Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	TIAM2
	Gene name	T-cell lymphoma invasion and metastasis 2
	Synonyms	STEF\|TIAM-2
	Cytomap	UCSC genome browser: 6q25.2
	Genomic location	chr6 :155538096-155578857
	Type of gene	protein-coding
	RefGenes	NM_001010927.2, NM_012454.3,
	Ensembl id	ENSG00000146426
	Description	SIF and TIAM1-like exchange factorT-lymphoma invasion and metastasis-inducing protein 2
	Modification date	20141207
dbXrefs	MIM : 604709
	HGNC : HGNC
	Ensembl : ENSG00000146426
	HPRD : 05273
	Vega : OTTHUMG00000015880
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TIAM2
	BioGPS: 26230
	Gene Expression Atlas: ENSG00000146426
	The Human Protein Atlas: ENSG00000146426
Pathway	NCI Pathway Interaction Database: TIAM2
	KEGG: TIAM2
	REACTOME: TIAM2
	ConsensusPathDB
	Pathway Commons: TIAM2
Metabolism	MetaCyc: TIAM2
	HUMANCyc: TIAM2
Regulation	Ensembl's Regulation: ENSG00000146426
	miRBase: chr6 :155,538,096-155,578,857
	TargetScan: NM_001010927
	cisRED: ENSG00000146426
Context	iHOP: TIAM2
	cancer metabolism search in PubMed: TIAM2
	UCL Cancer Institute: TIAM2
Assigned class in ccmGDB	C

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Phenotypic Information for TIAM2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: TIAM2
	MedGen: TIAM2 (Human Medical Genetics with Condition)
	ClinVar: TIAM2
Phenotype	MGI: TIAM2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TIAM2 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
BU629140	TIAM2	18	457	6	155284994	155285433	RAD1	457	523	5	34908559	34908625
BM993771	TIAM2	1	206	6	155578137	155578342	TFB1M	201	677	6	155580968	155581444
BI850472	TIAM2	13	405	6	155173929	155174321	TMEM57	396	613	1	25824898	25825116
CN479315	TIAM2	1	206	6	155578137	155578342	TFB1M	201	677	6	155580968	155581444
BG028067	TIAM2	12	404	6	155173929	155174321	TMEM57	395	670	1	25824898	25825182
BI010428	GORASP2	12	209	2	171807836	171811224	TIAM2	201	333	6	155272905	155273037
BQ371784	TIAM2	9	63	6	155161247	155161303	MKLN1	44	130	7	131124903	131124989
BF935734	TIAM2	12	189	6	155187561	155187739	PAPD4	184	467	5	78948775	78949058
T05134	TIAM2	83	264	6	155456767	155456944	NTN4	248	318	12	96111311	96111381

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=6

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Somatic 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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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
chr6:155574087-155574087	p.S1375S	6
chr6:155451141-155451141	p.E262K	3
chr6:155566797-155566797	p.A1195V	3
chr6:155504465-155504465	p.S965R	3
chr6:155469323-155469323	p.G628E	3
chr6:155578089-155578089	p.G1647E	2
chr6:155450636-155450636	p.T93T	2
chr6:155561777-155561777	p.L1094L	2
chr6:155575613-155575613	p.F1458F	2
chr6:155571042-155571042	p.Y1297C	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	6	5		25	6		11		3			14	6	5		1	25	24	3	20
# mutation	6	5		26	6		11		3			17	6	5		1	34	32	3	27
nonsynonymous SNV	6	4		22	5		9		2			14	4	3			21	23	3	15
synonymous SNV		1		4	1		2		1			3	2	2		1	13	9		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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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
chr6:155574087	p.S300S,TIAM2	5
chr6:155566797	p.A120V,TIAM2	3
chr6:155451237	p.E6K,TIAM2	2
chr6:155578089	p.S965R	2
chr6:155561736	p.E262K	2
chr6:155451141	p.T93T	2
chr6:155485641	p.S294P	2
chr6:155575144	p.P707P	2
chr6:155450636	p.T346T,TIAM2	2
chr6:155504465	p.G572E,TIAM2	2

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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