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 POMC

Basic gene info.	Gene symbol	POMC
	Gene name	proopiomelanocortin
	Synonyms	ACTH\|CLIP\|LPH\|MSH\|NPP\|POC
	Cytomap	UCSC genome browser: 2p23.3
	Genomic location	chr2 :25383721-25391559
	Type of gene	protein-coding
	RefGenes	NM_000939.2, NM_001035256.1,
	Ensembl id	ENSG00000115138
	Description	adrenocorticotropic hormoneadrenocorticotropinalpha-MSHalpha-melanocyte-stimulating hormonebeta-LPHbeta-MSHbeta-endorphinbeta-melanocyte-stimulating hormonecorticotropin-like intermediary peptidecorticotropin-lipotropingamma-LPHgamma-MSHlipotr
	Modification date	20141207
dbXrefs	MIM : 176830
	HGNC : HGNC
	Ensembl : ENSG00000115138
	HPRD : 01462
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POMC
	BioGPS: 5443
	Gene Expression Atlas: ENSG00000115138
	The Human Protein Atlas: ENSG00000115138
Pathway	NCI Pathway Interaction Database: POMC
	KEGG: POMC
	REACTOME: POMC
	ConsensusPathDB
	Pathway Commons: POMC
Metabolism	MetaCyc: POMC
	HUMANCyc: POMC
Regulation	Ensembl's Regulation: ENSG00000115138
	miRBase: chr2 :25,383,721-25,391,559
	TargetScan: NM_000939
	cisRED: ENSG00000115138
Context	iHOP: POMC
	cancer metabolism search in PubMed: POMC
	UCL Cancer Institute: POMC
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: POMC
	Familial Cancer Database: POMC

* 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
REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for POMC

* 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 POMC 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
AV750716	POMC	8	306	2	25384529	25391423	STK16	302	545	2	220110425	220110762
CD251046	POMC	1	217	2	25387510	25391431	RPL14	212	446	3	40503530	40503764

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=26)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=2)	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
chr2:25384121-25384121	p.V211V	3
chr2:25384084-25384084	p.E224K	2
chr2:25387619-25387619	p.R8H	2
chr2:25384322-25384322	p.F144L	2
chr2:25384144-25384144	p.D204N	2
chr2:25384587-25384587	p.A56V	2
chr2:25383986-25383986	p.N256N	1
chr2:25384367-25384367	p.K129K	1
chr2:25387560-25387560	p.C28G	1
chr2:25384074-25384074	p.R227H	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=1

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		4			1		1	2		3	2			1	3	6	1	5
# mutation		1		4			1		1	2		3	2			1	4	7	1	6
nonsynonymous SNV				3			1		1	2		1	2			1	3	6		4
synonymous SNV		1		1								2					1	1	1	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
chr2:25384011	p.G238S,POMC	1
chr2:25384191	p.K136E,POMC	1
chr2:25387536	p.D234Y,POMC	1
chr2:25384028	p.R133S,POMC	1
chr2:25384212	p.P231P,POMC	1
chr2:25387560	p.P132L,POMC	1
chr2:25384042	p.P231L,POMC	1
chr2:25384246	p.L37L,POMC	1
chr2:25387568	p.P220S,POMC	1
chr2:25384054	p.D36N,POMC	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 POMC 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 POMC

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


ABCG8,ADH4,ALG1L,DNPH1,CCDC102A,EPHB3,FAM101A, FLJ23867,HCCAT5,KCNN4,KIAA1755,MFI2,MIA,NDRG2, NRTN,POLR2F,POMC,PTH2,SNX22,SOX10,TPPP2	ATP5D,C17orf89,BABAM1,CDKN2D,CLTB,DEXI,FAM89B, HOMER3,HSPB1,KEAP1,LSM10,MAF1,MAP1LC3A,MRPL41, NDUFS8,NOSIP,POMC,PSMC3,PSMD4,TWF2,ZNF358

CPT1C,DPYSL4,FLG,GPR162,GRIN2A,HPCAL4,JPH4, KCNT2,NRG2,NTRK1,POMC,RAB39B,RGAG4,SCN1A, SLC17A7,SLITRK2,SSTR2,TCEAL5,TMEM59L,VENTXP1,ZNF385D	C10orf25,C20orf27,C9orf9,CDKN2C,CRELD1,FFAR3,GYPC, KCNJ5,LOC678655,NAT14,NINJ1,OAZ2,PELI3,PJA1, PLA2G2C,POMC,RAPSN,SLC22A2,SNN,TULP2,UBTD1

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 POMC

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
DB00836	proopiomelanocortin	approved	Loperamide
DB01497	proopiomelanocortin	illicit; experimental	Etorphine
DB01565	proopiomelanocortin	illicit; experimental	Dihydromorphine
DB00269	proopiomelanocortin	approved	Chlorotrianisene
DB00286	proopiomelanocortin	approved	Conjugated Estrogens
DB00890	proopiomelanocortin	approved	Dienestrol
DB00255	proopiomelanocortin	approved	Diethylstilbestrol
DB00783	proopiomelanocortin	approved; investigational	Estradiol
DB00655	proopiomelanocortin	approved	Estrone
DB00977	proopiomelanocortin	approved	Ethinyl Estradiol

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Cross referenced IDs for POMC

* 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