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 symbolIQGAP1
Gene nameIQ motif containing GTPase activating protein 1
SynonymsHUMORFA01|SAR1|p195
CytomapUCSC genome browser: 15q26.1
Genomic locationchr15 :90931472-91045475
Type of geneprotein-coding
RefGenesNM_003870.3,
Ensembl idENSG00000140575
DescriptionRasGAP-like with IQ motifsras GTPase-activating-like protein IQGAP1
Modification date20141222
dbXrefs MIM : 603379
HGNC : HGNC
Ensembl : ENSG00000140575
HPRD : 04541
Vega : OTTHUMG00000149832
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IQGAP1
BioGPS: 8826
Gene Expression Atlas: ENSG00000140575
The Human Protein Atlas: ENSG00000140575
PathwayNCI Pathway Interaction Database: IQGAP1
KEGG: IQGAP1
REACTOME: IQGAP1
ConsensusPathDB
Pathway Commons: IQGAP1
MetabolismMetaCyc: IQGAP1
HUMANCyc: IQGAP1
RegulationEnsembl's Regulation: ENSG00000140575
miRBase: chr15 :90,931,472-91,045,475
TargetScan: NM_003870
cisRED: ENSG00000140575
ContextiHOP: IQGAP1
cancer metabolism search in PubMed: IQGAP1
UCL Cancer Institute: IQGAP1
Assigned class in ccmGDBC

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Phenotypic Information for IQGAP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: IQGAP1
MedGen: IQGAP1 (Human Medical Genetics with Condition)
ClinVar: IQGAP1
PhenotypeMGI: IQGAP1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
NSIQGAP1chr159098113790981137chr159224674992246749
ovaryIQGAP1chr159094659790946617chr159052196890521988
ovaryIQGAP1chr159094778590947805IQGAP1chr159094447890944498
ovaryIQGAP1chr159099021990990239IQGAP1chr159094009690940116
ovaryIQGAP1chr159101303991013059chr159052263590522655
ovaryIQGAP1chr159102885191028871SEMA3Cchr78051902380519043
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows IQGAP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
L33075CAMK2D34004114615498114615896IQGAP13957573159093150191045470
BF351441TRPM3132997339902773442924IQGAP1325378159103462091034673
U51007IQGAP17128159104534491045467PSMD411913231151227233151239865
AI991234SH3BGRL31426512660776226608013IQGAP1264617159093400690934358
BF094243EFNA512525106880451106880703IQGAP1245370159103458191034706

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4    1       11  
GAIN (# sample)4    1       11  
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr15:91019925-91019925p.N941fs*83
chr15:91017005-91017005p.R803H3
chr15:90996087-90996087p.E415K3
chr15:91017007-91017007p.S804P3
chr15:90996157-90996157p.R438Q2
chr15:91017877-91017877p.L912L2
chr15:91029272-91029272p.D1311G2
chr15:91019920-91019920p.L937R2
chr15:90969438-90969438p.F84F2
chr15:91030268-91030268p.F1369F2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample51 251 5 51 782 2914114
# mutation61 261 5 61 782 21015117
nonsynonymous SNV31 211 4 51 562 2712111
synonymous SNV3  6  1 1  22   33 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr15:91027453p.R1264W4
chr15:91017007p.S804P3
chr15:91017851p.Q904K2
chr15:91029272p.D1311G2
chr15:91030268p.F1369F2
chr15:91019971p.Q954R2
chr15:91037964p.K1037K1
chr15:90977000p.K1165N1
chr15:91009655p.E29V1
chr15:91025201p.A1423V1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125IQ motif containing GTPase activating protein 1approved; nutraceuticalL-Arginine
DB00435IQ motif containing GTPase activating protein 1approvedNitric 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



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