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 TUBB4B

Basic gene info.	Gene symbol	TUBB4B
	Gene name	tubulin, beta 4B class IVb
	Synonyms	Beta2\|TUBB2\|TUBB2C
	Cytomap	UCSC genome browser: 9q34
	Genomic location	chr9 :140135710-140138159
	Type of gene	protein-coding
	RefGenes	NM_006088.5,
	Ensembl id	ENSG00000188229
	Description	class IVb beta tubulinclass IVb beta-tubulintubulin beta-2 chaintubulin beta-2C chaintubulin beta-4B chaintubulin, beta 2Ctubulin, beta, 2
	Modification date	20141207
dbXrefs	MIM : 602660
	HGNC : HGNC
	Ensembl : ENSG00000188229
	HPRD : 04043
	Vega : OTTHUMG00000131783
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TUBB4B
	BioGPS: 10383
	Gene Expression Atlas: ENSG00000188229
	The Human Protein Atlas: ENSG00000188229
Pathway	NCI Pathway Interaction Database: TUBB4B
	KEGG: TUBB4B
	REACTOME: TUBB4B
	ConsensusPathDB
	Pathway Commons: TUBB4B
Metabolism	MetaCyc: TUBB4B
	HUMANCyc: TUBB4B
Regulation	Ensembl's Regulation: ENSG00000188229
	miRBase: chr9 :140,135,710-140,138,159
	TargetScan: NM_006088
	cisRED: ENSG00000188229
Context	iHOP: TUBB4B
	cancer metabolism search in PubMed: TUBB4B
	UCL Cancer Institute: TUBB4B
Assigned class in ccmGDB	C

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Phenotypic Information for TUBB4B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TUBB4B
	Familial Cancer Database: TUBB4B

* 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: TUBB4B
	MedGen: TUBB4B (Human Medical Genetics with Condition)
	ClinVar: TUBB4B
Phenotype	MGI: TUBB4B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TUBB4B

Mutations for TUBB4B

* 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 TUBB4B 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
DA594703	TUBB4B	1	465	9	140135739	140137061	ITPRIP	465	565	10	106073634	106073733
AK310334	CDH5	1	1159	16	66410293	66424453	TUBB4B	1155	2052	9	140137262	140138159
DB150819	TUBB4B	1	402	9	140135739	140136997	A2M	398	584	12	9246089	9247668
BE903667	CTTNBP2NL	60	398	1	112959928	112960268	TUBB4B	399	812	9	140135754	140137031
BQ361837	TUBB4B	17	82	9	140137027	140137092	TUBB4B	81	308	9	140137109	140137333
BC071888	CTTNBP2NL	25	365	1	112959928	112960268	TUBB4B	366	1913	9	140135754	140138159
BQ319576	TUBB4B	10	90	9	140138079	140138159	PGAP2	91	600	11	3847053	3847574
BE902916	CTTNBP2NL	6	344	1	112959928	112960268	TUBB4B	345	773	9	140135754	140137057

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=0

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=0)	Stat. for Synonymous SNVs (# total SNVs=0)
There's no ns-snv.	There's no s-snv.
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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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

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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=4

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	3		8	1		3		2	1		4		1				2	1	2
# mutation	1	3		7	1		3		2	1		5		1				2	1	2
nonsynonymous SNV	1	3		4			1			1		4		1				2	1	2
synonymous SNV				3	1		2		2			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
chr9:140137892	p.F408L	3
chr9:140137041	p.A124V	2
chr9:140137531	p.D197D	1
chr9:140137897	p.S230S	1
chr9:140137057	p.F408F	1
chr9:140137547	p.L240P	1
chr9:140137915	p.T409T	1
chr9:140137109	p.L246L	1
chr9:140137606	p.M415I	1
chr9:140137952	p.M257I	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 TUBB4B 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 TUBB4B

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


C9orf142,C9orf69,RABL6,NELFB,DPM2,EDF1,NTMT1, NDOR1,NDUFA8,PMPCA,PTGES2,SIVA1,SSNA1,SURF2, TMEM203,TUBB4B,UBAC1,UCK1,WDR34,ZDHHC12,ZMYND19	ARHGDIA,CFL1,COPE,CRELD2,GIPC1,GNB2,GUK1, MBD3,MRPL28,PPP4C,PSMC4,RBM42,RHOC,SCO2, SLC39A3,TBCB,ALYREF,TSSC4,TUBB4B,UBE2J2,YIF1B

AURKAIP1,C14orf80,C9orf142,CDC20,COQ4,EDF1,MZT2B, EMC9,FPGS,MRPL41,MXD3,PMPCA,PTGES2,PTTG1, SSNA1,TACC3,TUBA1B,TUBA1C,TUBB4B,WDR34,ZDHHC12	ACTG1,ARHGDIA,ATP2A2,B3GNT3,BAIAP2L1,BCL10,DPP9, IPPK,KCTD5,NPLOC4,PHLDA2,PLAUR,PSME3,RAB35, RDH13,RPS6KA4,SFN,TRIM15,TUBA1C,TUBB4B,YWHAB

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 TUBB4B

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
DB00518	tubulin, beta 4B class IVb	approved	Albendazole
DB00643	tubulin, beta 4B class IVb	approved	Mebendazole
DB01873	tubulin, beta 4B class IVb	experimental; investigational	Epothilone D
DB03010	tubulin, beta 4B class IVb	experimental; investigational	Epothilone B

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Cross referenced IDs for TUBB4B

* 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