36R	3
chr12:6978532	p.F145L,TPI1	2
chr12:6979288	p.I26I,TPI1	1
chr12:6976808	p.D153D,TPI1	1
chr12:6978441	p.L29V,TPI1	1
chr12:6979473	p.V162I,TPI1	1
chr12:6976815	p.P45L,TPI1	1
chr12:6978443	p.T176N,TPI1	1
chr12:6979488	p.I49V,TPI1	1
chr12:6978046	p.A182S,TPI1	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 TPI1 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 TPI1

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


CCDC77,CDC20,CDCA3,DERA,EMG1,FOXM1,GAPDH, LDHB,LTBR,MAGOHB,MLF2,MRPL51,NCAPD2,NDUFA9, NOP2,PHB2,RAD51AP1,TEAD4,TPI1,UQCRH,USP5	AIMP2,AK1,ALDOA,CARM1,CCDC28B,COQ9,DYRK1B, ENDOG,FKBP3,GAMT,GAPDH,MDH2,MYL6B,LINC00116, NDUFS2,SH2B2,SHISA4,SLC25A11,TPI1,UBAC1,UQCRC1

ATP5B,CDCA3,COX6A1,EIF5A,EIF5AL1,ENO1,GAPDH, H2AFZ,MLF2,MRPL51,NDUFA9,PGAM1,PHB2,PSMD9, RAN,SRSF9,SLC25A3,TPI1,TUBA1B,TUBA1C,USP5	ANXA4,AP2S1,ASL,AURKAIP1,C2orf47,COX6B1,EDF1, ETFB,GDI2,LMAN2,MDH2,MGST2,MPDU1,NDUFC1, POP4,TACO1,TALDO1,EMC3,TMEM208,TPI1,UQCRC1

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 TPI1

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
DB01709	triosephosphate isomerase 1	experimental	2-Phosphoglyceric Acid
DB01779	triosephosphate isomerase 1	experimental	Glycerol-2-Phosphate
DB02515	triosephosphate isomerase 1	experimental	3-Phosphoglycerol
DB02726	triosephosphate isomerase 1	experimental	2-Phosphoglycolic Acid
DB02951	triosephosphate isomerase 1	experimental	3-Hydroxypyruvic Acid
DB04510	triosephosphate isomerase 1	experimental	3-Phosphoglyceric Acid
DB01695	triosephosphate isomerase 1	experimental	N-Hydroxy-4-Phosphono-Butanamide
DB03026	triosephosphate isomerase 1	experimental	Phosphoglycolohydroxamic Acid
DB03132	triosephosphate isomerase 1	experimental	3-(2-Benzothiazolylthio)-1-Propanesulfonic Acid
DB03135	triosephosphate isomerase 1	experimental	[2(Formyl-Hydroxy-Amino)-Ethyl]-Phosphonic Acid
DB03314	triosephosphate isomerase 1	experimental	Fluorotryptophane
DB03379	triosephosphate isomerase 1	experimental	2-Carboxyethylphosphonic Acid
DB03900	triosephosphate isomerase 1	experimental	2-Methyl-2-Propanol
DB04326	triosephosphate isomerase 1	experimental	1,3-Dihydroxyacetonephosphate
DB04447	triosephosphate isomerase 1	experimental	1,4-Dithiothreitol
DB07387	triosephosphate isomerase 1	experimental	3-(BUTYLSULPHONYL)-PROPANOIC ACID
DB00121	triosephosphate isomerase 1	approved; nutraceutical	Biotin

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Cross referenced IDs for TPI1

* 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