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 PABPC1

Basic gene info.	Gene symbol	PABPC1
	Gene name	poly(A) binding protein, cytoplasmic 1
	Synonyms	PAB1\|PABP\|PABP1\|PABPC2\|PABPL1
	Cytomap	UCSC genome browser: 8q22.2-q23
	Genomic location	chr8 :101715143-101734315
	Type of gene	protein-coding
	RefGenes	NM_002568.3,
	Ensembl id	ENSG00000070756
	Description	poly(A) binding protein, cytoplasmic 2polyadenylate-binding protein 1
	Modification date	20141222
dbXrefs	MIM : 604679
	HGNC : HGNC
	Ensembl : ENSG00000070756
	HPRD : 05247
	Vega : OTTHUMG00000164779
Protein	UniProt: P11940 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PABPC1
	BioGPS: 26986
	Gene Expression Atlas: ENSG00000070756
	The Human Protein Atlas: ENSG00000070756
Pathway	NCI Pathway Interaction Database: PABPC1
	KEGG: PABPC1
	REACTOME: PABPC1
	ConsensusPathDB
	Pathway Commons: PABPC1
Metabolism	MetaCyc: PABPC1
	HUMANCyc: PABPC1
Regulation	Ensembl's Regulation: ENSG00000070756
	miRBase: chr8 :101,715,143-101,734,315
	TargetScan: NM_002568
	cisRED: ENSG00000070756
Context	iHOP: PABPC1
	cancer metabolism search in PubMed: PABPC1
	UCL Cancer Institute: PABPC1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PABPC1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	604679; gene.
Orphanet
Disease	KEGG Disease: PABPC1
	MedGen: PABPC1 (Human Medical Genetics with Condition)
	ClinVar: PABPC1
Phenotype	MGI: PABPC1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PABPC1	chr8	101719215	101719235	PABPC1	chr8	101721351	101721371
pancreas	PABPC1	chr8	101719215	101719235	PABPC1	chr8	101721351	101721371

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PABPC1 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
AA731281	PABPC1	1	200	8	101733727	101733929	MGEA5	200	402	10	103577939	103578141
DA592957	HLA-DQB1	1	418	6	32629873	32634434	PABPC1	414	560	8	101730415	101733671
BQ348968	PABPC1	170	232	8	101721898	101721960	DPP4	223	512	2	162849781	162862283
AW629981	MFGE8	1	146	15	89445796	89445941	PABPC1	141	562	8	101730429	101733960
AW880952	PABPC1	35	352	8	101721812	101724949	PABPC1	351	424	8	101724944	101725017
BE612624	PABPC1	1	47	8	101715203	101715249	VCP	47	707	9	35057416	35060402
BG928171	PABPC1	61	207	8	101733914	101734059	NR4A1	190	628	12	52451247	52452841
BF087781	PABPC1	29	130	8	101719115	101719216	PABPC1	127	318	8	101721361	101721787
DB265528	PABPC1	1	213	8	101734039	101734251	MTMR14	206	592	3	9691293	9695557
DW419798	RFX3	18	90	9	3524905	3524977	PABPC1	89	302	8	101718881	101719175

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=5

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Somatic 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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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
chr8:101727750-101727750	p.I195V	5
chr8:101727766-101727766	p.E189E	5
chr8:101719201-101719201	p.I454T	4
chr8:101721709-101721709	p.Y408F	4
chr8:101719004-101719004	p.R493C	3
chr8:101718929-101718929	p.R518C	3
chr8:101718932-101718932	p.V517L	3
chr8:101730043-101730043	p.A154G	3
chr8:101730064-101730064	p.T147M	3
chr8:101721407-101721407	p.Q430Q	3

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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	4		9	1		1		13			7	4	3			5	2	1	11
# mutation	2	4		8	1		1		11			9	5	3			5	2	1	12
nonsynonymous SNV		2		5					9			6	5	3			3	2	1	11
synonymous SNV	2	2		3	1		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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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
chr8:101718929	p.R518C	3
chr8:101721709	p.Y408F	3
chr8:101724606	p.A181T	2
chr8:101727792	p.A154G	2
chr8:101730043	p.T147M	2
chr8:101730064	p.T319I	2
chr8:101724923	p.R278H	2
chr8:101721808	p.Q521R	1
chr8:101725345	p.P414S	1
chr8:101719214	p.E275K	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 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

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


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

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 PABPC1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P11940; -.
Chemistry	ChEMBL	CHEMBL1293286; -.
Organism-specific databases	PharmGKB	PA32880; -.
Organism-specific databases	CTD	26986; -.

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
DB00877	poly(A) binding protein, cytoplasmic 1	approved; investigational	Sirolimus

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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