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 TUBB2B

Basic gene info.	Gene symbol	TUBB2B
	Gene name	tubulin, beta 2B class IIb
	Synonyms	PMGYSA\|bA506K6.1
	Cytomap	UCSC genome browser: 6p25
	Genomic location	chr6 :3224494-3227968
	Type of gene	protein-coding
	RefGenes	NM_178012.4,
	Ensembl id	ENSG00000137285
	Description	class II beta-tubulin isotypeclass IIb beta-tubulintubulin beta-2B chaintubulin, beta polypeptide paralog
	Modification date	20141207
dbXrefs	MIM : 612850
	HGNC : HGNC
	Ensembl : ENSG00000137285
	HPRD : 14707
	Vega : OTTHUMG00000014143
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TUBB2B
	BioGPS: 347733
	Gene Expression Atlas: ENSG00000137285
	The Human Protein Atlas: ENSG00000137285
Pathway	NCI Pathway Interaction Database: TUBB2B
	KEGG: TUBB2B
	REACTOME: TUBB2B
	ConsensusPathDB
	Pathway Commons: TUBB2B
Metabolism	MetaCyc: TUBB2B
	HUMANCyc: TUBB2B
Regulation	Ensembl's Regulation: ENSG00000137285
	miRBase: chr6 :3,224,494-3,227,968
	TargetScan: NM_178012
	cisRED: ENSG00000137285
Context	iHOP: TUBB2B
	cancer metabolism search in PubMed: TUBB2B
	UCL Cancer Institute: TUBB2B
Assigned class in ccmGDB	C

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Phenotypic Information for TUBB2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TUBB2B
	Familial Cancer Database: TUBB2B

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: TUBB2B
	MedGen: TUBB2B (Human Medical Genetics with Condition)
	ClinVar: TUBB2B
Phenotype	MGI: TUBB2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TUBB2B

Mutations for TUBB2B

* 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 TUBB2B 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
AW498865	NACA	1	60	12	57112658	57112717	TUBB2B	61	352	6	3225938	3226861
DA506064	TUBB2B	1	484	6	3225949	3227887	DYRK2	484	572	12	68052307	68052395

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

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

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=16)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	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
chr6:3226446-3226446	p.S75L	3
chr6:3225015-3225015	p.F436F	3
chr6:3225000-3225000	p.G441G	2
chr6:3226486-3226486	p.R62R	2
chr6:3224993-3224993	p.E444K	1
chr6:3225694-3225694	p.I210S	1
chr6:3226475-3226475	p.L65L	1
chr6:3225711-3225711	p.N204N	1
chr6:3225005-3225005	p.E440K	1
chr6:3225760-3225760	p.S188L	1

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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=3

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		1		8					2			2				1		3	1	5
# mutation		1		6					2			2				1		3	1	5
nonsynonymous SNV		1		3					2			2				1		1	1	2
synonymous SNV				3														2		3

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
chr6:3225015	p.F436F	3
chr6:3225000	p.G441G	2
chr6:3226446	p.S168N	2
chr6:3225820	p.S75L	2
chr6:3225005	p.N14S	1
chr6:3226475	p.C12G	1
chr6:3226486	p.E440K	1
chr6:3225019	p.E435G	1
chr6:3226489	p.T409T	1
chr6:3225096	p.S188L	1

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 TUBB2B 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 TUBB2B

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


ATE1,COLCA2,LINC01551,KHDC3L,CCKBR,DCAF8L1,HSPB2, MAMLD1,NPM3,NSMCE4A,PCBP4,PGPEP1L,PRDM9,RSPO4, TRIM51,TBC1D21,TUBB2A,TUBB2B,UNC93A,ZCCHC18,ZNF232	ACTG2,CA11,CADM4,CNN1,CSRP1,FBXO2,IGFBP2, IL34,KRT14,KRT17,KRT5,PDLIM4,PLEKHA4,RAB34, SFN,TAGLN,TCEAL3,TGFB1I1,TUBB2B,VASP,ZYX

ASTN1,ATCAY,BSX,CLVS2,CNIH2,FERD3L,JPH4, KCNN1,LRRC4B,RGAG4,SLC17A7,SLC7A14,SYT4,SYT5, TAGLN3,TECRL,TMEM59L,TUBB2B,VWA5B2,ZCCHC12,ZDHHC22	ACTA2,ACTG2,AOC3,CNN1,COL22A1,DACT3,DGKG, RBFOX3,ILDR2,KIF26B,MAPT,NPTXR,PCP4L1,PCYT1B, PDLIM7,PYGM,REEP2,TAGLN,TUBA1A,TUBB2B,ZFHX4

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 TUBB2B

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
DB07574	tubulin, beta 2B class IIb	experimental	2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE

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Cross referenced IDs for TUBB2B

* 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