Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 GIP
Basic gene info.Gene symbolGIP
Gene namegastric inhibitory polypeptide
Synonyms-
CytomapUCSC genome browser: 17q21.3-q22
Genomic locationchr17 :47035917-47045955
Type of geneprotein-coding
RefGenesNM_004123.2,
Ensembl idENSG00000159224
Descriptionglucose-dependent insulinotropic polypeptideincretin hormone
Modification date20141207
dbXrefs MIM : 137240
HGNC : HGNC
Ensembl : ENSG00000159224
HPRD : 15925
Vega : OTTHUMG00000161171
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GIP
BioGPS: 2695
Gene Expression Atlas: ENSG00000159224
The Human Protein Atlas: ENSG00000159224
PathwayNCI Pathway Interaction Database: GIP
KEGG: GIP
REACTOME: GIP
ConsensusPathDB
Pathway Commons: GIP
MetabolismMetaCyc: GIP
HUMANCyc: GIP
RegulationEnsembl's Regulation: ENSG00000159224
miRBase: chr17 :47,035,917-47,045,955
TargetScan: NM_004123
cisRED: ENSG00000159224
ContextiHOP: GIP
cancer metabolism search in PubMed: GIP
UCL Cancer Institute: GIP
Assigned class in ccmGDBC

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Phenotypic Information for GIP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GIP
Familial Cancer Database: GIP
* 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: GIP
MedGen: GIP (Human Medical Genetics with Condition)
ClinVar: GIP
PhenotypeMGI: GIP (International Mouse Phenotyping Consortium)
PhenomicDB: GIP

Mutations for GIP
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GIP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample2                
GAIN (# sample)2                
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=11)
Stat. for Synonymous SNVs
(# total SNVs=3)
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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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
chr17:47044539-47044539p.G19E2
chr17:47039132-47039132p.S103G2
chr17:47041683-47041683p.G82G2
chr17:47041724-47041724p.H69Y1
chr17:47038307-47038307p.D131D1
chr17:47041735-47041735p.M65T1
chr17:47044562-47044562p.L11L1
chr17:47038312-47038312p.R130W1
chr17:47041781-47041781p.P50S1
chr17:47038345-47038345p.P119T1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2         41   3213
# mutation 2         41   3213
nonsynonymous SNV 2         31   2 12
synonymous SNV           1    12 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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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
chr17:47041841p.P119A1
chr17:47038345p.S118F1
chr17:47044509p.A102V1
chr17:47038347p.E95E1
chr17:47044511p.G82G1
chr17:47039134p.K81K1
chr17:47044526p.A79S1
chr17:47039154p.H69Y1
chr17:47044539p.P50S1
chr17:47041683p.S33F1

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 GIP 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 GIP

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

ATP5G1,B4GALNT2,PRAC2,CALCOCO2,CBX1,NSRP1,CXCL17,
DNAH8,EFCAB5,GIP,GIT1,GSK3A,HOXB2,KRTAP20-2,
NUFIP2,PAFAH1B3,PRR15L,SMARCE1,SNF8,SSH2,UBE2Z
ACTL6B,CARTPT,CPLX2,EPYC,AMER3,FLJ36000,GIP,
HMP19,IBSP,IFNA14,LCE2D,LOC650293,LOC729121,LOC732275,
NEU2,OR8B2,OR8H3,PCSK1,SEZ6,SYT4,TRIM48

CPLX3,CSH1,DEFB107A,FAM197Y2,FAM27L,GIP,KRTAP20-4,
LCE1A,LOC642929,OR2L8,OR5H2,RBMY1A3P,RNF17,SCGB1D4,
SLC6A5,TFAP2D,TSPY1,TSPY2,TSPY4,VCY,ZNF645
NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA,
NA,NA,NA,NA,NA,NA,NA
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 GIP
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
DB00363gastric inhibitory polypeptideapprovedClozapine


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Cross referenced IDs for GIP
* 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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