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 PAIP1

Basic gene info.	Gene symbol	PAIP1
	Gene name	poly(A) binding protein interacting protein 1
	Synonyms	-
	Cytomap	UCSC genome browser: 5p12
	Genomic location	chr5 :43526369-43557195
	Type of gene	protein-coding
	RefGenes	NM_006451.4, NM_182789.3,NM_183323.2,
	Ensembl id	ENSG00000172239
	Description	PABC1-interacting protein 1PABP-interacting protein 1PAIP-1poly(A)-binding protein-interacting protein 1polyadenylate binding protein-interacting protein 1polyadenylate-binding protein-interacting protein 1
	Modification date	20141207
dbXrefs	MIM : 605184
	HGNC : HGNC
	Ensembl : ENSG00000172239
	HPRD : 05539
	Vega : OTTHUMG00000096960
Protein	UniProt: Q9H074 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAIP1
	BioGPS: 10605
	Gene Expression Atlas: ENSG00000172239
	The Human Protein Atlas: ENSG00000172239
Pathway	NCI Pathway Interaction Database: PAIP1
	KEGG: PAIP1
	REACTOME: PAIP1
	ConsensusPathDB
	Pathway Commons: PAIP1
Metabolism	MetaCyc: PAIP1
	HUMANCyc: PAIP1
Regulation	Ensembl's Regulation: ENSG00000172239
	miRBase: chr5 :43,526,369-43,557,195
	TargetScan: NM_006451
	cisRED: ENSG00000172239
Context	iHOP: PAIP1
	cancer metabolism search in PubMed: PAIP1
	UCL Cancer Institute: PAIP1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PAIP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PAIP1
	Familial Cancer Database: PAIP1

* 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 BLCA ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	605184; gene.
Orphanet
Disease	KEGG Disease: PAIP1
	MedGen: PAIP1 (Human Medical Genetics with Condition)
	ClinVar: PAIP1
Phenotype	MGI: PAIP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PAIP1

Mutations for PAIP1

* 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 PAIP1 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
BU734173	HSP90AA1	15	282	14	102550822	102551205	PAIP1	278	657	5	43535707	43543212
BM709680	PAIP1	1	381	5	43535707	43543212	HSP90AA1	377	644	14	102550822	102551205
BU732881	HSP90AA1	15	282	14	102550822	102551205	PAIP1	278	553	5	43535707	43539139

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr5:43527537-43527537	p.E461Q	2
chr5:43543191-43543191	p.M217V	2
chr5:43543175-43543175	p.C222Y	2
chr5:43556069-43556069	p.S100A	2
chr5:43543182-43543182	p.R220C	2
chr5:43529971-43529971	p.E421D	1
chr5:43548014-43548014	p.E146A	1
chr5:43536983-43536983	p.L304L	1
chr5:43556088-43556088	p.P93P	1
chr5:43533846-43533846	p.D416N	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=1

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	6			5			3		4			7	4	1			7	3		6
# mutation	6			6			4		4			9	4	1			7	4		7
nonsynonymous SNV	6			6			4		3			8	2	1			6	2		6
synonymous SNV									1			1	2				1	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
chr5:43543182	p.R220S,PAIP1	2
chr5:43529961	p.E464Q,PAIP1	1
chr5:43555944	p.E350Q,PAIP1	1
chr5:43536991	p.Y216Y,PAIP1	1
chr5:43527528	p.L94M,PAIP1	1
chr5:43543192	p.E463Q,PAIP1	1
chr5:43529971	p.G338E,PAIP1	1
chr5:43555957	p.S210C,PAIP1	1
chr5:43537010	p.P93P,PAIP1	1
chr5:43527531	p.E461Q,PAIP1	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 PAIP1 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 PAIP1

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


BRIX1,C5orf22,C5orf28,C5orf34,C5orf51,CCT5,DNAJC21, FASTKD3,GOLPH3,ICE1,MTMR12,NIPBL,NUP155,PAIP1, RAD1,DROSHA,SKP2,TARS,TRIP13,ZFR,ZNF131	ARL5A,ATAD1,BTF3L4,URI1,CAPZA2,CCDC91,DNAJC24, EIF1AX,EIF2S1,FAM175B,ISCA1,MMADHC,NT5C3A,PAIP1, PPP1CC,PRKRA,RAB6A,UBE2V2,UCHL5,VBP1,VPS37A

BRIX1,C11orf58,C3orf38,C5orf28,CCT5,CENPQ,CRBN, FASTKD3,GOLPH3,GPN1,PAIP1,PCNP,RAD1,SUB1, TBPL1,TTC33,UBA3,WDR70,ZFR,ZNF131,ZNF627	ARL1,BTF3L4,FAM204A,C11orf58,CWC15,SMIM11,GNG10, METTL5,MRPL33,NMD3,NSL1,PAIP1,PCNP,PIGY, PRKAG1,RSL24D1,RWDD1,SNX3,STARD3NL,ZCRB1,ZFAND1

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 PAIP1

There's no related Drug.

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Cross referenced IDs for PAIP1

* 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