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 IMPDH1
Basic gene info.Gene symbolIMPDH1
Gene nameIMP (inosine 5'-monophosphate) dehydrogenase 1
SynonymsIMPD|IMPD1|LCA11|RP10|sWSS2608
CytomapUCSC genome browser: 7q31.3-q32
Genomic locationchr7 :128032330-128046024
Type of geneprotein-coding
RefGenesNM_000883.3,
NM_001102605.1,NM_001142573.1,NM_001142574.1,NM_001142575.1,
NM_001142576.1,NM_183243.2,
Ensembl idENSG00000106348
DescriptionIMP (inosine monophosphate) dehydrogenase 1IMP dehydrogenase 1IMPD 1IMPDH 1IMPDH-Iinosine-5'-monophosphate dehydrogenase 1
Modification date20141219
dbXrefs MIM : 146690
HGNC : HGNC
Ensembl : ENSG00000106348
HPRD : 08853
Vega : OTTHUMG00000157713
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IMPDH1
BioGPS: 3614
Gene Expression Atlas: ENSG00000106348
The Human Protein Atlas: ENSG00000106348
PathwayNCI Pathway Interaction Database: IMPDH1
KEGG: IMPDH1
REACTOME: IMPDH1
ConsensusPathDB
Pathway Commons: IMPDH1
MetabolismMetaCyc: IMPDH1
HUMANCyc: IMPDH1
RegulationEnsembl's Regulation: ENSG00000106348
miRBase: chr7 :128,032,330-128,046,024
TargetScan: NM_000883
cisRED: ENSG00000106348
ContextiHOP: IMPDH1
cancer metabolism search in PubMed: IMPDH1
UCL Cancer Institute: IMPDH1
Assigned class in ccmGDBC

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Phenotypic Information for IMPDH1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: IMPDH1
Familial Cancer Database: IMPDH1
* 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
KEGG_PURINE_METABOLISM
KEGG_DRUG_METABOLISM_OTHER_ENZYMES
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: IMPDH1
MedGen: IMPDH1 (Human Medical Genetics with Condition)
ClinVar: IMPDH1
PhenotypeMGI: IMPDH1 (International Mouse Phenotyping Consortium)
PhenomicDB: IMPDH1

Mutations for IMPDH1
* 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 IMPDH1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG954732CDV362813133306634133306914IMPDH12723667128043784128045890

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 # sample        1        
GAIN (# sample)        1        
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=33)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr7:128035304-128035304p.G429V2
chr7:128038490-128038490p.A351V2
chr7:128040946-128040946p.?2
chr7:128037021-128037021p.Q377R2
chr7:128037057-128037057p.S365*2
chr7:128034631-128034631p.A525T1
chr7:128038653-128038653p.V297I1
chr7:128040569-128040569p.D202Y1
chr7:128033072-128033072p.R597W1
chr7:128049846-128049846p.S37N1

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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 32 2 1  932  77 8
# mutation 2 32 3 1  1042  77 8
nonsynonymous SNV 2 32 3 1  831  25 6
synonymous SNV           211  52 2
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
chr7:128034398p.G461A,IMPDH12
chr7:128034978p.M395I,IMPDH11
chr7:128041077p.N205N,IMPDH11
chr7:128038487p.A81T,IMPDH11
chr7:128033072p.K384N,IMPDH11
chr7:128040160p.A198D,IMPDH11
chr7:128035011p.D77Y,IMPDH11
chr7:128041089p.T369T,IMPDH11
chr7:128038490p.I197I,IMPDH11
chr7:128034338p.S68F,IMPDH11

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 IMPDH1 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 IMPDH1

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

AGAP3,ARF5,ATAD3A,ATP6V1F,B4GALT2,DAZAP1,FASTK,
GUK1,IMPDH1,LRWD1,NDUFB2,NSUN5,PDAP1,PPP1R14B,
RBM28,RPUSD1,SLC12A9,TBRG4,TMUB1,ZC3HC1,ZNF598
AP1M1,BCAP31,TANGO2,CD81,DOK1,FURIN,GPX4,
IMPDH1,INF2,LGALS1,LZTR1,MGAT1,NADK,PALM,
PHLDA3,PLXND1,POR,PRR5,RNPEPL1,RRAS,TPD52L2

ABCF2,ADCK1,ANKRD13B,BRAT1,C7orf50,CPSF4,EIF3B,
FTSJ2,HEATR2,HYAL3,IMPDH1,MGC72080,NSUN5,PDAP1,
POLD2,PUS1,RBM28,RRP9,SAC3D1,SLC19A1,WBSCR16
B3GNT9,CBX2,CD276,COPS7B,DUSP7,EPOR,HDAC7,
IMPDH1,LEPRE1,AGAP2-AS1,MAP3K12,MAP3K6,NR2F1,NUP62,
PHF19,SCN1B,SLC43A1,SLC43A3,SRPX2,TIMP1,UBFD1
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 IMPDH1
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
DB00157IMP (inosine 5'-monophosphate) dehydrogenase 1approved; nutraceuticalNADH
DB00688IMP (inosine 5'-monophosphate) dehydrogenase 1approved; investigationalMycophenolate mofetil
DB00811IMP (inosine 5'-monophosphate) dehydrogenase 1approvedRibavirin
DB01024IMP (inosine 5'-monophosphate) dehydrogenase 1approvedMycophenolic acid
DB03948IMP (inosine 5'-monophosphate) dehydrogenase 1experimental6-Chloropurine Riboside, 5'-Monophosphate
DB00993IMP (inosine 5'-monophosphate) dehydrogenase 1approvedAzathioprine


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Cross referenced IDs for IMPDH1
* 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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