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 IQGAP1

Basic gene info.	Gene symbol	IQGAP1
	Gene name	IQ motif containing GTPase activating protein 1
	Synonyms	HUMORFA01\|SAR1\|p195
	Cytomap	UCSC genome browser: 15q26.1
	Genomic location	chr15 :90931472-91045475
	Type of gene	protein-coding
	RefGenes	NM_003870.3,
	Ensembl id	ENSG00000140575
	Description	RasGAP-like with IQ motifsras GTPase-activating-like protein IQGAP1
	Modification date	20141222
dbXrefs	MIM : 603379
	HGNC : HGNC
	Ensembl : ENSG00000140575
	HPRD : 04541
	Vega : OTTHUMG00000149832
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_IQGAP1
	BioGPS: 8826
	Gene Expression Atlas: ENSG00000140575
	The Human Protein Atlas: ENSG00000140575
Pathway	NCI Pathway Interaction Database: IQGAP1
	KEGG: IQGAP1
	REACTOME: IQGAP1
	ConsensusPathDB
	Pathway Commons: IQGAP1
Metabolism	MetaCyc: IQGAP1
	HUMANCyc: IQGAP1
Regulation	Ensembl's Regulation: ENSG00000140575
	miRBase: chr15 :90,931,472-91,045,475
	TargetScan: NM_003870
	cisRED: ENSG00000140575
Context	iHOP: IQGAP1
	cancer metabolism search in PubMed: IQGAP1
	UCL Cancer Institute: IQGAP1
Assigned class in ccmGDB	C

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Phenotypic Information for IQGAP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: IQGAP1
	Familial Cancer Database: IQGAP1

* 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: IQGAP1
	MedGen: IQGAP1 (Human Medical Genetics with Condition)
	ClinVar: IQGAP1
Phenotype	MGI: IQGAP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: IQGAP1

Mutations for IQGAP1

* 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
NS	IQGAP1	chr15	90981137	90981137		chr15	92246749	92246749
ovary	IQGAP1	chr15	90946597	90946617		chr15	90521968	90521988
ovary	IQGAP1	chr15	90947785	90947805	IQGAP1	chr15	90944478	90944498
ovary	IQGAP1	chr15	90990219	90990239	IQGAP1	chr15	90940096	90940116
ovary	IQGAP1	chr15	91013039	91013059		chr15	90522635	90522655
ovary	IQGAP1	chr15	91028851	91028871	SEMA3C	chr7	80519023	80519043

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 IQGAP1 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
L33075	CAMK2D	3	400	4	114615498	114615896	IQGAP1	395	7573	15	90931501	91045470
BF351441	TRPM3	1	329	9	73399027	73442924	IQGAP1	325	378	15	91034620	91034673
U51007	IQGAP1	7	128	15	91045344	91045467	PSMD4	119	1323	1	151227233	151239865
AI991234	SH3BGRL3	14	265	1	26607762	26608013	IQGAP1	264	617	15	90934006	90934358
BF094243	EFNA5	1	252	5	106880451	106880703	IQGAP1	245	370	15	91034581	91034706

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=101)	Stat. for Synonymous SNVs (# total SNVs=27)

Stat. for Deletions (# total SNVs=6)	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
chr15:91019925-91019925	p.N941fs*8	3
chr15:91017005-91017005	p.R803H	3
chr15:90996087-90996087	p.E415K	3
chr15:91017007-91017007	p.S804P	3
chr15:91029272-91029272	p.D1311G	2
chr15:91019920-91019920	p.L937R	2
chr15:90969438-90969438	p.F84F	2
chr15:91030268-91030268	p.F1369F	2
chr15:91019954-91019954	p.M948I	2
chr15:91025277-91025277	p.R1139W	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=4

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	5	1		25	1		5		5	1		7	8	2		2	9	14	1	14
# mutation	6	1		26	1		5		6	1		7	8	2		2	10	15	1	17
nonsynonymous SNV	3	1		21	1		4		5	1		5	6	2		2	7	12	1	11
synonymous SNV	3			6			1		1			2	2				3	3		6

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
chr15:91027453	p.R1264W	4
chr15:91017007	p.S804P	3
chr15:91029272	p.Q904K	2
chr15:91030268	p.D1311G	2
chr15:91019971	p.F1369F	2
chr15:91017851	p.Q954R	2
chr15:90984750	p.A1501A	1
chr15:91016190	p.M246V	1
chr15:91025320	p.L558L	1
chr15:91040551	p.R847Q	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 IQGAP1 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 IQGAP1

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


ADAM10,ASXL2,BIRC6,CRTC3,DPP8,GTF2A1,IQGAP1, IREB2,LIMS1,MAP3K2,MGA,MYO9A,PAFAH1B2,PPP4R2, RANBP2,RNF111,ROCK1,SON,STAG1,TCF12,ZNF774	ATF6,CAMSAP2,CREB3L2,CTTNBP2NL,FNDC3A,FRMD4B,HIVEP1, IPO8,IQGAP1,CFAP97,MAPK1,MOB1A,NIPAL2,PARP4, PDCD6IP,RASAL2,SETX,SLC37A3,SWAP70,TCF12,TM9SF3

ACBD3,ADAM10,AKAP13,CCDC186,DPP8,EFTUD1,FAM63B, FNIP2,GNAQ,IQGAP1,MYO9A,RNF111,SECISBP2L,PEAK1, SPG11,SPRED1,STXBP5,TMOD3,TRIP11,UBR1,USP8	ATP2A2,BIRC6,CLTC,EGFR,EIF4G3,ENTPD4,IGF2R, IQGAP1,MYH9,NCOR1,NFKB1,PAK2,RCOR1,ROCK2, RRBP1,SEC16A,SCAF4,SLC38A1,SPTBN1,TOP1,TRIP12

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 IQGAP1

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
DB00125	IQ motif containing GTPase activating protein 1	approved; nutraceutical	L-Arginine
DB00435	IQ motif containing GTPase activating protein 1	approved	Nitric Oxide

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Cross referenced IDs for IQGAP1

* 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