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 GAPDH

Basic gene info.	Gene symbol	GAPDH
	Gene name	glyceraldehyde-3-phosphate dehydrogenase
	Synonyms	G3PD\|GAPD\|HEL-S-162eP
	Cytomap	UCSC genome browser: 12p13
	Genomic location	chr12 :6644408-6647537
	Type of gene	protein-coding
	RefGenes	NM_001256799.2, NM_001289745.1,NM_001289746.1,NM_002046.5,
	Ensembl id	ENSG00000111640
	Description	aging-associated gene 9 proteinepididymis secretory sperm binding protein Li 162ePpeptidyl-cysteine S-nitrosylase GAPDH
	Modification date	20141222
dbXrefs	MIM : 138400
	HGNC : HGNC
	Ensembl : ENSG00000111640
	HPRD : 00713
	Vega : OTTHUMG00000137379
Protein	UniProt: P04406 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GAPDH
	BioGPS: 2597
	Gene Expression Atlas: ENSG00000111640
	The Human Protein Atlas: ENSG00000111640
Pathway	NCI Pathway Interaction Database: GAPDH
	KEGG: GAPDH
	REACTOME: GAPDH
	ConsensusPathDB
	Pathway Commons: GAPDH
Metabolism	MetaCyc: GAPDH
	HUMANCyc: GAPDH
Regulation	Ensembl's Regulation: ENSG00000111640
	miRBase: chr12 :6,644,408-6,647,537
	TargetScan: NM_001256799
	cisRED: ENSG00000111640
Context	iHOP: GAPDH
	cancer metabolism search in PubMed: GAPDH
	UCL Cancer Institute: GAPDH
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GAPDH in cancer cell metabolism	1. Zhang JY, Zhang F, Hong CQ, Giuliano AE, Cui XJ, et al. (2015) Critical protein GAPDH and its regulatory mechanisms in cancer cells. Cancer Biol Med 12: 10-22. doi: 10.7497/j.issn.2095-3941.2014.0019. pmid: 4383849. go to article 2. Jing Z, Heng W, Xia L, Ning W, Yafei Q, et al. (2015) Downregulation of phosphoglycerate dehydrogenase inhibits proliferation and enhances cisplatin sensitivity in cervical adenocarcinoma cells by regulating Bcl-2 and caspase-3. Cancer Biol Ther 16: 541-548. doi: 10.1080/15384047.2015.1017690. go to article 3. Hjerpe E, Brage SE, Frostvik Stolt M, Johansson H, Shoshan M, et al. (2014) Metabolic markers and HSP60 in chemonaive serous solid ovarian cancer versus ascites. Int J Gynecol Cancer 24: 1389-1394. doi: 10.1097/IGC.0000000000000246. go to article

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

Cancer Description
Cancer	CGAP: GAPDH
	Familial Cancer Database: GAPDH

* 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 BIOCARTA_GLYCOLYSIS_PATHWAY REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	138400; gene.
Orphanet
Disease	KEGG Disease: GAPDH
	MedGen: GAPDH (Human Medical Genetics with Condition)
	ClinVar: GAPDH
Phenotype	MGI: GAPDH (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GAPDH

Mutations for GAPDH

* 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

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

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 GAPDH 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
DA446259	GAPDH	1	251	12	6643686	6645897	SON	247	572	21	34927473	34929562
BI117444	CDKN1A	2	160	6	36654392	36654550	GAPDH	160	873	12	6643705	6646888
BQ314752	GAPDH	1	191	12	6645734	6646143	JUP	187	499	17	39847268	39847581
BQ314754	GAPDH	1	191	12	6645734	6646143	JUP	187	535	17	39847268	39847617
BF815183	MALAT1	16	285	11	65268063	65268332	GAPDH	275	392	12	6646152	6646359
BE255519	PRMT2	1	466	21	48069565	48081784	GAPDH	467	552	12	6645706	6645881
BQ314753	GAPDH	1	193	12	6645734	6646143	JUP	189	446	17	39847268	39847526
DB548780	ZNF836	1	411	19	52659282	52659692	GAPDH	403	455	12	6647484	6647536
BQ314756	GAPDH	1	191	12	6645734	6646143	JUP	187	499	17	39847268	39847580
CD387579	GAPDH	16	541	12	6643686	6646484	UBQLN4	535	592	1	156005092	156005149
BG574895	GAPDH	1	618	12	6646531	6647444	PEA15	612	670	1	160184354	160184412
BG926120	PDCD4	92	422	10	112635795	112641287	GAPDH	415	667	12	6646488	6646932
DA778207	GAPDH	1	95	12	6643686	6644020	FAM3C	92	574	7	121000124	121023065
BQ314755	GAPDH	1	191	12	6645734	6646143	JUP	187	538	17	39847268	39847620
DW440511	GAPDH	18	187	12	6643683	6646535	RPL23	185	386	17	37008897	37009979
BQ314751	GAPDH	1	191	12	6645734	6646143	JUP	187	551	17	39847268	39847635
BQ019603	GAPDH	18	132	12	6647423	6647537	AHNAK	129	687	11	62284554	62285112
AW498880	RPL28	1	160	19	55899375	55899730	GAPDH	161	391	12	6644002	6645955
BC009430	GAPDH	61	997	12	6646122	6647537	RPN2	997	1744	20	35857110	35870026
BF816390	GAPDH	1	162	12	6643686	6645719	MRPS17	155	219	7	56022696	56022760
CB147232	GAPDH	1	327	12	6646881	6647311	SERPINA1	326	459	14	94849493	94854945
AJ711772	PRICKLE4	1	421	6	41755449	41757469	GAPDH	422	531	12	6647011	6647120
BC013852	GAPDH	1	618	12	6646530	6647444	PEA15	612	681	1	160184354	160184423
CV312017	SKP1	6	213	5	133497362	133497575	GAPDH	213	428	12	6646910	6647125
BQ671968	GAPDH	35	141	12	6647431	6647537	FBXL7	141	766	5	15937518	15938142
BM041208	CPT1A	2	681	11	68552431	68575053	GAPDH	662	705	12	6647494	6647537
BQ420306	CALML4	17	473	15	68484020	68490023	GAPDH	463	516	12	6647483	6647536
BI003826	GAPDH	11	63	12	6643683	6643735	GAPDH	60	169	12	6643978	6645719
BG391044	GAPDH	22	84	12	6646125	6646277	GAPDH	82	600	12	6646154	6647044
BC044944	ZNF638	1	1612	2	71601071	71603450	GAPDH	1604	1659	12	6647482	6647537
BF820683	SRRT	17	221	7	100483975	100484540	GAPDH	211	420	12	6647322	6647532

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=20)	Stat. for Synonymous SNVs (# total SNVs=3)

Stat. for Deletions (# total SNVs=1)	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
chr12:6647098-6647098	p.S292A	2
chr12:6646853-6646853	p.S210F	2
chr12:6646152-6646152	p.V101V	2
chr12:6647313-6647313	p.A329T	1
chr12:6644014-6644014	p.V6I	1
chr12:6646278-6646278	p.G115fs*21	1
chr12:6646941-6646941	p.N239K	1
chr12:6645733-6645733	p.D35Y	1
chr12:6646281-6646281	p.G114G	1
chr12:6646994-6646999	p.D257_K259>E	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		1	1	1	1		2					3	2	1			1	1		3
# mutation		1	1	1	1		2					2	2	1			1	1		3
nonsynonymous SNV		1	1	1	1							2	2	1			1	1		2
synonymous SNV							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
chr12:6646512	p.A119S,GAPDH	2
chr12:6645733	p.I165I,GAPDH	1
chr12:6646882	p.V178L,GAPDH	1
chr12:6645907	p.V219A,GAPDH	1
chr12:6647006	p.S250A,GAPDH	1
chr12:6646115	p.T252T,GAPDH	1
chr12:6647098	p.G258D,GAPDH	1
chr12:6646132	p.D35Y,GAPDH	1
chr12:6647106	p.E21K,GAPDH	1
chr12:6646283	p.D47G,GAPDH	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 GAPDH 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 GAPDH

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.

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Protein Expression Plot (RPPA)

*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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


ASPRV1,C1orf68,CCL27,FLG2,GAPDHS,KPRP,KRT1, KRT2,LCE1A,LCE1B,LCE1C,LCE1D,LCE1E,LCE1F, LCE2B,LCE2C,LCE2D,LCE5A,LCE6A,LOR,MLANA	ARID1A,CCDC57,CRAMP1L,ERN1,GAPDHS,ITPR3,CLUHP3, LDB1,LOC100131193,LOC646471,MAML1,NCKAP5,NEK8,PRDM15, SLC26A1,SPATA13,TUBGCP6,URB1,ZNF335,ZNF500,ZNF710

AHSA2,SNHG20,GAPDHS,KLHL31,LENG8,LOC100129387,LOC100130557, LOC256880,LOC440944,NSUN5P2,OGT,PMS2P3,TRMT10B,SEPT7P2, SNORA71E,STAG3L3,TCTE3,TRIM52,WDR27,DPH7,ZNF767P	AHI1,ALG1L2,ASPH,SYNE4,TDRP,COG5,COG6, FIBCD1,GAPDHS,GPRIN3,KCTD12,KIR2DL1,PRPS1L1,RARRES1, RGS17,SEC24D,SLC16A7,SLC26A4,SLC6A12,SULT1C2,TBC1D8B

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 GAPDH

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P04406; -.
Chemistry	ChEMBL	CHEMBL2284; -.
Organism-specific databases	PharmGKB	PA28554; -.
Organism-specific databases	CTD	2597; -.

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
DB00157	glyceraldehyde-3-phosphate dehydrogenase	approved; nutraceutical	NADH
DB01907	glyceraldehyde-3-phosphate dehydrogenase	experimental	Nicotinamide-Adenine-Dinucleotide
DB02059	glyceraldehyde-3-phosphate dehydrogenase	experimental	Adenosine-5-Diphosphoribose
DB03893	glyceraldehyde-3-phosphate dehydrogenase	experimental	Thionicotinamide-Adenine-Dinucleotide
DB07347	glyceraldehyde-3-phosphate dehydrogenase	experimental	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
DB02263	glyceraldehyde-3-phosphate dehydrogenase	experimental	Glyceraldehyde-3-Phosphate
DB00269	glyceraldehyde-3-phosphate dehydrogenase	approved	Chlorotrianisene
DB00286	glyceraldehyde-3-phosphate dehydrogenase	approved	Conjugated Estrogens
DB00890	glyceraldehyde-3-phosphate dehydrogenase	approved	Dienestrol
DB00255	glyceraldehyde-3-phosphate dehydrogenase	approved	Diethylstilbestrol
DB00783	glyceraldehyde-3-phosphate dehydrogenase	approved; investigational	Estradiol
DB00655	glyceraldehyde-3-phosphate dehydrogenase	approved	Estrone
DB00977	glyceraldehyde-3-phosphate dehydrogenase	approved	Ethinyl Estradiol

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Cross referenced IDs for GAPDH

* 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