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 AHCYL1

Basic gene info.	Gene symbol	AHCYL1
	Gene name	adenosylhomocysteinase-like 1
	Synonyms	DCAL\|IRBIT\|PPP1R78\|PRO0233\|XPVKONA
	Cytomap	UCSC genome browser: 1p13.2
	Genomic location	chr1 :110527386-110566364
	Type of gene	protein-coding
	RefGenes	NM_001242673.1, NM_001242674.1,NM_001242675.1,NM_001242676.1,NM_006621.5,
	Ensembl id	ENSG00000168710
	Description	DC-expressed AHCY-like moleculeS-adenosyl homocysteine hydrolase homologS-adenosyl-L-homocysteine hydrolase 2S-adenosylhomocysteine hydrolase-like protein 1adoHcyase 2dendritic cell expressed AHCY-like proteininositol 1,4,5-trisphosphate receptor-bi
	Modification date	20141207
dbXrefs	MIM : 607826
	HGNC : HGNC
	Ensembl : ENSG00000168710
	HPRD : 07613
	Vega : OTTHUMG00000011652
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_AHCYL1
	BioGPS: 10768
	Gene Expression Atlas: ENSG00000168710
	The Human Protein Atlas: ENSG00000168710
Pathway	NCI Pathway Interaction Database: AHCYL1
	KEGG: AHCYL1
	REACTOME: AHCYL1
	ConsensusPathDB
	Pathway Commons: AHCYL1
Metabolism	MetaCyc: AHCYL1
	HUMANCyc: AHCYL1
Regulation	Ensembl's Regulation: ENSG00000168710
	miRBase: chr1 :110,527,386-110,566,364
	TargetScan: NM_001242673
	cisRED: ENSG00000168710
Context	iHOP: AHCYL1
	cancer metabolism search in PubMed: AHCYL1
	UCL Cancer Institute: AHCYL1
Assigned class in ccmGDB	C

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Phenotypic Information for AHCYL1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: AHCYL1
	Familial Cancer Database: AHCYL1

* 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
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: AHCYL1
	MedGen: AHCYL1 (Human Medical Genetics with Condition)
	ClinVar: AHCYL1
Phenotype	MGI: AHCYL1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: AHCYL1

Mutations for AHCYL1

* 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
breast	AHCYL1	chr1	110543945	110543945	CAPZA1	chr1	113190387	113190387

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 AHCYL1 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
CA841960	MDC1	1	88	6	2005120	2005207	AHCYL1	82	595	1	110563832	110564345
DA647181	AHCYL1	1	544	1	110564420	110564963	LRRC58	545	782	3	120047152	120047390
AA207072	AHCYL1	1	24	1	110535028	110535051	RNFT2	21	141	12	117217168	117217288
BQ774807	AHCYL1	18	123	1	110566259	110566364	AHCYL1	120	765	1	110564873	110565518
AI800578	AHCYL1	1	148	1	110564858	110565005	AHCYL1	143	598	1	110565532	110565987
AI862468	AHCYL1	1	246	1	110564750	110564995	CDK6	237	476	7	92366341	92366578
BQ776309	AHCYL1	1	43	1	110565797	110566217	AHCYL1	28	692	1	110565596	110566197
AA830163	RBFOX2	14	115	22	36234279	36234400	AHCYL1	105	434	1	110561072	110563417
DA382933	PDXDC1	1	423	16	15130378	15130799	AHCYL1	415	632	1	110561585	110562230

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=38)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	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
chr1:110560608-110560608	p.R365W	3
chr1:110553838-110553838	p.A79T	2
chr1:110563436-110563436	p.L517F	2
chr1:110558115-110558115	p.I248I	2
chr1:110560120-110560120	p.G323S	2
chr1:110561083-110561083	p.I404I	2
chr1:110561085-110561085	p.D405A	2
chr1:110560622-110560622	p.V369V	2
chr1:110559066-110559066	p.E295*	2
chr1:110561048-110561048	p.I393L	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=2

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	1	1	9			1		3		1	6	2	3			1	8		6
# mutation	1	1	1	8			1		3		1	6	2	3			1	8		7
nonsynonymous SNV		1	1	7			1		3			5	1	3				6		4
synonymous SNV	1			1							1	1	1				1	2		3

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
chr1:110557445	p.R167H,AHCYL1	2
chr1:110561083	p.I357I,AHCYL1	2
chr1:110561031	p.M1I,AHCYL1	1
chr1:110551702	p.N232N,AHCYL1	1
chr1:110561730	p.P404L,AHCYL1	1
chr1:110558065	p.T9I,AHCYL1	1
chr1:110561046	p.R247Q,AHCYL1	1
chr1:110551754	p.A412T,AHCYL1	1
chr1:110562188	p.D26D,AHCYL1	1
chr1:110558117	p.R256S,AHCYL1	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 AHCYL1 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 AHCYL1

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


ABCD3,AHCYL1,ATP8B1,CPEB4,DBT,DNAJC16,DNAL1, STRIP1,FAM73A,FBXL5,FPGT,GOLGB1,IPP,EFCAB14, PCYOX1,SLC25A24,SPG11,STXBP3,TMEM167B,USP33,WDR47	AHCYL1,ASPH,ATP9A,CCPG1,COBLL1,DDHD2,DYNC1LI2, IMPAD1,ITGB1,JAK1,KCTD20,KLHL5,PARVA,PCYOX1, PTPN11,RABL3,RNF14,SEC22B,SEPT11,SNX19,STS

ABCD3,AGL,AHCYL1,ALG6,CEPT1,CLCC1,CSDE1, DBT,DDAH1,FAM102B,GNAI3,HIPK1,MAGI3,PKN2, RSBN1,SCP2,SERBP1,SLC25A24,SLC35A3,STXBP3,TAF13	AHCYL1,ALS2,AQP1,BCO2,CDR2L,CREB3L2,CYP2U1, DEFB131,ESRRG,HOXC11,HOXC5,KCTD3,KIFC3,MAOB, NBAS,PHYHIPL,PMP22,SFXN3,SUSD2,TIAM2,TMEM25

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 AHCYL1

There's no related Drug.

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Cross referenced IDs for AHCYL1

* 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