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 ANKRD1

Basic gene info.	Gene symbol	ANKRD1
	Gene name	ankyrin repeat domain 1 (cardiac muscle)
	Synonyms	ALRP\|C-193\|CARP\|CVARP\|MCARP\|bA320F15.2
	Cytomap	UCSC genome browser: 10q23.31
	Genomic location	chr10 :92671856-92681032
	Type of gene	protein-coding
	RefGenes	NM_014391.2,
	Ensembl id	ENSG00000148677
	Description	ankyrin repeat domain-containing protein 1cardiac ankyrin repeat proteincytokine-inducible gene C-193 proteincytokine-inducible nuclear proteinliver ankyrin repeat domain 1
	Modification date	20141219
dbXrefs	MIM : 609599
	HGNC : HGNC
	Ensembl : ENSG00000148677
	HPRD : 10647
	Vega : OTTHUMG00000018734
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ANKRD1
	BioGPS: 27063
	Gene Expression Atlas: ENSG00000148677
	The Human Protein Atlas: ENSG00000148677
Pathway	NCI Pathway Interaction Database: ANKRD1
	KEGG: ANKRD1
	REACTOME: ANKRD1
	ConsensusPathDB
	Pathway Commons: ANKRD1
Metabolism	MetaCyc: ANKRD1
	HUMANCyc: ANKRD1
Regulation	Ensembl's Regulation: ENSG00000148677
	miRBase: chr10 :92,671,856-92,681,032
	TargetScan: NM_014391
	cisRED: ENSG00000148677
Context	iHOP: ANKRD1
	cancer metabolism search in PubMed: ANKRD1
	UCL Cancer Institute: ANKRD1
Assigned class in ccmGDB	C

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Phenotypic Information for ANKRD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ANKRD1
	Familial Cancer Database: ANKRD1

* 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_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ANKRD1
	MedGen: ANKRD1 (Human Medical Genetics with Condition)
	ClinVar: ANKRD1
Phenotype	MGI: ANKRD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ANKRD1

Mutations for ANKRD1

* 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 ANKRD1 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
BP260187	ANKRD1	1	397	10	92678893	92680843	CAV1	398	584	7	116165090	116166708
BP259299	ANKRD1	1	263	10	92679932	92680847	ATP8B5P	259	579	9	35406896	35407216

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=44)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr10:92677580-92677580	p.R154P	4
chr10:92675935-92675935	p.R215Q	3
chr10:92672639-92672639	p.R315H	2
chr10:92679998-92679998	p.L45L	2
chr10:92672640-92672640	p.R315C	2
chr10:92678998-92678998	p.S79P	2
chr10:92677503-92677503	p.E180K	2
chr10:92675581-92675581	p.E236E	2
chr10:92677521-92677521	p.E174K	2
chr10:92678945-92678945	p.R96R	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=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	1			9			1		3			8	2	2			3	3		5
# mutation	1			10			1		3			8	2	2			3	3		6
nonsynonymous SNV	1			9			1		2			7	1	2			1	3		6
synonymous SNV				1					1			1	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
chr10:92675935	p.R215Q	3
chr10:92680081	p.G18W	2
chr10:92675581	p.E236E	2
chr10:92675612	p.E43D	1
chr10:92677534	p.R315H	1
chr10:92679982	p.E180K	1
chr10:92675931	p.L39S	1
chr10:92678659	p.R315C	1
chr10:92672639	p.I179I	1
chr10:92680004	p.L39V	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 ANKRD1 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 ANKRD1

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


ADAMTSL4,AMOTL2,ANKRD1,CYP1A2,COL26A1,FNDC1,GRIN2A, ICAM5,KCNA5,KLHL38,KRT84,LEFTY2,MYOZ1,NRARP, OR2A12,PDE1C,PIM1,SLC7A5P1,SPTB,THBS3,TTC7A	ACTA1,ACTN2,ANKRD1,ASB10,MIR1-1HG,SMCO1,CASQ1, PPP1R27,KLHL41,KLHL40,LMOD2,LMOD3,LOC151300,MYH2, MYH6,NEB,OR5H15,P2RX6P,PPP1R3A,SLN,SMPX

ANKRD1,CD274,CXCL10,DIRAS3,FRMD5,HMX2,IL17C, IL31RA,KIR2DL1,KIR2DL3,KPRP,LCE1F,LOC153910,LOC285735, LOC400696,LRRTM1,OR5B17,PAEP,PMAIP1,TM4SF18,WARS	ANKRD1,CCIN,CELA3A,DRD5,DUSP21,FGF5,HSPA6, IAPP,LOC645166,LINC00152,NEUROD4,PAK1IP1,PCCB,PKD2L1, PSG1,SLC14A2,SLC37A2,SSX8,TMEM211,VCY,XKR3

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 ANKRD1

There's no related Drug.

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Cross referenced IDs for ANKRD1

* 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