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 GNAI1

Basic gene info.	Gene symbol	GNAI1
	Gene name	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1
	Synonyms	Gi
	Cytomap	UCSC genome browser: 7q21
	Genomic location	chr7 :79765070-79848725
	Type of gene	protein-coding
	RefGenes	NM_001256414.1, NM_002069.5,
	Ensembl id	ENSG00000127955
	Description	Gi1 protein alpha subunitadenylate cyclase-inhibiting G alpha proteinguanine nucleotide-binding protein G(i) subunit alpha-1
	Modification date	20141207
dbXrefs	MIM : 139310
	HGNC : HGNC
	Ensembl : ENSG00000127955
	HPRD : 00756
	Vega : OTTHUMG00000023523
Protein	UniProt: P63096 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNAI1
	BioGPS: 2770
	Gene Expression Atlas: ENSG00000127955
	The Human Protein Atlas: ENSG00000127955
Pathway	NCI Pathway Interaction Database: GNAI1
	KEGG: GNAI1
	REACTOME: GNAI1
	ConsensusPathDB
	Pathway Commons: GNAI1
Metabolism	MetaCyc: GNAI1
	HUMANCyc: GNAI1
Regulation	Ensembl's Regulation: ENSG00000127955
	miRBase: chr7 :79,765,070-79,848,725
	TargetScan: NM_001256414
	cisRED: ENSG00000127955
Context	iHOP: GNAI1
	cancer metabolism search in PubMed: GNAI1
	UCL Cancer Institute: GNAI1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GNAI1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNAI1
	Familial Cancer Database: GNAI1

* 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	139310; gene. 139310; gene.
Orphanet
Disease	KEGG Disease: GNAI1
	MedGen: GNAI1 (Human Medical Genetics with Condition)
	ClinVar: GNAI1
Phenotype	MGI: GNAI1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNAI1

Mutations for GNAI1

* 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	GNAI1	chr7	79767058	79767058	GNAI1	chr7	79778501	79778501
ovary	GNAI1	chr7	79845375	79845395		chr7	80050819	80050839

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 GNAI1 related fusion information.

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

AI982766

GNAI1

253

79848348

79848600

MALAT1

247

497

65269640

65269890

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=43)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr7:79818546-79818546	p.A101V	4
chr7:79842125-79842125	p.D272Y	2
chr7:79842176-79842176	p.E289Q	2
chr7:79842041-79842041	p.H244N	1
chr7:79818438-79818438	p.E65G	1
chr7:79846687-79846687	p.D315N	1
chr7:79828599-79828599	p.A121G	1
chr7:79840297-79840297	p.V201V	1
chr7:79842045-79842045	p.E245G	1
chr7:79818476-79818476	p.I78V	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	1		9			1		1	1		3	3				3	3		6
# mutation	1	1		8			1		1	1		3	3				3	3		6
nonsynonymous SNV	1	1		5			1		1			3	3				1	2		5
synonymous SNV				3						1							2	1		1

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
chr7:79840317	p.R156Q,GNAI1	2
chr7:79818503	p.K225K,GNAI1	1
chr7:79846672	p.L39L,GNAI1	1
chr7:79818508	p.T232I,GNAI1	1
chr7:79840331	p.D45G,GNAI1	1
chr7:79846687	p.N242T,GNAI1	1
chr7:79818515	p.D50H,GNAI1	1
chr7:79840336	p.Y250C,GNAI1	1
chr7:79846721	p.R53H,GNAI1	1
chr7:79818534	p.L258V,GNAI1	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 GNAI1 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 GNAI1

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


B3GNT5,BMP2,BNC1,C11orf87,CAV1,CAV2,CPNE8, CSRP2,DFNA5,EPHA2,FAM126A,FSCN1,GNAI1,KRT5, MID1,MOB3B,MSN,PLEK2,PRNP,RBMS1,TES	ACADL,ACO1,ANO6,ANTXR2,FAM213A,PQLC2L,EIF4EBP2, FAM89A,FBXO27,FERMT2,GHR,GNAI1,GYG2,HRASLS5, LOC283392,MARC1,PDE8A,PEX19,PLIN1,RHOBTB3,SIK2

ABCC9,ARHGAP24,CFL2,CLIC4,DIXDC1,FERMT2,GNAI1, HCFC2,JAZF1,MEF2A,PDE4D,PDLIM5,PJA2,PLN, POU6F1,PPAP2A,RGS2,SECISBP2L,SETBP1,SGCE,STRN3	CNR1,ELOVL4,EPM2A,FBXO17,FGF2,GAS1,GNAI1, GPM6A,HABP4,JAZF1,LSAMP,MARK1,MTMR9,NEGR1, NKX3-2,NUDT10,PGR,SCD5,SOCS5,SSPN,ZDHHC15

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 GNAI1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P63096; -.
Chemistry	ChEMBL	CHEMBL4741; -.
Chemistry	BindingDB	P63096; -.
Chemistry	ChEMBL	CHEMBL4741; -.
Organism-specific databases	PharmGKB	PA172; -.
Organism-specific databases	PharmGKB	PA172; -.
Organism-specific databases	CTD	2770; -.
Organism-specific databases	CTD	2770; -.

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
DB00945	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved	Acetylsalicylic acid
DB00125	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved; nutraceutical	L-Arginine
DB00435	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved	Nitric Oxide
DB00396	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved	Progesterone
DB00171	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved; nutraceutical	Adenosine triphosphate
DB01064	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved	Isoproterenol
DB00938	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	approved	Salmeterol

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Cross referenced IDs for GNAI1

* 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