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 GNAI2

Basic gene info.	Gene symbol	GNAI2
	Gene name	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2
	Synonyms	GIP\|GNAI2B\|H_LUCA15.1\|H_LUCA16.1
	Cytomap	UCSC genome browser: 3p21.31
	Genomic location	chr3 :50273646-50296786
	Type of gene	protein-coding
	RefGenes	NM_001166425.1, NM_001282617.1,NM_001282618.1,NM_001282619.1,NM_001282620.1, NM_002070.3,
	Ensembl id	ENSG00000263156
	Description	GTP-binding regulatory protein Gi alpha-2 chainadenylate cyclase-inhibiting G alpha proteinguanine nucleotide-binding protein G(i) subunit alpha-2guanine nucleotide-binding protein G(i), alpha-2 subunit
	Modification date	20141207
dbXrefs	MIM : 139360
	HGNC : HGNC
	Ensembl : ENSG00000114353
	HPRD : 00764
	Vega : OTTHUMG00000156940
Protein	UniProt: P04899 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNAI2
	BioGPS: 2771
	Gene Expression Atlas: ENSG00000263156
	The Human Protein Atlas: ENSG00000263156
Pathway	NCI Pathway Interaction Database: GNAI2
	KEGG: GNAI2
	REACTOME: GNAI2
	ConsensusPathDB
	Pathway Commons: GNAI2
Metabolism	MetaCyc: GNAI2
	HUMANCyc: GNAI2
Regulation	Ensembl's Regulation: ENSG00000263156
	miRBase: chr3 :50,273,646-50,296,786
	TargetScan: NM_001166425
	cisRED: ENSG00000263156
Context	iHOP: GNAI2
	cancer metabolism search in PubMed: GNAI2
	UCL Cancer Institute: GNAI2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GNAI2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNAI2
	Familial Cancer Database: GNAI2

* 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 SKCM ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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.sciencedirect.com/science/article/pii/S0092867415006340,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	139360; gene.
Orphanet
Disease	KEGG Disease: GNAI2
	MedGen: GNAI2 (Human Medical Genetics with Condition)
	ClinVar: GNAI2
Phenotype	MGI: GNAI2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNAI2

Mutations for GNAI2

* 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 GNAI2 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
BM931874	MBD5	1	102	2	149024645	149024746	GNAI2	89	194	3	50268507	50268611
BM450613	HSP90AA1	24	130	14	102549430	102549540	GNAI2	114	204	3	50296695	50296785
BY797642	GNAI2	1	198	3	50273688	50273885	NT5DC2	198	586	3	52562484	52563351
BE707091	GNAI2	20	206	3	50295821	50296003	PSAP	205	296	10	73579624	73580054
BM684932	GNAI2	19	123	3	50268507	50268611	MBD5	110	211	2	149024645	149024746
BI031334	NPIPB7	198	234	16	28512657	28512693	GNAI2	227	480	3	50281808	50282061
DB337573	LOC100128993	1	65	8	19102360	19102424	GNAI2	59	552	3	50294486	50296040
CK725123	GNAI2	7	209	3	50296583	50296785	PRKAG1	208	654	12	49396800	49397246
BI051043	GNAI2	9	145	3	50293693	50294232	GNAI2	140	310	3	50290505	50293682
AI377593	GNAI2	1	195	3	50296586	50296780	H19	185	414	11	2018056	2018286

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=28)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr3:50293695-50293695	p.R179H	4
chr3:50293689-50293689	p.R177Q	3
chr3:50290580-50290580	p.R143H	3
chr3:50290615-50290615	p.Y155H	2
chr3:50294446-50294446	p.L267L	2
chr3:50293704-50293704	p.T182I	2
chr3:50290492-50290492	p.A114T	2
chr3:50290494-50290494	p.A114A	2
chr3:50289876-50289876	p.R70Q	2
chr3:50294255-50294255	p.D232Y	2

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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	1	4			1		4	1	1			1			6	2		5
# mutation		3	1	6			1		4	1	1			1			6	2		5
nonsynonymous SNV		2	1	2					2	1	1			1			3	2		5
synonymous SNV		1		4			1		2								3

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
chr3:50294242	p.R98C,GNAI2	2
chr3:50294255	p.A146A,GNAI2	2
chr3:50293694	p.D151Y,GNAI2	2
chr3:50290578	p.C271Y,GNAI2	1
chr3:50293708	p.A83V,GNAI2	1
chr3:50273779	p.D86D,GNAI2	1
chr3:50290580	p.T4T	1
chr3:50273876	p.T90A,GNAI2	1
chr3:50293634	p.L37M	1
chr3:50289871	p.R96Q,GNAI2	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 GNAI2 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 GNAI2

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


ABI3,ACVRL1,C1orf54,EMP3,ENG,TMEM255B,GNAI2, GPX1,HYAL2,IFFO1,LST1,LYL1,NCF4,PLEKHO2, PPM1M,RHOG,SPI1,TGFB1,TNFSF12,TWF2,TYROBP	ACVRL1,C10orf54,CCM2L,TOR4A,CST3,EFEMP2,ENG, GIMAP5,GMFG,GNAI2,ICAM2,ILK,MAPK3,MFNG, MGAT1,PLXND1,SYDE1,TNFRSF1A,TNFSF12,TSPAN4,VAT1

BASP1,C1R,CMTM3,COL6A2,EFEMP2,EHD2,EMP3, GNAI2,GYPC,LAMB2,LOXL1,MAFB,MAP7D1,MRAS, MRC2,NRP1,PLEKHO2,PTRF,TIMP2,TSPAN4,VIM	CCDC102A,CD81,CHST10,COPZ2,DOCK11,EFEMP2,FIBIN, GNAI2,GYPC,LIX1L,NAT14,PELI3,PJA1,PLSCR3, PRAF2,PRDM8,QKI,SHISA4,SNN,SULF1,TUBG2

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 GNAI2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA24347; -.
Organism-specific databases	CTD	2771; -.

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
DB00125	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	approved; nutraceutical	L-Arginine
DB00435	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	approved	Nitric Oxide
DB00938	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	approved	Salmeterol

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Cross referenced IDs for GNAI2

* 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