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 GEMIN4
Basic gene info.Gene symbolGEMIN4
Gene namegem (nuclear organelle) associated protein 4
SynonymsHC56|HCAP1|HHRF-1|p97
CytomapUCSC genome browser: 17p13
Genomic locationchr17 :647660-655501
Type of geneprotein-coding
RefGenesNM_015721.2,
Ensembl idENSG00000179409
DescriptionHCC-associated protein 1component of gems 4gem-associated protein 4gemin-4
Modification date20141207
dbXrefs MIM : 606969
HGNC : HGNC
Ensembl : ENSG00000179409
HPRD : 07370
Vega : OTTHUMG00000177495
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GEMIN4
BioGPS: 50628
Gene Expression Atlas: ENSG00000179409
The Human Protein Atlas: ENSG00000179409
PathwayNCI Pathway Interaction Database: GEMIN4
KEGG: GEMIN4
REACTOME: GEMIN4
ConsensusPathDB
Pathway Commons: GEMIN4
MetabolismMetaCyc: GEMIN4
HUMANCyc: GEMIN4
RegulationEnsembl's Regulation: ENSG00000179409
miRBase: chr17 :647,660-655,501
TargetScan: NM_015721
cisRED: ENSG00000179409
ContextiHOP: GEMIN4
cancer metabolism search in PubMed: GEMIN4
UCL Cancer Institute: GEMIN4
Assigned class in ccmGDBC

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Phenotypic Information for GEMIN4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GEMIN4
Familial Cancer Database: GEMIN4
* 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_METABOLISM_OF_NON_CODING_RNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GEMIN4
MedGen: GEMIN4 (Human Medical Genetics with Condition)
ClinVar: GEMIN4
PhenotypeMGI: GEMIN4 (International Mouse Phenotyping Consortium)
PhenomicDB: GEMIN4

Mutations for GEMIN4
* 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 GEMIN4 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 # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
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=52)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=3)
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
chr17:649505-649505p.E593V3
chr17:650284-650284p.A333A2
chr17:650077-650077p.I402I2
chr17:650551-650551p.A244A2
chr17:650090-650090p.A398D2
chr17:649487-649487p.S599C2
chr17:650033-650033p.R417H1
chr17:650836-650836p.T149T1
chr17:649180-649180p.L701F1
chr17:648290-648290p.C998Y1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1281 3 211514  66 8
# mutation 1281 3 211514  66 8
nonsynonymous SNV 1231 3 2112 2  22 4
synonymous SNV   5       312  44 4
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
chr17:650077p.I402I2
chr17:649630p.S304L1
chr17:648573p.S829S1
chr17:650285p.L607H1
chr17:651064p.T303T1
chr17:649336p.G810E1
chr17:649755p.L582V1
chr17:650372p.H285H1
chr17:648796p.L756L1
chr17:649339p.Q580H1

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 GEMIN4 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 GEMIN4

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

C1QBP,COX10,DVL2,ELAC2,FAM57A,GEMIN4,GLOD4,
CLUH,MYBBP1A,NUP88,PELP1,PRPF8,RNMTL1,RPA1,
SCO1,SENP3,TIMM22,TSR1,VPS53,YWHAE,ZNF232
C10orf2,SNHG20,CCDC120,CD3EAP,CHRM1,DDX31,DKC1,
DTNB,EFNB3,GEMIN4,GNG7,LIG1,MKS1,LINC00086,
PDCD11,PLEKHG4,PTK7,TMPRSS2,UNK,WDR6,WWC1

C1QBP,COX10,CRK,DPH1,EIF4A1,ELAC2,FAM57A,
GEMIN4,GLOD4,GSG2,CLUH,PELP1,PRPF8,RNMTL1,
RPA1,SCO1,TIMM22,TOP3A,TSR1,WRAP53,YWHAE
ANAPC1,C10orf2,EARS2,FARSA,GEMIN4,GRWD1,KDM1A,
LAS1L,NAT10,NOC2L,NOP14,POLR1B,PPAN,PTDSS1,
RRP1,SSRP1,TRAP1,TTC27,UTP14A,WDR3,ZBTB9
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 GEMIN4


There's no related Drug.
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Cross referenced IDs for GEMIN4
* 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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