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 GPHN

Basic gene info.	Gene symbol	GPHN
	Gene name	gephyrin
	Synonyms	GEPH\|GPH\|GPHRYN\|HKPX1\|MOCODC
	Cytomap	UCSC genome browser: 14q23.3
	Genomic location	chr14 :66974124-67648525
	Type of gene	protein-coding
	RefGenes	NM_001024218.1, NM_020806.4,
	Ensembl id	ENSG00000171723
	Description	-
	Modification date	20141219
dbXrefs	MIM : 603930
	HGNC : HGNC
	Ensembl : ENSG00000171723
	HPRD : 04893
	Vega : OTTHUMG00000029785
Protein	UniProt: Q9NQX3 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GPHN
	BioGPS: 10243
	Gene Expression Atlas: ENSG00000171723
	The Human Protein Atlas: ENSG00000171723
Pathway	NCI Pathway Interaction Database: GPHN
	KEGG: GPHN
	REACTOME: GPHN
	ConsensusPathDB
	Pathway Commons: GPHN
Metabolism	MetaCyc: GPHN
	HUMANCyc: GPHN
Regulation	Ensembl's Regulation: ENSG00000171723
	miRBase: chr14 :66,974,124-67,648,525
	TargetScan: NM_001024218
	cisRED: ENSG00000171723
Context	iHOP: GPHN
	cancer metabolism search in PubMed: GPHN
	UCL Cancer Institute: GPHN
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: GPHN
	Familial Cancer Database: GPHN

* 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_VITAMINS_AND_COFACTORS

Others
OMIM	603930; gene. 615501; phenotype.
Orphanet	308400; Sulfite oxidase deficiency due to molybdenum cofactor deficiency type C. 3197; Hereditary hyperekplexia.
Disease	KEGG Disease: GPHN
	MedGen: GPHN (Human Medical Genetics with Condition)
	ClinVar: GPHN
Phenotype	MGI: GPHN (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GPHN

Mutations for GPHN

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
ovary	GPHN	chr14	67283998	67284018	GPHN	chr14	67284199	67284219
ovary	GPHN	chr14	67482168	67482188	GPHN	chr14	67482499	67482519
pancreas	GPHN	chr14	67087992	67088192	GPHN	chr14	67083708	67083908
pancreas	GPHN	chr14	67588674	67588694	GPHN	chr14	67623116	67623136
pancreas	GPHN	chr14	67620693	67620713	GPHN	chr14	67610533	67610553
prostate	GPHN	chr14	66990562	66992562	RGS6	chr14	72644723	72646723
prostate	GPHN	chr14	66990882	66992882	RGS6	chr14	72808787	72810787
prostate	GPHN	chr14	67161914	67163914	DPF3	chr14	73349955	73351955

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 GPHN 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
DB087988	USP6NL	1	225	10	11639629	11653573	GPHN	225	462	14	67291192	67382765
BX509307	GPHN	1	88	14	67102484	67102571	CCDC12	83	658	3	46982228	46982802
BE172739	DNM1L	23	143	12	32896833	32896951	GPHN	125	245	14	67625457	67625577

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	5	2	1				1				1			1	2
GAIN (# sample)	1	1													1
LOSS (# sample)	4	1	1				1				1			1	1

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=11)	Stat. for Synonymous SNVs (# total SNVs=0)
	There's no s-snv.
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
chr14:67578599-67578599	p.R479*	2
chr14:67626169-67626169	p.A625V	1
chr14:67631930-67631930	p.I654M	1
chr14:67635728-67635728	p.P685L	1
chr14:67147816-67147816	p.?	1
chr14:67346678-67346678	p.R106W	1
chr14:67346679-67346679	p.R106Q	1
chr14:67389434-67389434	p.R170C	1
chr14:67389594-67389594	p.G223A	1
chr14:67525489-67525489	p.I377N	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		15			1		4	1		3	1	2			9	8		11
# mutation	1	3		14			1		4	1		3	1	2			11	10		20
nonsynonymous SNV	1	2		12			1		3	1		3		2			8	10		16
synonymous SNV		1		2					1				1				3			4

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
chr14:67626169	p.R527C,GPHN	3
chr14:67589024	p.A592V,GPHN	3
chr14:67525490	p.I344I,GPHN	2
chr14:67631930	p.R387C,GPHN	2
chr14:67567593	p.I621M,GPHN	2
chr14:67389594	p.L484F,GPHN	1
chr14:67610133	p.P652L,GPHN	1
chr14:67646301	p.T139T,GPHN	1
chr14:67525414	p.S270L,GPHN	1
chr14:67346678	p.V490F,GPHN	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 GPHN 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 GPHN

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


ATP6V1C1,DHRS4-AS1,LINC00238,C8orf37,DNAL1,EARS2,EBAG9, EXD2,FLNB,GPHN,MAPT,MBLAC2,OCIAD1,PARD6B, RAD17,SLC39A9,STAU2,TMEM128,TRPS1,UBXN2B,WWP1	ABCB7,AGPAT9,ALDH1L1,AMBN,BMP3,C17orf53,IZUMO4, CTH,EYA1,GLUL,GMCL1,GPD1L,GPHN,HADH, MOCS1,NTSR2,PMM1,PXMP2,RASL10B,TCEB3,USP30

ALDH6A1,LINC00238,CDKL1,DHRS4L2,DLST,EPHB3,GPHN, IMPDH2,KIAA0586,L2HGDH,LRP4,MMACHC,MTHFD1,AP5M1, OXA1L,RGMB,SAMM50,SETD3,SIPA1L1,TRMT5,WDR89	ANAPC1,AQR,ATIC,PROSER1,CBX5,CCDC15,DCAF7, EXOSC10,GANAB,GPHN,INCENP,INTS9,FOCAD,NCAPD2, PAXIP1,PTK7,SND1,SPTLC2,SSRP1,TOP2A,VPRBP

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 GPHN

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28840; -.
Organism-specific databases	CTD	10243; -.

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
DB01942	gephyrin	experimental	Formic Acid
DB03766	gephyrin	experimental	Propanoic Acid

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Cross referenced IDs for GPHN

* 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