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 TUBA4A

Basic gene info.	Gene symbol	TUBA4A
	Gene name	tubulin, alpha 4a
	Synonyms	H2-ALPHA\|TUBA1
	Cytomap	UCSC genome browser: 2q35
	Genomic location	chr2 :220115000-220118638
	Type of gene	protein-coding
	RefGenes	NM_001278552.1, NM_006000.2,
	Ensembl id	ENSG00000127824
	Description	tubulin H2-alphatubulin alpha-1 chaintubulin alpha-4A chaintubulin, alpha 1 (testis specific)
	Modification date	20141207
dbXrefs	MIM : 191110
	HGNC : HGNC
	Ensembl : ENSG00000127824
	HPRD : 01851
	Vega : OTTHUMG00000133126
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TUBA4A
	BioGPS: 7277
	Gene Expression Atlas: ENSG00000127824
	The Human Protein Atlas: ENSG00000127824
Pathway	NCI Pathway Interaction Database: TUBA4A
	KEGG: TUBA4A
	REACTOME: TUBA4A
	ConsensusPathDB
	Pathway Commons: TUBA4A
Metabolism	MetaCyc: TUBA4A
	HUMANCyc: TUBA4A
Regulation	Ensembl's Regulation: ENSG00000127824
	miRBase: chr2 :220,115,000-220,118,638
	TargetScan: NM_001278552
	cisRED: ENSG00000127824
Context	iHOP: TUBA4A
	cancer metabolism search in PubMed: TUBA4A
	UCL Cancer Institute: TUBA4A
Assigned class in ccmGDB	C

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Phenotypic Information for TUBA4A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TUBA4A
	Familial Cancer Database: TUBA4A

* 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: TUBA4A
	MedGen: TUBA4A (Human Medical Genetics with Condition)
	ClinVar: TUBA4A
Phenotype	MGI: TUBA4A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TUBA4A

Mutations for TUBA4A

* 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 TUBA4A related fusion information.

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

DA812020

TM9SF4

402

30697533

30729350

TUBA4A

395

788

220116326

220118638

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=36)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=2)	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
chr2:220115768-220115768	p.D218G	3
chr2:220116426-220116426	p.R79Q	3
chr2:220115938-220115938	p.Y161Y	2
chr2:220115764-220115764	p.I219I	2
chr2:220115939-220115939	p.Y161F	2
chr2:220115877-220115877	p.V182I	2
chr2:220115880-220115880	p.V181M	2
chr2:220115736-220115736	p.R229C	1
chr2:220116808-220116808	p.T50P	1
chr2:220115919-220115919	p.E168K	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		12	1		3		2	1		3	1	3		1	5	1		10
# mutation		1		8	1		3		2	1		3	1	3		1	6	1		15
nonsynonymous SNV		1		7	1		1		2	1		3		3			4	1		10
synonymous SNV				1			2						1			1	2			5

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
chr2:220115768	p.D203G,TUBA4A	3
chr2:220116426	p.R64Q,TUBA4A	3
chr2:220115938	p.T58T,TUBA4A	2
chr2:220115939	p.Y146Y,TUBA4A	2
chr2:220116737	p.Y146F,TUBA4A	2
chr2:220116310	p.P246S,TUBA4A	1
chr2:220115512	p.L104L,TUBA4A	1
chr2:220116755	p.S221F,TUBA4A	1
chr2:220115769	p.V103L,TUBA4A	1
chr2:220116329	p.R214H,TUBA4A	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 TUBA4A 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 TUBA4A

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


ARHGEF4,BNC1,CA9,ENO1,FERMT1,FGFBP1,FSCN1, GJB3,GJB5,GPR87,KRT5,KRT6B,MYO7B,PCSK9, PLEK2,RPSAP52,S100A2,SFN,SOX15,TNFSF9,TUBA4A	PERM1,CACNB1,CHRNA10,YBX3,FEM1A,FHL3,GAMT, GAPDH,GMPR,GOT2,IDI2,MYL6B,PDLIM3,RBM38, RTN2,SH2B2,SHISA4,TCEA3,TPM1,TPM2,TUBA4A

ATPIF1,UQCC3,CD320,DTYMK,EXOSC7,MZT2B,HNRNPAB, ILKAP,LSM4,LSM7,MRPS34,MXD3,NOP16,PPIH, PRELID1,STARD10,TIMM13,TUBA1C,TUBA4A,TUBB4B,UQCRQ	AGR2,ARF4,CCT7,CDC37,CGB,GALE,GARS, GORASP2,KCTD14,KDELR3,NABP2,PPP5C,RGS8,S100P, SLC16A14,SYNGR2,TFF1,TMED9,TTC39A,TUBA4A,TUBG1

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 TUBA4A

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
DB00541	tubulin, alpha 4a	approved; investigational	Vincristine
DB01179	tubulin, alpha 4a	approved	Podofilox
DB01873	tubulin, alpha 4a	experimental; investigational	Epothilone D
DB03010	tubulin, alpha 4a	experimental; investigational	Epothilone B
DB06772	tubulin, alpha 4a	approved	Cabazitaxel
DB01033	tubulin, alpha 4a	approved	Mercaptopurine
DB00563	tubulin, alpha 4a	approved	Methotrexate

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Cross referenced IDs for TUBA4A

* 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