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 TIAM2
Basic gene info.Gene symbolTIAM2
Gene nameT-cell lymphoma invasion and metastasis 2
SynonymsSTEF|TIAM-2
CytomapUCSC genome browser: 6q25.2
Genomic locationchr6 :155538096-155578857
Type of geneprotein-coding
RefGenesNM_001010927.2,
NM_012454.3,
Ensembl idENSG00000146426
DescriptionSIF and TIAM1-like exchange factorT-lymphoma invasion and metastasis-inducing protein 2
Modification date20141207
dbXrefs MIM : 604709
HGNC : HGNC
Ensembl : ENSG00000146426
HPRD : 05273
Vega : OTTHUMG00000015880
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TIAM2
BioGPS: 26230
Gene Expression Atlas: ENSG00000146426
The Human Protein Atlas: ENSG00000146426
PathwayNCI Pathway Interaction Database: TIAM2
KEGG: TIAM2
REACTOME: TIAM2
ConsensusPathDB
Pathway Commons: TIAM2
MetabolismMetaCyc: TIAM2
HUMANCyc: TIAM2
RegulationEnsembl's Regulation: ENSG00000146426
miRBase: chr6 :155,538,096-155,578,857
TargetScan: NM_001010927
cisRED: ENSG00000146426
ContextiHOP: TIAM2
cancer metabolism search in PubMed: TIAM2
UCL Cancer Institute: TIAM2
Assigned class in ccmGDBC

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Phenotypic Information for TIAM2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TIAM2
Familial Cancer Database: TIAM2
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TIAM2
MedGen: TIAM2 (Human Medical Genetics with Condition)
ClinVar: TIAM2
PhenotypeMGI: TIAM2 (International Mouse Phenotyping Consortium)
PhenomicDB: TIAM2

Mutations for TIAM2
* 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 TIAM2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU629140TIAM2184576155284994155285433RAD145752353490855934908625
BM993771TIAM212066155578137155578342TFB1M2016776155580968155581444
BI850472TIAM2134056155173929155174321TMEM5739661312582489825825116
CN479315TIAM212066155578137155578342TFB1M2016776155580968155581444
BG028067TIAM2124046155173929155174321TMEM5739567012582489825825182
BI010428GORASP2122092171807836171811224TIAM22013336155272905155273037
BQ371784TIAM29636155161247155161303MKLN1441307131124903131124989
BF935734TIAM2121896155187561155187739PAPD418446757894877578949058
T05134TIAM2832646155456767155456944NTN4248318129611131196111381

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    11  
GAIN (# sample)             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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=122)
Stat. for Synonymous SNVs
(# total SNVs=51)
Stat. for Deletions
(# total SNVs=6)
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
chr6:155574087-155574087p.S1375S6
chr6:155451141-155451141p.E262K3
chr6:155566797-155566797p.A1195V3
chr6:155504465-155504465p.S965R3
chr6:155469323-155469323p.G628E3
chr6:155561736-155561736p.E1081K2
chr6:155572049-155572049p.V1318V2
chr6:155450781-155450781p.G142R2
chr6:155451255-155451255p.R300W2
chr6:155577988-155577988p.P1613P2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample65 256 11 3  1465 12524320
# mutation65 266 11 3  1765 13432327
nonsynonymous SNV64 225 9 2  1443  2123315
synonymous SNV 1 41 2 1  322 1139 12
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
chr6:155574087p.S300S,TIAM25
chr6:155566797p.A120V,TIAM23
chr6:155575144p.T346T,TIAM22
chr6:155450636p.E6K,TIAM22
chr6:155504465p.S965R2
chr6:155451237p.E262K2
chr6:155578089p.T93T2
chr6:155561736p.G572E,TIAM22
chr6:155451141p.P707P2
chr6:155485641p.S294P2

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 TIAM2 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 TIAM2

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

ARHGAP21,C22orf23,C4orf51,CHST3,FAT1,GLS,LGR5,
MAML2,MFGE8,MICALL1,MTMR2,NRP2,OR2S2,PLEKHG1,
PTPN14,SHC4,SOX6,TIAM2,TRPV4,WWTR1,ZNF532
NRDE2,FAM227B,ESYT3,FAM83B,FLJ22536,GRAMD3,INADL,
LY75,MTMR1,NAA16,NT5C2,PDE7A,PM20D2,RPS6KA5,
SLC2A12,TIAM2,TP63,ZNF202,ZNF543,ZNF711,ZNF782

AEBP1,CLDN18,COL8A2,DLL1,DPYSL2,ETV1,ETV5,
FKBP15,FZD1,LOC100129034,PCDHB12,PCDHGA1,PCDHGA2,PCDHGA3,
PCDHGA5,PCDHGA6,ROR1,TIAM2,TRIM8,ZFPM1,ZNF618
CPS1,DAB1,DFNA5,FTCD,GRIA4,HOXC11,HOXC8,
KHK,LRAT,MTTP,OAT,PDZD7,PHYHIPL,PMP22,
RHOBTB2,SEC14L2,SUSD2,TIAM2,TM4SF4,TMPRSS15,TNFSF15
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 TIAM2


There's no related Drug.
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Cross referenced IDs for TIAM2
* 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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