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 TUBA1A

Basic gene info.	Gene symbol	TUBA1A
	Gene name	tubulin, alpha 1a
	Synonyms	B-ALPHA-1\|LIS3\|TUBA3
	Cytomap	UCSC genome browser: 12q13.12
	Genomic location	chr12 :49578582-49582861
	Type of gene	protein-coding
	RefGenes	NM_001270399.1, NM_001270400.1,NM_006009.3,
	Ensembl id	ENSG00000167552
	Description	hum-a-tub1hum-a-tub2tubulin B-alpha-1tubulin alpha-1A chaintubulin alpha-3 chaintubulin, alpha, brain-specific
	Modification date	20141222
dbXrefs	MIM : 602529
	HGNC : HGNC
	Ensembl : ENSG00000167552
	HPRD : 03959
	Vega : OTTHUMG00000169511
Protein	UniProt: Q71U36 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TUBA1A
	BioGPS: 7846
	Gene Expression Atlas: ENSG00000167552
	The Human Protein Atlas: ENSG00000167552
Pathway	NCI Pathway Interaction Database: TUBA1A
	KEGG: TUBA1A
	REACTOME: TUBA1A
	ConsensusPathDB
	Pathway Commons: TUBA1A
Metabolism	MetaCyc: TUBA1A
	HUMANCyc: TUBA1A
Regulation	Ensembl's Regulation: ENSG00000167552
	miRBase: chr12 :49,578,582-49,582,861
	TargetScan: NM_001270399
	cisRED: ENSG00000167552
Context	iHOP: TUBA1A
	cancer metabolism search in PubMed: TUBA1A
	UCL Cancer Institute: TUBA1A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for TUBA1A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TUBA1A
	Familial Cancer Database: TUBA1A

* 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	602529; gene. 611603; phenotype.
Orphanet	171680; Lissencephaly due to TUBA1A mutation.
Disease	KEGG Disease: TUBA1A
	MedGen: TUBA1A (Human Medical Genetics with Condition)
	ClinVar: TUBA1A
Phenotype	MGI: TUBA1A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TUBA1A

Mutations for TUBA1A

* 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 TUBA1A 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
AI198453	TUBA1A	8	242	12	49578582	49578816	SNRNP27	234	452	2	70122273	70124540
AU099292	PTPN13	9	90	4	87622394	87622475	TUBA1A	90	300	12	49580508	49582861
AI199092	TUBA1A	1	232	12	49578585	49578816	SNRNP27	224	401	2	70122314	70124540

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=1

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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
chr12:49579743-49579743	p.L136L	1
chr12:49580453-49580453	p.T56M	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=2

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	2	1		2	1		1		1		1	4	1		1		3	3	1	10
# mutation	2	1		2	1		1		1		1	5	1		1		3	3	1	10
nonsynonymous SNV	2	1		1	1				1		1	4	1		1		3	2		9
synonymous SNV				1			1					1						1	1	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
chr12:49580453	p.T56M,TUBA1A	2
chr12:49579554	p.G412E,TUBA1A	1
chr12:49580452	p.R214C,TUBA1A	1
chr12:49579153	p.A400V,TUBA1A	1
chr12:49579664	p.D199N,TUBA1A	1
chr12:49579170	p.R390H,TUBA1A	1
chr12:49579682	p.G162D,TUBA1A	1
chr12:49580492	p.S379S,TUBA1A	1
chr12:49579227	p.R156H,TUBA1A	1
chr12:49579767	p.S379N,TUBA1A	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 TUBA1A 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 TUBA1A

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


NREP,CCDC23,CLIP2,DBN1,DIRAS1,GPR161,H2BFXP, HDAC2,KDM1A,KIF3C,MAD2L2,MEX3A,MEX3B,NCS1, NXN,SOX4,STMN1,TMEFF1,TMSB15B,TUBA1A,TUBA1B	ACTB,ACTG1,CFL1,CRIP2,FXYD5,JUND,KIF9, MED27,NXT1,OVCA2,PDLIM1,RAB34,S100A16,SERTAD1, SF3B4,SLC10A3,TAGLN2,TNFRSF12A,TUBA1A,TUBA1C,ZYX

BNC2,CNRIP1,COX7A1,DZIP1,EFEMP2,FERMT2,FEZ1, ARHGEF25,GYPC,HSPB2,JAM3,LAYN,MSRB3,NAP1L3, PRKD1,RAB34,SYT11,TCEAL7,TGFB1I1,TUBA1A,TUBB6	CASQ2,CSRP1,DACT3,DES,ILK,KCNMB1,LGALS1, LMO3,MYL9,MYLK,PDLIM3,PDLIM7,PNCK,SMTN, TAGLN,TMEM35,TPM1,TPM2,TSPAN2,TUBA1A,TUBB6

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 TUBA1A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q71U36; -.
Chemistry	ChEMBL	CHEMBL2095182; -.
Organism-specific databases	PharmGKB	PA162407319; -.
Organism-specific databases	CTD	7846; -.

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, alpha 1a	approved	Albendazole
DB00570	tubulin, alpha 1a	approved	Vinblastine
DB00643	tubulin, alpha 1a	approved	Mebendazole
DB01873	tubulin, alpha 1a	experimental; investigational	Epothilone D
DB03010	tubulin, alpha 1a	experimental; investigational	Epothilone B
DB07574	tubulin, alpha 1a	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 TUBA1A

* 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