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 ANP32A

Basic gene info.	Gene symbol	ANP32A
	Gene name	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A
	Synonyms	C15orf1\|HPPCn\|I1PP2A\|LANP\|MAPM\|PHAP1\|PHAPI\|PP32
	Cytomap	UCSC genome browser: 15q23
	Genomic location	chr15 :69070874-69113261
	Type of gene	protein-coding
	RefGenes	NM_006305.3,
	Ensembl id	ENSG00000140350
	Description	acidic leucine-rich nuclear phosphoprotein 32 family member Aacidic nuclear phosphoprotein pp32cerebellar leucine rich acidic nuclear proteinhepatopoietin Cninhibitor-1 of protein phosphatase-2Aleucine-rich acidic nuclear proteinmapmodulinpotent he
	Modification date	20141207
dbXrefs	MIM : 600832
	HGNC : HGNC
	Ensembl : ENSG00000140350
	HPRD : 09014
	Vega : OTTHUMG00000154502
Protein	UniProt: P39687 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ANP32A
	BioGPS: 8125
	Gene Expression Atlas: ENSG00000140350
	The Human Protein Atlas: ENSG00000140350
Pathway	NCI Pathway Interaction Database: ANP32A
	KEGG: ANP32A
	REACTOME: ANP32A
	ConsensusPathDB
	Pathway Commons: ANP32A
Metabolism	MetaCyc: ANP32A
	HUMANCyc: ANP32A
Regulation	Ensembl's Regulation: ENSG00000140350
	miRBase: chr15 :69,070,874-69,113,261
	TargetScan: NM_006305
	cisRED: ENSG00000140350
Context	iHOP: ANP32A
	cancer metabolism search in PubMed: ANP32A
	UCL Cancer Institute: ANP32A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for ANP32A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ANP32A
	Familial Cancer Database: ANP32A

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	600832; gene.
Orphanet
Disease	KEGG Disease: ANP32A
	MedGen: ANP32A (Human Medical Genetics with Condition)
	ClinVar: ANP32A
Phenotype	MGI: ANP32A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ANP32A

Mutations for ANP32A

* 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

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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ANP32A	chr15	69103657	69103677	ANP32A	chr15	69110856	69110876

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 ANP32A 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
AA634993	ANP32A	1	341	15	69072759	69076924	ANKRD12	336	389	18	9256041	9256094
AI990804	ANP32A	5	195	15	69076744	69076935	MIR548F1	188	299	1	186283023	186283134
BG002858	ANP32A	11	154	15	69103700	69103844	HES2	150	323	1	6476149	6476322
T20169	ANP32A	187	413	15	69071722	69071952	C1orf87	404	423	1	60458727	60458746
AA173919	POMT1	1	290	9	134398890	134399180	ANP32A	286	486	15	69072041	69072241

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=16)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr15:69072792-69072792	p.N215N	2
chr15:69076789-69076789	p.S158L	2
chr15:69113080-69113080	p.G4D	1
chr15:69076799-69076799	p.A155S	1
chr15:69080146-69080146	p.S56L	1
chr15:69076826-69076826	p.D146N	1
chr15:69080153-69080153	p.L54V	1
chr15:69076829-69076829	p.L145F	1
chr15:69080154-69080154	p.G53G	1
chr15:69076865-69076865	p.E133*	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	2			1				1				4	1				2	1	1	3
# mutation	2			1				1				4	1				2	1	1	3
nonsynonymous SNV	1			1				1				4	1				2		1	2
synonymous SNV	1																	1		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
chr15:69079816	p.K65T	1
chr15:69080119	p.A58T	1
chr15:69080141	p.S56L	1
chr15:69080146	p.G53G	1
chr15:69072434	p.S29S	1
chr15:69080154	p.N13K	1
chr15:69072764	p.R12L	1
chr15:69080226	p.L9L	1
chr15:69076789	p.E246Q	1
chr15:69113052	p.E225K	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 ANP32A 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 ANP32A

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


AAGAB,ANP32A,VWA9,C15orf61,CLN6,COX5A,EDC3, GTF2A2,HNRNPC,IMP3,LOC723972,MAP2K5,OAZ2,PPCDC, PSMA4,RPL4,SNAPC5,SNUPN,TRIP4,UBL7,WDR61	ANP32A,CFDP1,CLNS1A,CNPY2,HNRNPC,MEA1,MFAP1, MRFAP1L1,MRPL9,PA2G4,PDCD6,PTMA,RANBP1,RBMX2, RPS24,SF3B14,SRSF9,STYXL1,UBE2I,UFC1,ZMAT2

ANP32A,BLM,BUB1B,CLN6,CLPX,CSK,EDC3, EIF3J,FAM98B,FBXO22,HMG20A,KIF23,LEO1,MESDC2, PDCD7,RPL4,SLTM,SPATA5L1,TIPIN,UBL7,ZWILCH	ANP32A,ANP32B,ATP2C1,BCL11A,CAPRIN1,CCDC15,CRLF2, DCP2,GPHN,HNRNPA1,HNRNPH3,L3MBTL3,MED17,MEX3C, NPAT,PHF6,RHOV,SBK1,STX6,SUDS3,USP48

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 ANP32A

There's no related Drug.

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Cross referenced IDs for ANP32A

* 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