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 GFER
Basic gene info.Gene symbolGFER
Gene namegrowth factor, augmenter of liver regeneration
SynonymsALR|ERV1|HERV1|HPO|HPO1|HPO2|HSS
CytomapUCSC genome browser: 16p13.3-p13.12
Genomic locationchr16 :2034149-2037750
Type of geneprotein-coding
RefGenesNM_005262.2,
Ensembl idENSG00000127554
DescriptionERV1 homologFAD-linked sulfhydryl oxidase ALRerv1-like growth factorhepatic regenerative stimulation substancehepatopoietin protein
Modification date20141207
dbXrefs MIM : 600924
HGNC : HGNC
Ensembl : ENSG00000127554
HPRD : 02954
Vega : OTTHUMG00000176896
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GFER
BioGPS: 2671
Gene Expression Atlas: ENSG00000127554
The Human Protein Atlas: ENSG00000127554
PathwayNCI Pathway Interaction Database: GFER
KEGG: GFER
REACTOME: GFER
ConsensusPathDB
Pathway Commons: GFER
MetabolismMetaCyc: GFER
HUMANCyc: GFER
RegulationEnsembl's Regulation: ENSG00000127554
miRBase: chr16 :2,034,149-2,037,750
TargetScan: NM_005262
cisRED: ENSG00000127554
ContextiHOP: GFER
cancer metabolism search in PubMed: GFER
UCL Cancer Institute: GFER
Assigned class in ccmGDBC

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

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

Mutations for GFER
* 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
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 GFER 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
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
chr16:2035969-2035969p.F186F2
chr16:2035868-2035868p.L153L1
chr16:2035896-2035896p.T162I1
chr16:2035898-2035898p.R163W1
chr16:2035934-2035934p.N175H1
chr16:2035935-2035935p.N175S1
chr16:2035946-2035946p.R179S1
chr16:2035967-2035967p.F186I1
chr16:2034418-2034418p.R67G1
chr16:2034434-2034434p.R72L1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   1    11 21   11 2
# mutation   1    12 21   11 2
nonsynonymous SNV         2 21   11 1
synonymous SNV   1    1          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
chr16:2035969p.F186F2
chr16:2035934p.R179S1
chr16:2035935p.F186I1
chr16:2035946p.E193A1
chr16:2035967p.L153L1
chr16:2035989p.R161S1
chr16:2035868p.T162I1
chr16:2035892p.R163W1
chr16:2035896p.N175H1
chr16:2035898p.N175S1

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 GFER 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 GFER

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

TSR3,CD2BP2,ECI1,FAM173A,FAM195A,FLYWCH2,GFER,
JMJD8,MLST8,MPG,MRPL28,MRPS34,NARFL,NDUFB10,
NME3,NUBP2,PGP,RHOT2,STUB1,TBL3,ZNF205
ARFRP1,ARL6IP4,UQCC3,TSR3,C17orf59,NELFB,DGCR6L,
EDF1,GFER,HRAS,MPG,MRPL28,MRPS34,NTHL1,
NUBP2,PRPF31,RPS19BP1,SSNA1,SURF2,WDR83,ZNF688

ATP6V0C,AXIN1,C16orf13,TSR3,CHMP1A,GFER,HAGH,
HMOX2,MRPS34,NARFL,NAA60,NDUFB10,NTHL1,NUBP2,
RAB40C,RHOT2,RNPS1,SPSB3,STUB1,TCEB2,UBE2I
ACY1,BCL2L1,C11orf52,GUCD1,CCL14-CCL15,CES2,DCAF11,
DHRS11,EPS8L2,FAM132A,GFER,GLOD5,KIAA2013,NGEF,
RAB17,SLC39A5,STRADB,TMEM120A,TMEM150B,TNNC2,USH1C
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 GFER
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
DB00260growth factor, augmenter of liver regenerationapprovedCycloserine
DB01993growth factor, augmenter of liver regenerationexperimentalN-(5'-Phosphopyridoxyl)-D-Alanine
DB02142growth factor, augmenter of liver regenerationexperimentalPyridoxamine-5'-Phosphate
DB03097growth factor, augmenter of liver regenerationexperimentalPmp-Hydroxyisoxazole, Pyridoxamine-5-Phosphate-Hydroxyisoxazole
DB03327growth factor, augmenter of liver regenerationexperimental{1-[(3-Hydroxy-Methyl-5-Phosphonooxy-Methyl-Pyridin-4-Ylmethyl)-Amino]-Ethyl}-Phosphonic Acid
DB03579growth factor, augmenter of liver regenerationexperimentalPyridoxyl-N,O-Cycloserylamide-5-Monophosphate
DB03766growth factor, augmenter of liver regenerationexperimentalPropanoic Acid
DB03801growth factor, augmenter of liver regenerationexperimentalLysine Nz-Carboxylic Acid
DB04467growth factor, augmenter of liver regenerationexperimentalPyridoxyl-Alanine-5-Phosphate


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Cross referenced IDs for GFER
* 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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