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 PABPC1
Basic gene info.Gene symbolPABPC1
Gene namepoly(A) binding protein, cytoplasmic 1
SynonymsPAB1|PABP|PABP1|PABPC2|PABPL1
CytomapUCSC genome browser: 8q22.2-q23
Genomic locationchr8 :101715143-101734315
Type of geneprotein-coding
RefGenesNM_002568.3,
Ensembl idENSG00000070756
Descriptionpoly(A) binding protein, cytoplasmic 2polyadenylate-binding protein 1
Modification date20141222
dbXrefs MIM : 604679
HGNC : HGNC
Ensembl : ENSG00000070756
HPRD : 05247
Vega : OTTHUMG00000164779
ProteinUniProt: P11940
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PABPC1
BioGPS: 26986
Gene Expression Atlas: ENSG00000070756
The Human Protein Atlas: ENSG00000070756
PathwayNCI Pathway Interaction Database: PABPC1
KEGG: PABPC1
REACTOME: PABPC1
ConsensusPathDB
Pathway Commons: PABPC1
MetabolismMetaCyc: PABPC1
HUMANCyc: PABPC1
RegulationEnsembl's Regulation: ENSG00000070756
miRBase: chr8 :101,715,143-101,734,315
TargetScan: NM_002568
cisRED: ENSG00000070756
ContextiHOP: PABPC1
cancer metabolism search in PubMed: PABPC1
UCL Cancer Institute: PABPC1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PABPC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PABPC1
Familial Cancer Database: PABPC1
* 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
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 604679; gene.
Orphanet
DiseaseKEGG Disease: PABPC1
MedGen: PABPC1 (Human Medical Genetics with Condition)
ClinVar: PABPC1
PhenotypeMGI: PABPC1 (International Mouse Phenotyping Consortium)
PhenomicDB: PABPC1

Mutations for PABPC1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryPABPC1chr8101719215101719235PABPC1chr8101721351101721371
pancreasPABPC1chr8101719215101719235PABPC1chr8101721351101721371
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 PABPC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA731281PABPC112008101733727101733929MGEA520040210103577939103578141
DA592957HLA-DQB1141863262987332634434PABPC14145608101730415101733671
BQ348968PABPC11702328101721898101721960DPP42235122162849781162862283
AW629981MFGE81146158944579689445941PABPC11415628101730429101733960
AW880952PABPC1353528101721812101724949PABPC13514248101724944101725017
BE612624PABPC11478101715203101715249VCP4770793505741635060402
BG928171PABPC1612078101733914101734059NR4A1190628125245124752452841
BF087781PABPC1291308101719115101719216PABPC11273188101721361101721787
DB265528PABPC112138101734039101734251MTMR14206592396912939695557
DW419798RFX31890935249053524977PABPC1893028101718881101719175

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 # sample1                
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=23)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr8:101727750-101727750p.I195V5
chr8:101727766-101727766p.E189E5
chr8:101719201-101719201p.I454T4
chr8:101721709-101721709p.Y408F4
chr8:101721407-101721407p.Q430Q3
chr8:101718965-101718965p.R506C3
chr8:101718968-101718968p.V505I3
chr8:101718987-101718987p.A498A3
chr8:101719004-101719004p.R493C3
chr8:101718929-101718929p.R518C3

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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
# sample24 91 1 13  743  52111
# mutation24 81 1 11  953  52112
nonsynonymous SNV 2 5    9  653  32111
synonymous SNV22 31 1 2  3    2  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
chr8:101718929p.Y408F3
chr8:101721709p.R518C3
chr8:101730064p.R278H2
chr8:101724923p.A181T2
chr8:101724606p.A154G2
chr8:101727792p.T147M2
chr8:101730043p.T319I2
chr8:101719181p.R436C1
chr8:101721752p.L296L1
chr8:101733795p.A65A1

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 PABPC1 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 PABPC1

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

AZIN1,DCAF13,EIF3E,ENY2,ESRP1,INTS8,MTDH,
MTERF3,NUDCD1,PABPC1,PABPC3,POLR2K,PTDSS1,RAD54B,
RPL30,RPL7,SLC25A32,TATDN1,UQCRB,YWHAZ,ZNF706
NOA1,CCNB1IP1,CHRM1,EEF1A1,EIF2A,EIF3E,EIF3L,
ELF5,FOLH1,NONO,NPM1,PABPC1,PABPC3,PDCD4,
ROPN1,ROPN1B,RPL17,RSL1D1,SLC13A2,TMEM87A,TOMM20

ANKRD46,ARFGEF1,AZIN1,CPNE3,DCAF13,EIF3E,EIF3H,
GRHL2,HSF1,INTS8,KIAA1429,PABPC1,PTDSS1,PTK2,
RPL30,RRS1,SLC25A32,TATDN1,TOP1MT,EMC2,ZNF7
TMEM254,NOA1,CRB2,EIF3D,FOXA1,FOXD2,KREMEN1,
LGR5,LIMD1,MAZ,MTL5,PABPC1,PABPC3,PIK3R2,
PTK7,QARS,REPIN1,SUMF1,TOP1MT,VGLL4,NELFA
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 PABPC1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P11940; -.
ChemistryChEMBL CHEMBL1293286; -.
Organism-specific databasesPharmGKB PA32880; -.
Organism-specific databasesCTD 26986; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877poly(A) binding protein, cytoplasmic 1approved; investigationalSirolimus


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Cross referenced IDs for PABPC1
* 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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