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 TP53

Basic gene info.	Gene symbol	TP53
	Gene name	tumor protein p53
	Synonyms	BCC7\|LFS1\|P53\|TRP53
	Cytomap	UCSC genome browser: 17p13.1
	Genomic location	chr17 :7571719-7578811
	Type of gene	protein-coding
	RefGenes	NM_000546.5, NM_001126112.2,NM_001126113.2,NM_001126114.2,NM_001126115.1, NM_001126116.1,NM_001126117.1,NM_001126118.1,NM_001276695.1, NM_001276696.1,NM_001276697.1,NM_001276698.1,NM_001276699.1, NM_001276760.1,NM_001276761.1,
	Ensembl id	ENSG00000141510
	Description	antigen NY-CO-13cellular tumor antigen p53mutant tumor protein 53p53 tumor suppressorphosphoprotein p53transformation-related protein 53tumor protein 53
	Modification date	20141222
dbXrefs	MIM : 191170
	HGNC : HGNC
	Ensembl : ENSG00000141510
	HPRD : 01859
	Vega : OTTHUMG00000162125
Protein	UniProt: P04637 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TP53
	BioGPS: 7157
	Gene Expression Atlas: ENSG00000141510
	The Human Protein Atlas: ENSG00000141510
Pathway	NCI Pathway Interaction Database: TP53
	KEGG: TP53
	REACTOME: TP53
	ConsensusPathDB
	Pathway Commons: TP53
Metabolism	MetaCyc: TP53
	HUMANCyc: TP53
Regulation	Ensembl's Regulation: ENSG00000141510
	miRBase: chr17 :7,571,719-7,578,811
	TargetScan: NM_000546
	cisRED: ENSG00000141510
Context	iHOP: TP53
	cancer metabolism search in PubMed: TP53
	UCL Cancer Institute: TP53
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TP53 in cancer cell metabolism	1. Wong EYL, Wong SCC, Chan CML, Lam EKY, Ho LY, et al. (2015) TP53-induced glycolysis and apoptosis regulator promotes proliferation and invasiveness of nasopharyngeal carcinoma cells. Oncology letters 9: 569-574. go to article 2. Shen L, O’Shea JM, Kaadige MR, Cunha S, Wilde BR, et al. (2015) Metabolic reprogramming in triple-negative breast cancer through Myc suppression of TXNIP. Proceedings of the National Academy of Sciences 112: 5425-5430. go to article 3. Mishra P, Ambs S (2015) Metabolic signatures of human breast cancer. Molecular & cellular oncology 2: e992217. go to article

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Phenotypic Information for TP53(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TP53
	Familial Cancer Database: TP53

* 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 BLCA ⁶, BRCA ⁷, CLL ⁸, COAD ⁹, CRC ¹⁰, DLBCL ¹¹, ESO ¹², GBM ¹³, HNSC ¹⁴, KIRC ¹⁵, LAML ¹⁶, LUAD ¹⁷, LUSC ¹⁸, MEL ¹⁹, MM ²⁰, OV ²¹, PRAD ²², UCEC ²³, STAD ²⁴, STAD ²⁵, SKCM ²⁶, THCA ²⁷, GBM ²⁸, HNSC ²⁹, SCLC ³⁰, PAAD ³¹,	Therapeutic Vulnerabilities in Cancer³²

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,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
8 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
9 http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html,
10 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
11 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
12 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
13 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
14 https://www.sciencemag.org/content/333/6046/1157,
15 http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html,
16 http://www.nejm.org/doi/full/10.1056/NEJMoa1301689,
17 http://www.sciencedirect.com/science/article/pii/S0092867412010227,
18 http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html,
19 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
20 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
21 http://www.nature.com/nature/journal/v474/n7353/full/nature10166.html,
22 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
23 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
24 http://www.nature.com/ng/journal/v46/n6/full/ng.2983.html,
25 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
26 http://www.sciencedirect.com/science/article/pii/S0092867415006340,
27 http://www.sciencedirect.com/science/article/pii/S0092867414012380,
28 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
29 http://www.nature.com/nature/journal/v517/n7536/full/nature14129.html,
30 http://www.nature.com/nature/journal/v524/n7563/full/nature14664.html,
31 http://www.nature.com/nature/journal/v518/n7540/full/nature14169.html,
32Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

Others
OMIM	133239; phenotype. 133239; phenotype. 151623; phenotype. 151623; phenotype. 191170; gene+phenotype. 191170; gene+phenotype. 202300; phenotype. 202300; phenotype. 211980; phenotype. 211980; phenotype. 260500; phenotype. 260500; phenotype. 275355; phenotype. 275355; phenotype. 614740; phenotype. 614740; phenotype.
Orphanet	1333; Familial pancreatic carcinoma. 1333; Familial pancreatic carcinoma. 1501; Adrenocortical carcinoma. 1501; Adrenocortical carcinoma. 251576; Gliosarcoma. 251576; Gliosarcoma. 251579; Giant cell glioblastoma. 251579; Giant cell glioblastoma. 2807; Papilloma of choroid plexus. 2807; Papilloma of choroid plexus. 3318; Essential thrombocythemia. 3318; Essential thrombocythemia. 524; Li-Fraumeni syndrome. 524; Li-Fraumeni syndrome. 67038; B-cell chronic lymphocytic leukemia. 67038; B-cell chronic lymphocytic leukemia. 99860; Precursor B-cell acute lymphoblastic leukemia. 99860; Precursor B-cell acute lymphoblastic leukemia.
Disease	KEGG Disease: TP53
	MedGen: TP53 (Human Medical Genetics with Condition)
	ClinVar: TP53
Phenotype	MGI: TP53 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TP53

Mutations for TP53

* 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
pancreas	TP53	chr17	7576890	7576910	TP53	chr17	7576823	7576843

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 TP53 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
CB048242	TP53	27	239	17	7571739	7571951	ARHGAP26	236	307	5	142297940	142298011
BM991038	MLF2	13	305	12	6857164	6857456	TP53	297	614	17	7572411	7572728
AA947588	TP53	2	325	17	7572945	7573268	OSBPL10	320	521	3	31964262	31964463

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=1424

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=13383)	Stat. for Synonymous SNVs (# total SNVs=428)

Stat. for Deletions (# total SNVs=1122)	Stat. for Insertions (# total SNVs=390)

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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
chr17:7578406-7578406	p.R175H	951
chr17:7577538-7577538	p.R248Q	723
chr17:7577120-7577120	p.R273H	713
chr17:7577121-7577121	p.R273fs*72	598
chr17:7577539-7577539	p.R248W	553
chr17:7577094-7577094	p.R282G	483
chr17:7577548-7577548	p.G245C	404
chr17:7577534-7577534	p.R249S	342
chr17:7578190-7578190	p.Y220S	277
chr17:7578212-7578212	p.R213*	273

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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=64

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	25	161	1	210	75		136	9	11	1	12	105	101	218	4	7	23	68		57
# mutation	25	80	1	204	51		80	9	12	1	12	78	65	94	4	7	20	45		38
nonsynonymous SNV	23	78	1	151	48		79	9	11	1	11	77	62	91	4	7	19	43		36
synonymous SNV	2	2		55	3		3		1		1	1	4	3			1	2		2

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
chr17:7578406	p.R43H,TP53	64
chr17:7577120	p.R141P,TP53	63
chr17:7577121	p.R141C,TP53	61
chr17:7577538	p.R116Q,TP53	43
chr17:7577539	p.R116W,TP53	37
chr17:7578190	p.Y88C,TP53	34
chr17:7577094	p.R150W,TP53	32
chr17:7578271	p.H61R,TP53	29
chr17:7578394	p.H47R,TP53	27
chr17:7577548	p.G113S,TP53	26

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 TP53 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 TP53

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


C1QBP,COX10,CTDNEP1,EIF4A1,EIF5AL1,ELAC2,GEMIN4, METTL16,MYBBP1A,NDEL1,NUP88,PFAS,PITPNA,PLD2, RPA1,RPL26,SCO1,SENP3,TP53,TSR1,YWHAE	BCL11A,DIRAS1,DKC1,DTNB,ETV6,GYLTL1B,H2AFY2, IPO4,KCTD14,LAD1,LRRC8D,NONO,POLR1C,PTK7, RCC2,SOX10,TGIF2,TP53,TRIM27,TTLL4,UCK2

COX10,DPH1,DRG2,CTDNEP1,EIF4A1,ELAC2,FXR2, GEMIN4,GLOD4,CLUH,MED9,MYBBP1A,PELP1,RNMTL1, SENP3,SHMT1,TMEM102,TP53,TRAPPC1,TTC19,YWHAE	ARHGEF10L,BEND3,CASP2,CDT1,EPHB2,EPHB3,FAM171A1, GPR56,HUNK,INTS5,MAZ,MEN1,METTL13,MLEC, MTL5,PROM2,PVRL1,RCC2,TARS2,TP53,NELFA

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 TP53

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P04637; -.
Chemistry	ChEMBL	CHEMBL2221344; -.
Chemistry	BindingDB	P04637; -.
Chemistry	ChEMBL	CHEMBL2221344; -.
Organism-specific databases	PharmGKB	PA36679; -.
Organism-specific databases	PharmGKB	PA36679; -.
Organism-specific databases	CTD	7157; -.
Organism-specific databases	CTD	7157; -.

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
DB01008	tumor protein p53	approved; investigational	Busulfan
DB00675	tumor protein p53	approved	Tamoxifen
DB00269	tumor protein p53	approved	Chlorotrianisene
DB00286	tumor protein p53	approved	Conjugated Estrogens
DB00890	tumor protein p53	approved	Dienestrol
DB00255	tumor protein p53	approved	Diethylstilbestrol
DB00783	tumor protein p53	approved; investigational	Estradiol
DB00655	tumor protein p53	approved	Estrone
DB00977	tumor protein p53	approved	Ethinyl Estradiol
DB00958	tumor protein p53	approved	Carboplatin
DB00531	tumor protein p53	approved; investigational	Cyclophosphamide
DB01248	tumor protein p53	approved; investigational	Docetaxel
DB00997	tumor protein p53	approved; investigational	Doxorubicin
DB00773	tumor protein p53	approved	Etoposide
DB00544	tumor protein p53	approved	Fluorouracil
DB01229	tumor protein p53	approved	Paclitaxel
DB01030	tumor protein p53	approved; investigational	Topotecan
DB00515	tumor protein p53	approved	Cisplatin
DB01033	tumor protein p53	approved	Mercaptopurine
DB00563	tumor protein p53	approved	Methotrexate
DB01050	tumor protein p53	approved	Ibuprofen
DB00291	tumor protein p53	approved	Chlorambucil

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Cross referenced IDs for TP53

* 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