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 GEMIN6
Basic gene info.Gene symbolGEMIN6
Gene namegem (nuclear organelle) associated protein 6
Synonyms-
CytomapUCSC genome browser: 2p22.1
Genomic locationchr2 :39005326-39009106
Type of geneprotein-coding
RefGenesNM_024775.9,
Ensembl idENSG00000152147
DescriptionSIP2gem-associated protein 6gemin 6gemin-6
Modification date20141207
dbXrefs MIM : 607006
HGNC : HGNC
HPRD : 06110
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GEMIN6
BioGPS: 79833
Gene Expression Atlas: ENSG00000152147
The Human Protein Atlas: ENSG00000152147
PathwayNCI Pathway Interaction Database: GEMIN6
KEGG: GEMIN6
REACTOME: GEMIN6
ConsensusPathDB
Pathway Commons: GEMIN6
MetabolismMetaCyc: GEMIN6
HUMANCyc: GEMIN6
RegulationEnsembl's Regulation: ENSG00000152147
miRBase: chr2 :39,005,326-39,009,106
TargetScan: NM_024775
cisRED: ENSG00000152147
ContextiHOP: GEMIN6
cancer metabolism search in PubMed: GEMIN6
UCL Cancer Institute: GEMIN6
Assigned class in ccmGDBC

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Phenotypic Information for GEMIN6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GEMIN6
Familial Cancer Database: GEMIN6
* 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: GEMIN6
MedGen: GEMIN6 (Human Medical Genetics with Condition)
ClinVar: GEMIN6
PhenotypeMGI: GEMIN6 (International Mouse Phenotyping Consortium)
PhenomicDB: GEMIN6

Mutations for GEMIN6
* 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 GEMIN6 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
There's no copy number variation information in COSMIC data for this gene.

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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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
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
chr2:39008979-39008979p.I150S1
chr2:39008760-39008760p.R77T1
chr2:39008997-39008997p.Q156R1
chr2:39008778-39008778p.M83K1
chr2:39009027-39009027p.S166F1
chr2:39008788-39008788p.F86F1
chr2:39008826-39008826p.L99Q1
chr2:39008833-39008833p.E101E1
chr2:39006139-39006139p.E3*1
chr2:39008851-39008851p.K107N1

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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   3    1       1  1
# mutation   4    1       1  1
nonsynonymous SNV   4            1  1
synonymous SNV        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
chr2:39008932p.S166F1
chr2:39008979p.D14Y1
chr2:39008997p.G59R1
chr2:39009027p.M61V1
chr2:39006172p.K107N1
chr2:39008705p.T134T1
chr2:39008711p.I150S1
chr2:39008851p.Q156R1

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 GEMIN6 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 GEMIN6

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

AUP1,BOLA3,C17orf89,C19orf53,COX7B,DGUOK,DPY30,
EIF5A,GEMIN6,KRTCAP2,MORN2,MPV17,MRPL17,MRPS15,
NDUFA1,OST4,PFDN6,PPM1G,SHFM1,SNRPG,TIMM8B
APOA1BP,EIF3I,FIBP,GEMIN6,LOC152217,LSM2,MEA1,
MRFAP1,MRPL17,MRPL51,MRPS21,NABP2,PFDN5,POLR2G,
PPIA,SMUG1,SNRPF,TIMM22,TMEM223,TOMM22,UFC1

BOLA3,C19orf53,C8orf59,CCDC58,DPY30,GEMIN6,HSPE1,
MEMO1,METTL5,NIFK,MRPL40,MRPS23,NME1,POLR2F,
RPL26L1,SF3B14,SNRPG,SS18L2,SSBP1,SUMO1,TPRKB
ELP6,COMMD10,CWC15,DRG1,GEMIN6,HAX1,ICT1,
LSM2,MED31,MRPS15,MRPS23,NDUFA4,NUP54,POLE3,
PRDX3,PSMD10,SNRPD2,THOC7,TMEM126A,TMEM126B,TOMM6
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 GEMIN6


There's no related Drug.
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Cross referenced IDs for GEMIN6
* 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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