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 TRAM1
Basic gene info.Gene symbolTRAM1
Gene nametranslocation associated membrane protein 1
SynonymsPNAS8|TRAM|TRAMP
CytomapUCSC genome browser: 8q13.3
Genomic locationchr8 :71485452-71520694
Type of geneprotein-coding
RefGenesNM_014294.5,
Ensembl idENSG00000067167
Descriptiontranslocating chain-associated membrane protein 1translocating chain-associating membrane proteintranslocation-associating membrane protein 1
Modification date20141207
dbXrefs MIM : 605190
HGNC : HGNC
Ensembl : ENSG00000067167
HPRD : 05545
Vega : OTTHUMG00000164428
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TRAM1
BioGPS: 23471
Gene Expression Atlas: ENSG00000067167
The Human Protein Atlas: ENSG00000067167
PathwayNCI Pathway Interaction Database: TRAM1
KEGG: TRAM1
REACTOME: TRAM1
ConsensusPathDB
Pathway Commons: TRAM1
MetabolismMetaCyc: TRAM1
HUMANCyc: TRAM1
RegulationEnsembl's Regulation: ENSG00000067167
miRBase: chr8 :71,485,452-71,520,694
TargetScan: NM_014294
cisRED: ENSG00000067167
ContextiHOP: TRAM1
cancer metabolism search in PubMed: TRAM1
UCL Cancer Institute: TRAM1
Assigned class in ccmGDBC

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Phenotypic Information for TRAM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TRAM1
Familial Cancer Database: TRAM1
* 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: TRAM1
MedGen: TRAM1 (Human Medical Genetics with Condition)
ClinVar: TRAM1
PhenotypeMGI: TRAM1 (International Mouse Phenotyping Consortium)
PhenomicDB: TRAM1

Mutations for TRAM1
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryTRAM1chr87148690871486928NCOA2chr87105531471055334
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 TRAM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
W89040AUTS216576962460869624672TRAM15823787150729171507470
AI207431TRAM1121687151608171516296RAP1A2096731112255277112255741

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 # sample3     1   1      
GAIN (# sample)2     1          
LOSS (# sample)1         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=27)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr8:71512313-71512313p.T43M2
chr8:71520314-71520314p.E41Q2
chr8:71510383-71510383p.E99Q2
chr8:71495976-71495976p.L267I2
chr8:71508498-71508498p.T162I2
chr8:71495481-71495481p.W323*1
chr8:71499153-71499153p.F241L1
chr8:71508503-71508503p.L160L1
chr8:71495485-71495485p.R322M1
chr8:71499155-71499155p.F241I1

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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
# sample3 19  3 2  431 143 4
# mutation2 110  3 2  431 133 4
nonsynonymous SNV1 17  2 1  431 132 3
synonymous SNV1  3  1 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
chr8:71520314p.L267F2
chr8:71495976p.L259F2
chr8:71495998p.E41Q2
chr8:71508498p.T162I2
chr8:71495485p.G275G1
chr8:71520431p.A127V1
chr8:71499155p.T271S1
chr8:71510466p.E99Q1
chr8:71495488p.S71F1
chr8:71499189p.K45N1

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 TRAM1 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 TRAM1

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

ARFGEF1,ARMC1,ATP6V1C1,CPNE3,FAM91A1,IMPAD1,LACTB2,
MTDH,MTFR1,PEX2,RAB2A,RB1CC1,SLC25A32,STAU2,
TCEA1,TERF1,TRAM1,EMC2,UBE2W,VCPIP1,YTHDF3
CASC4,FAM3C,HIAT1,LIN7C,MIER1,NUS1,PCNP,
PIGK,RAB14,RBM7,SPTLC1,SSR1,SYPL1,TM9SF3,
TMED7,TMX1,TRAM1,TROVE2,TWSG1,UBLCP1,YIPF5

ARMC1,AZIN1,CPNE3,DERL1,DPY19L4,FAM91A1,HNF4G,
LACTB2,MAL2,MTDH,MTFR1,NUDCD1,PEX2,PLEKHF2,
RNF139,SLC25A32,STK3,TRAM1,UBE2W,YTHDF3,YWHAZ
ATG5,BET1,C18orf32,CCNC,CISD2,CNIH1,DNAJB9,
HSBP1,MAGT1,MMADHC,OSTC,PEX2,RAP1B,SEP15,
SNX6,SUB1,TPT1,TRAM1,UBE2D3,UBE2W,ZNF410
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 TRAM1
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
DB08081translocation associated membrane protein 1experimental3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE


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Cross referenced IDs for TRAM1
* 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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