Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 ACTB
Basic gene info.Gene symbolACTB
Gene nameactin, beta
SynonymsBRWS1|PS1TP5BP1
CytomapUCSC genome browser: 7p22
Genomic locationchr7 :5566778-5570232
Type of geneprotein-coding
RefGenesNM_001101.3,
Ensembl idENSG00000075624
DescriptionPS1TP5-binding protein 1actin, cytoplasmic 1beta cytoskeletal actin
Modification date20141207
dbXrefs MIM : 102630
HGNC : HGNC
Ensembl : ENSG00000075624
HPRD : 00032
Vega : OTTHUMG00000023268
ProteinUniProt: P60709
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ACTB
BioGPS: 60
Gene Expression Atlas: ENSG00000075624
The Human Protein Atlas: ENSG00000075624
PathwayNCI Pathway Interaction Database: ACTB
KEGG: ACTB
REACTOME: ACTB
ConsensusPathDB
Pathway Commons: ACTB
MetabolismMetaCyc: ACTB
HUMANCyc: ACTB
RegulationEnsembl's Regulation: ENSG00000075624
miRBase: chr7 :5,566,778-5,570,232
TargetScan: NM_001101
cisRED: ENSG00000075624
ContextiHOP: ACTB
cancer metabolism search in PubMed: ACTB
UCL Cancer Institute: ACTB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ACTB in cancer cell metabolism1. Carrascoso I, Sanchez-Jimenez C, Izquierdo JM (2014) Long-term reduction of T-cell intracellular antigens leads to increased beta-actin expression. Mol Cancer 13: 90. doi: 10.1186/1476-4598-13-90. pmid: 4113145. go to article
2. Mandelbaum J, Rollins N, Shah P, Bowman D, Lee JY, et al. (2015) Identification of a lung cancer cell line deficient in atg7-dependent autophagy. Autophagy: 0. doi: 10.1080/15548627.2015.1056966. go to article

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Phenotypic Information for ACTB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ACTB
Familial Cancer Database: ACTB
* 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 102630; gene.
102630; gene.
243310; phenotype.
243310; phenotype.
607371; phenotype.
607371; phenotype.
Orphanet 2995; Baraitser-Winter syndrome.
2995; Baraitser-Winter syndrome.
79107; Developmental malformations - deafness - dystonia.
79107; Developmental malformations - deafness - dystonia.
DiseaseKEGG Disease: ACTB
MedGen: ACTB (Human Medical Genetics with Condition)
ClinVar: ACTB
PhenotypeMGI: ACTB (International Mouse Phenotyping Consortium)
PhenomicDB: ACTB

Mutations for ACTB
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryACTBchr755668075566827FBXL18chr755295695529589
ovaryACTBchr755689455568965chr755084545508474
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ACTB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG874502ACTB27349755676595568077ISY1-RAB433493993128849393128849443
BG773769ACTB2272755689575570222RPS16272538193992432339926573
DA891854ACTB1332755689075570232ACO2331486224190393341907914
BP379102ACTB1419755688205570232BSG41956819580716581397
DA501316ACTB1144755692295570232LOC100507412138569?110001110430
BP371810ACTB1434755688055570232LOC100507412431581?110070110220
BP286903ACTB1341755688985570232THBS33415781155176037155178773
BF213980LOC100507412147?110244110290ACTB46603755671875567947
BP309743ACTB1341755688985570232LOC100507412338583?117691117936
BQ321009PITPNA5791714448901451611ACTB78339755673035567674
BM352323ACTB1437755680395568916HERPUD243851973567291935673000
DB103450SNHG1163116262113862621200ACTB64559755683005570230
BG473536ACTB2273755689575570222RPS16273685193992398239926573
BI019526VAMP2331111780662138066292ACTB102208755669315567037
BE732178ACTB1248755689575570201RPS16248764193992387239926573
BI019850ACTB8184755679825568158ACTB167360755677675568066
AW949281ACTB1151755672635567413OSBPL314020972488725624969581
BG258572ACTB16159755691935570198ACTB158737755680495569213
BE707882ACTB1142755688265568971AGAP11321562237015903237015931
BQ320988ACTB1179755682015568820FMN1179464153326150033357202
AW970008TSNARE1792218143454297143454439ACTB219401755674795567773
BF376499JPH354401168771548787715835ACTB387485755671745567272
AW803684SPTLC214107147797242877972521ACTB92182755672585567348
DA184434ACTB2217755689815570190CBX5216518125462481754625118
BI063294ACTB11317755673575567775SUPV3L1309385107096758470967660
BF803193MAOA15235X4360122743603397ACTB229334755679115568016
BE828383ACTB38232755673685567674HIPK22272497139477503139477526
DA571523LOC1005074123103?117006117106ACTB103699755682605570232

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)		Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=3)		Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr7:5569032-5569032p.?12
chr7:5568242-5568242p.G158R5
chr7:5567464-5567464p.S348L4
chr7:5568871-5568871p.R95H3
chr7:5569212-5569212p.A26D2
chr7:5567474-5567474p.I345V2
chr7:5567936-5567936p.A260T2
chr7:5568044-5568044p.E224Q2
chr7:5569226-5569226p.F21F2
chr7:5567476-5567476p.S344C2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample4315  2  3 411  5712
# mutation3315  2  3 411  5812
nonsynonymous SNV3214  2  3 411  4612
synonymous SNV 1 1            12  
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr7:5567464p.S348L2
chr7:5567738p.R254Q1
chr7:5568123p.A114T1
chr7:5568857p.Y240C1
chr7:5567755p.H101R1
chr7:5568124p.E224Q1
chr7:5568878p.E100K1
chr7:5567921p.A220T1
chr7:5568128p.E93Q1
chr7:5567393p.R372C1

check002.gifOther 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

check002.gifCopy Number for ACTB 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 ACTB

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ACOT9,ACTB,AVEN,CNN2,FAM127A,FHL3,LIMK1,
LOC541471,LOC644936,PFN1,RAC1,RAP2B,RHOG,S100A10,
S100A11,SH3BGRL3,TAX1BP3,TMSB10,TMSB4XP8,TNFRSF12A,ZYX		ACTB,CFL1,CRIP2,FTSJ1,FXYD5,LINC00152,PFN1,
PLP2,PRAF2,PSENEN,RHOG,S100A11,SEC61B,SF3B4,
TAGLN2,TAX1BP3,TRIM47,TUBA1A,TUBA1C,VASP,ZYX

ACTB,ACTR1A,AGR2___C11orf96,CAPZB,CCM2,CYB5R3,KLF2,
LOC644936,PDLIM7,PHLDA2,PLAUR,PLK3,RAC1,RHOC,
RHOG,RRAS,S100A10,TPM4,TUBB6,UPP1,ZYX		ACTB,BVES,CACNA1C,CTXN1,ITGB1,JPH2,LOC401093,
MAP7D1,MICALL1,MYLK,PDLIM7,PNMA1,REEP2,SLC2A4,
SRF,TBC1D1,TES,TUBA1A,TUBB6,VCL,ZYX
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 ACTB
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2062353; -.
ChemistryChEMBL CHEMBL2062353; -.
Organism-specific databasesPharmGKB PA24457; -.
Organism-specific databasesPharmGKB PA24457; -.
Organism-specific databasesCTD 60; -.
Organism-specific databasesCTD 60; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00394actin, betaapprovedBeclomethasone
DB00443actin, betaapprovedBetamethasone
DB01222actin, betaapproved; investigationalBudesonide
DB01410actin, betaapproved; investigationalCiclesonide
DB01260actin, betaapproved; investigationalDesonide
DB01234actin, betaapproved; investigationalDexamethasone
DB00180actin, betaapproved; investigationalFlunisolide
DB00588actin, betaapproved; investigationalFluticasone Propionate
DB00741actin, betaapprovedHydrocortisone
DB00959actin, betaapprovedMethylprednisolone
DB00764actin, betaapprovedMometasone
DB01384actin, betaapprovedParamethasone
DB00860actin, betaapprovedPrednisolone
DB00635actin, betaapprovedPrednisone
DB00896actin, betaapprovedRimexolone
DB00620actin, betaapprovedTriamcinolone


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Cross referenced IDs for ACTB
* 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



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