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 TUBA1B

Basic gene info.	Gene symbol	TUBA1B
	Gene name	tubulin, alpha 1b
	Synonyms	K-ALPHA-1
	Cytomap	UCSC genome browser: 12q13.12
	Genomic location	chr12 :49521566-49525304
	Type of gene	protein-coding
	RefGenes	NM_006082.2,
	Ensembl id	ENSG00000123416
	Description	alpha tubulinalpha-tubulin ubiquitoustubulin K-alpha-1tubulin alpha-1B chaintubulin alpha-ubiquitous chaintubulin, alpha, ubiquitous
	Modification date	20141207
dbXrefs	MIM : 602530
	HGNC : HGNC
	Ensembl : ENSG00000123416
	HPRD : 03960
	Vega : OTTHUMG00000170410
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TUBA1B
	BioGPS: 10376
	Gene Expression Atlas: ENSG00000123416
	The Human Protein Atlas: ENSG00000123416
Pathway	NCI Pathway Interaction Database: TUBA1B
	KEGG: TUBA1B
	REACTOME: TUBA1B
	ConsensusPathDB
	Pathway Commons: TUBA1B
Metabolism	MetaCyc: TUBA1B
	HUMANCyc: TUBA1B
Regulation	Ensembl's Regulation: ENSG00000123416
	miRBase: chr12 :49,521,566-49,525,304
	TargetScan: NM_006082
	cisRED: ENSG00000123416
Context	iHOP: TUBA1B
	cancer metabolism search in PubMed: TUBA1B
	UCL Cancer Institute: TUBA1B
Assigned class in ccmGDB	C

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Phenotypic Information for TUBA1B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: TUBA1B
	Familial Cancer Database: TUBA1B

* 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: TUBA1B
	MedGen: TUBA1B (Human Medical Genetics with Condition)
	ClinVar: TUBA1B
Phenotype	MGI: TUBA1B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: TUBA1B

Mutations for TUBA1B

* 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 TUBA1B 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
BE143246	PTPN18	7	83	2	131132487	131132563	TUBA1B	77	178	12	49521691	49521792
DA127449	TUBA1B	1	100	12	49525079	49525178	GRM4	98	584	6	34101152	34101637
CN426333	TUBA1B	1	515	12	49522507	49523433	ZSCAN29	510	628	15	43651109	43651227
CD621808	NPTXR	1	201	22	39215153	39215353	TUBA1B	201	504	12	49523142	49525129
H93515	FTL	1	199	19	49468581	49468779	TUBA1B	192	377	12	49522392	49522573
BE960893	TUBA1B	1	130	12	49521750	49521880	F8A3	124	559	X	154686903	154687339
CD621809	NPTXR	1	201	22	39215153	39215353	TUBA1B	201	504	12	49523142	49525129
DA368267	SNRPN	1	91	15	25336937	25337026	TUBA1B	90	581	12	49522701	49525178
AV718300	KIF1B	1	130	1	10401387	10401516	TUBA1B	124	157	12	49521741	49521774
DA077791	TUBA1B	1	99	12	49525080	49525178	PFKM	98	502	12	48531503	48534653
AI880459	TUBA1B	1	72	12	49521577	49521648	RNU5F-1	71	155	1	220160714	220161983
BC001209	TMEM246	44	1985	9	104237608	104249328	TUBA1B	1986	3598	12	49521565	49525164
DB368876	TUBA1B	1	131	12	49521569	49521699	CNOT7	132	523	8	17087282	17087676

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=11

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr12:49523173-49523173	p.D76A	11
chr12:49522719-49522719	p.A126A	3
chr12:49523353-49523353	p.F52F	2
chr12:49522578-49522578	p.P173P	2
chr12:49522602-49522602	p.S165S	2
chr12:49522057-49522057	p.C347F	2
chr12:49521785-49521785	p.D438Y	2
chr12:49523033-49523033	p.R123C	2
chr12:49521833-49521833	p.R422C	1
chr12:49522238-49522238	p.S287T	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		2	1	6	1		3					2	2				7	3		5
# mutation		2	1	5	1		3					2	2				6	3		5
nonsynonymous SNV		2	1	5	1		2					1	2				4	1		5
synonymous SNV							1					1					2	2

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
chr12:49522057	p.G29D	2
chr12:49523423	p.R123C	2
chr12:49523033	p.C347F	2
chr12:49523492	p.G43W	1
chr12:49523058	p.I335M	1
chr12:49522081	p.R308C	1
chr12:49523061	p.G29R	1
chr12:49522092	p.A278V	1
chr12:49523074	p.S6F	1
chr12:49522175	p.P175P	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 TUBA1B 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 TUBA1B

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


AURKB,CDC20,CDC25C,CDC45,CDT1,E2F1,FEN1, H2AFZ,LMNB1,PKMYT1,PLK1,PTTG1,RAD54L,RNASEH2A, TACC3,ALYREF,TROAP,TUBA1B,TUBA1C,UBE2C,UBE2S	AP2M1,ARPC1B,ARPC4,CFL1,EFHD2,FAM109B,IFI27L2, NECAP2,PFN1,PLOD3,PLSCR3,RGS19,RHOG,SHISA5, SHKBP1,TAGLN2,TAX1BP3,TIMP1,TMSB10,TUBA1B,TUBA1C

AURKB,CDC20,CDC45,CDCA8,CENPM,H2AFZ,HMGN2, ORC1,PSMD9,RACGAP1,RAD51,RAN,RCC1,RFC5, SRSF9,SKA1,TK1,TPI1,TUBA1B,TUBA1C,TYMS	ATXN10,CMSS1,CCT7,CENPW,CSE1L,GSTCD,HAUS7, IARS,LDHB,MLH1,NUP93,PA2G4,POLA2,PSMC3, RANBP1,RUVBL1,S100A11,TCF19,TIPIN,TUBA1B,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 TUBA1B

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
DB01873	tubulin, alpha 1b	experimental; investigational	Epothilone D
DB03010	tubulin, alpha 1b	experimental; investigational	Epothilone B
DB07574	tubulin, alpha 1b	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 TUBA1B

* 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