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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for TRAM1 |
Basic gene info. | Gene symbol | TRAM1 |
Gene name | translocation associated membrane protein 1 | |
Synonyms | PNAS8|TRAM|TRAMP | |
Cytomap | UCSC genome browser: 8q13.3 | |
Genomic location | chr8 :71485452-71520694 | |
Type of gene | protein-coding | |
RefGenes | NM_014294.5, | |
Ensembl id | ENSG00000067167 | |
Description | translocating chain-associated membrane protein 1translocating chain-associating membrane proteintranslocation-associating membrane protein 1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 605190 | |
HGNC : HGNC | ||
Ensembl : ENSG00000067167 | ||
HPRD : 05545 | ||
Vega : OTTHUMG00000164428 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TRAM1 | |
BioGPS: 23471 | ||
Gene Expression Atlas: ENSG00000067167 | ||
The Human Protein Atlas: ENSG00000067167 | ||
Pathway | NCI Pathway Interaction Database: TRAM1 | |
KEGG: TRAM1 | ||
REACTOME: TRAM1 | ||
ConsensusPathDB | ||
Pathway Commons: TRAM1 | ||
Metabolism | MetaCyc: TRAM1 | |
HUMANCyc: TRAM1 | ||
Regulation | Ensembl's Regulation: ENSG00000067167 | |
miRBase: chr8 :71,485,452-71,520,694 | ||
TargetScan: NM_014294 | ||
cisRED: ENSG00000067167 | ||
Context | iHOP: TRAM1 | |
cancer metabolism search in PubMed: TRAM1 | ||
UCL Cancer Institute: TRAM1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for TRAM1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: TRAM1 |
Familial Cancer Database: TRAM1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: TRAM1 |
MedGen: TRAM1 (Human Medical Genetics with Condition) | |
ClinVar: TRAM1 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | TRAM1 | chr8 | 71486908 | 71486928 | NCOA2 | chr8 | 71055314 | 71055334 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TRAM1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
W89040 | AUTS2 | 1 | 65 | 7 | 69624608 | 69624672 | TRAM1 | 58 | 237 | 8 | 71507291 | 71507470 | |
AI207431 | TRAM1 | 1 | 216 | 8 | 71516081 | 71516296 | RAP1A | 209 | 673 | 1 | 112255277 | 112255741 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 3 |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=27) | (# total SNVs=6) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr8:71495976-71495976 | p.L267I | 2 |
chr8:71508498-71508498 | p.T162I | 2 |
chr8:71512313-71512313 | p.T43M | 2 |
chr8:71520314-71520314 | p.E41Q | 2 |
chr8:71510383-71510383 | p.E99Q | 2 |
chr8:71499401-71499401 | p.P194H | 1 |
chr8:71495415-71495415 | p.S345S | 1 |
chr8:71512306-71512306 | p.K45N | 1 |
chr8:71496023-71496023 | p.S251F | 1 |
chr8:71506818-71506818 | p.M165V | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 3 |   | 1 | 9 |   |   | 3 |   | 2 |   |   | 4 | 3 | 1 |   | 1 | 4 | 3 |   | 4 |
# mutation | 2 |   | 1 | 10 |   |   | 3 |   | 2 |   |   | 4 | 3 | 1 |   | 1 | 3 | 3 |   | 4 |
nonsynonymous SNV | 1 |   | 1 | 7 |   |   | 2 |   | 1 |   |   | 4 | 3 | 1 |   | 1 | 3 | 2 |   | 3 |
synonymous SNV | 1 |   |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr8:71520314 | p.T162I | 2 |
chr8:71495976 | p.L267F | 2 |
chr8:71495998 | p.L259F | 2 |
chr8:71508498 | p.E41Q | 2 |
chr8:71496023 | p.R367Q | 1 |
chr8:71508503 | p.V229L | 1 |
chr8:71495415 | p.S15I | 1 |
chr8:71520395 | p.S345S | 1 |
chr8:71496025 | p.Y211S | 1 |
chr8:71510176 | p.L14L | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for TRAM1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB08081 | translocation associated membrane protein 1 | experimental | 3-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 |
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