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 GNAO1

Basic gene info.	Gene symbol	GNAO1
	Gene name	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O
	Synonyms	EIEE17\|G-ALPHA-o\|GNAO
	Cytomap	UCSC genome browser: 16q13
	Genomic location	chr16 :56225250-56382111
	Type of gene	protein-coding
	RefGenes	NM_020988.2, NM_138736.2,
	Ensembl id	ENSG00000087258
	Description	guanine nucleotide-binding protein G(o) subunit alpha
	Modification date	20141207
dbXrefs	MIM : 139311
	HGNC : HGNC
	Ensembl : ENSG00000087258
	HPRD : 00757
	Vega : OTTHUMG00000133241
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNAO1
	BioGPS: 2775
	Gene Expression Atlas: ENSG00000087258
	The Human Protein Atlas: ENSG00000087258
Pathway	NCI Pathway Interaction Database: GNAO1
	KEGG: GNAO1
	REACTOME: GNAO1
	ConsensusPathDB
	Pathway Commons: GNAO1
Metabolism	MetaCyc: GNAO1
	HUMANCyc: GNAO1
Regulation	Ensembl's Regulation: ENSG00000087258
	miRBase: chr16 :56,225,250-56,382,111
	TargetScan: NM_020988
	cisRED: ENSG00000087258
Context	iHOP: GNAO1
	cancer metabolism search in PubMed: GNAO1
	UCL Cancer Institute: GNAO1
Assigned class in ccmGDB	C

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Phenotypic Information for GNAO1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNAO1
	Familial Cancer Database: GNAO1

* 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_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GNAO1
	MedGen: GNAO1 (Human Medical Genetics with Condition)
	ClinVar: GNAO1
Phenotype	MGI: GNAO1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNAO1

Mutations for GNAO1

* 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
breast	GNAO1	chr16	56232647	56232647	GNAO1	chr16	56252900	56252900
large_intestine	GNAO1	chr16	56312514	56312514		chr16	79703505	79703505

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 GNAO1 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
DB344809	FBRSL1	1	64	12	133160815	133160878	GNAO1	59	550	16	56374478	56377743
DA491290	ZNF711	1	126	X	84498997	84499122	GNAO1	125	553	16	56225702	56226130
BF362557	TBC1D5	2	74	3	17780626	17780698	GNAO1	71	328	16	56378567	56378824
AW014453	GNAO1	11	61	16	56390199	56390249	GNAO1	54	393	16	56389963	56390302
M78823	GNAO1	1	89	16	56390777	56390865	FAM81A	83	441	15	59732524	59732880

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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=33)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr16:56388797-56388797	p.D299D	3
chr16:56388909-56388909	p.D337H	3
chr16:56388841-56388841	p.S314L	2
chr16:56370655-56370655	p.V202V	2
chr16:56385325-56385325	p.F251F	2
chr16:56370674-56370674	p.R209C	2
chr16:56362664-56362664	p.N142S	2
chr16:56370728-56370728	p.A227T	2
chr16:56362673-56362673	p.R145Q	2
chr16:56362569-56362569	p.V111fs*1	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	3	3		11	1		2		1			9			1	1	3	1		10
# mutation	3	3		11	1		2		1			8			1	1	3	1		11
nonsynonymous SNV	1	2		9	1		2		1			2				1	2			7
synonymous SNV	2	1		2								6			1		1	1		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
chr16:56388797	p.D337N	2
chr16:56374870	p.P283Q	2
chr16:56370656	p.F251F	2
chr16:56388909	p.G203R,GNAO1	2
chr16:56385325	p.D299D	2
chr16:56362673	p.G92D,GNAO1	1
chr16:56374784	p.A227T,GNAO1	1
chr16:56385394	p.A301A	1
chr16:56309890	p.I93I,GNAO1	1
chr16:56362683	p.A227A,GNAO1	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 GNAO1 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 GNAO1

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


APLP1,BSN,CPLX2,DISP2,DKFZP434H168,AMER3,GNAO1, UNC79,LOC283856,MAPK8IP1,PHF21B,PSD,PTPRN2,RUNDC3A, SNAP25,SPTBN4,SYN1,SYP,SYT4,TMEM145,UNC13A	C11orf94,FOXL2NB,CDSN,COL4A6,CWH43,CYP4F22,FOXD4L6, FOXL2,GNAO1,HS6ST2,KLK2,LOC283856,LPHN3,NETO2, NRK,OR52W1,RAP1GDS1,SCRG1,UPK3A,WIF1,ZNF689

ASB2,CAND2,CLIP3,GNAO1,GPM6A,GRIK5,HSPB8, KIAA2022,LDB3,LMOD1,LONRF2,LRCH2,MAB21L2,MAP6, MYH11,MYLK,MYOCD,PDZRN4,REEP2,SPEG,TCEAL2	ATP2B4,CACNA1C,CACNA1H,DMD,FRMPD4,GNAO1,GRIK5, ITGA7,KCNB1,KCNMA1,MRVI1,MYH11,TENM3___TENM1,PPP1R12B, PRUNE2,PTGS1,SPEG,SVIL,TACR2,TNS1,TSPAN18

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 GNAO1

There's no related Drug.

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Cross referenced IDs for GNAO1

* 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