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 MARCKS
Basic gene info.Gene symbolMARCKS
Gene namemyristoylated alanine-rich protein kinase C substrate
Synonyms80K-L|MACS|PKCSL|PRKCSL
CytomapUCSC genome browser: 6q22.2
Genomic locationchr6 :114178526-114184652
Type of geneprotein-coding
RefGenesNM_002356.5,
Ensembl idENSG00000155130
Descriptionmyristoylated alanine-rich C-kinase substratemyristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)phosphomyristinprotein kinase C substrate, 80 kDa protein, light chain
Modification date20141207
dbXrefs MIM : 177061
HGNC : HGNC
Ensembl : ENSG00000277443
HPRD : 07519
Vega : OTTHUMG00000188327
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MARCKS
BioGPS: 4082
Gene Expression Atlas: ENSG00000155130
The Human Protein Atlas: ENSG00000155130
PathwayNCI Pathway Interaction Database: MARCKS
KEGG: MARCKS
REACTOME: MARCKS
ConsensusPathDB
Pathway Commons: MARCKS
MetabolismMetaCyc: MARCKS
HUMANCyc: MARCKS
RegulationEnsembl's Regulation: ENSG00000155130
miRBase: chr6 :114,178,526-114,184,652
TargetScan: NM_002356
cisRED: ENSG00000155130
ContextiHOP: MARCKS
cancer metabolism search in PubMed: MARCKS
UCL Cancer Institute: MARCKS
Assigned class in ccmGDBC

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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MARCKS
MedGen: MARCKS (Human Medical Genetics with Condition)
ClinVar: MARCKS
PhenotypeMGI: MARCKS (International Mouse Phenotyping Consortium)
PhenomicDB: MARCKS

Mutations for MARCKS
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MARCKS related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG118012MARCKS16796114183688114183751MARCKS768026114183719114184445
AW451126MARCKS11496114181218114181366MARCKS1452356114181780114181870

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample                1
GAIN (# sample)                1
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr6:114181729-114181730p.A328fs*>62
chr6:114181210-114181210p.K155fs*122
chr6:114181248-114181248p.F164F2
chr6:114180958-114180958p.D68N1
chr6:114181730-114181730p.P327fs*>61
chr6:114181750-114181750p.E332Q1
chr6:114181255-114181255p.S167C1
chr6:114181309-114181309p.E185K1
chr6:114181338-114181338p.D194D1
chr6:114181567-114181567p.E271*1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1       1  11   11  
# mutation1       1  11   11  
nonsynonymous SNV1       1  11   1   
synonymous SNV                 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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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
chr6:114181338p.D194D1
chr6:114181669p.A305T1
chr6:114181750p.E332Q1
chr6:114178975p.R18S1
chr6:114179007p.S29F1
chr6:114181255p.S167C1

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 MARCKS 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 MARCKS

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

ACVR2A,ARHGAP10,ARPC2,ARSB,CCDC102B,DSE,FKBP7,
GNAI1,GUCY1B3,IKBIP,JAZF1,LAMA4,LOX,LY96,
MAF,MAP4K4,MARCKS,MYO1B,PRRX1,RAP2B,RBMS1
ALG2,SMIM15,CBX3,CISD2,DUSP11,EIF4E,FAM3C,
GCA,H3F3A,HPRT1,IQCK,LOC653566,MARCKS,MPZL2,
NPTN,RAB14,SEP15,SERP1,SPCS2,TMEM9B,YWHAQ

ATL1,BMPR2,CDK19,CLIC4,CMTM3,CNTN4,CYBRD1,
FKBP7,FZD1,LTBP1,MARCKS,OLFML1,OSTM1,PPAP2A,
RNF180,SEC31A,SERINC1,SPIN1,SSPN,TAB2,TGFBR1
AGFG2,AMACR,CNPPD1,CCNJL,CDX2,FAM134A,HIST1H2BD,
KCNJ2,MARCKS,MKRN1,NBR1,PAK1,TINCR,PLCL2,
PPARG,PWWP2A,SLC16A1,SLC26A2,SP3,TRAF3IP2,WDR78
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 MARCKS
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00864myristoylated alanine-rich protein kinase C substrateapproved; investigationalTacrolimus


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Cross referenced IDs for MARCKS
* 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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