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 SLC44A4

Basic gene info.	Gene symbol	SLC44A4
	Gene name	solute carrier family 44, member 4
	Synonyms	C6orf29\|CTL4\|NG22\|TPPT
	Cytomap	UCSC genome browser: 6p21.3
	Genomic location	chr6_ssto_hap7 :3163717-3179566
	Type of gene	protein-coding
	RefGenes	NM_001178044.1, NM_001178045.1,NM_025257.2,
	Ensembl id	ENSG00000204385
	Description	choline transporter-like protein 4
	Modification date	20141207
dbXrefs	MIM : 606107
	HGNC : HGNC
	Ensembl : ENSG00000204385
	HPRD : 12087
	Vega : OTTHUMG00000031133
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC44A4
	BioGPS: 80736
	Gene Expression Atlas: ENSG00000204385
	The Human Protein Atlas: ENSG00000204385
Pathway	NCI Pathway Interaction Database: SLC44A4
	KEGG: SLC44A4
	REACTOME: SLC44A4
	ConsensusPathDB
	Pathway Commons: SLC44A4
Metabolism	MetaCyc: SLC44A4
	HUMANCyc: SLC44A4
Regulation	Ensembl's Regulation: ENSG00000204385
	miRBase: chr6_ssto_hap7 :3,163,717-3,179,566
	TargetScan: NM_001178044
	cisRED: ENSG00000204385
Context	iHOP: SLC44A4
	cancer metabolism search in PubMed: SLC44A4
	UCL Cancer Institute: SLC44A4
Assigned class in ccmGDB	C

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Phenotypic Information for SLC44A4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC44A4
	Familial Cancer Database: SLC44A4

* 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_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: SLC44A4
	MedGen: SLC44A4 (Human Medical Genetics with Condition)
	ClinVar: SLC44A4
Phenotype	MGI: SLC44A4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC44A4

Mutations for SLC44A4

* 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 SLC44A4 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
BI026665	MYH9	2	140	22	36727986	36728125	SLC44A4	129	281	6	3171348	3171501
BF509779	SLC44A4	141	313	6	3164418	3164590	SLC44A4	307	409	6	3164214	3164316
BC014659	SLC44A4	92	2565	6	3163722	3176652	ANKRD17	2562	2583	4	74084357	74084378

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=39)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=7)

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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
chr6:31842534-31842535	p.N144fs*55	3
chr6:31833864-31833864	p.V425L	2
chr6:31838832-31838832	p.?	2
chr6:31838468-31838468	p.A317T	2
chr6:31842535-31842536	p.N144fs*55	2
chr6:31836957-31836957	p.P403L	2
chr6:31846741-31846741	p.R6L	2
chr6:31833482-31833482	p.D523H	2
chr6:31833747-31833747	p.V464I	2
chr6:31833528-31833528	p.L507L	2

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

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
chr6:31838664	p.A246T,SLC44A4	2
chr6:31832449	p.D622G,SLC44A4	2
chr6:31833833	p.V17V,SLC44A4	1
chr6:31832450	p.G605V,SLC44A4	1
chr6:31838621	p.F443S,SLC44A4	1
chr6:31842560	p.R242Q,SLC44A4	1
chr6:31833349	p.Y13C,SLC44A4	1
chr6:31833838	p.D586N,SLC44A4	1
chr6:31832499	p.P437P,SLC44A4	1
chr6:31838641	p.Y233C,SLC44A4	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 SLC44A4 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 SLC44A4

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


ARFIP2,CCDC176,C9orf152,CCDC125,CCDC160,CD46,CREB3L1, CREB3L4,ERBB3,ERGIC1,FOXA1,GALNT6,GALNT7,GPR160, MIA3,MLPH,MUC1,SEC16A,SLC44A4,SPDEF,ZBTB42	C3orf52,CANT1,CLDN7,DLG3,GALNT6,GOLM1,HN1L, LEO1,LRRC46,MAGED2,MAPK13,MLPH,MUC1,PRR15, PRR15L,SEC14L2,SEZ6L2,SLC35A2,SLC44A4,SLC9A3R1,XBP1

BCAS1,C1orf106,C4orf19,CAPN5,CASP7,CDHR5,DNM2, FA2H,GPA33,HECTD3,ITM2C,MGLL,MUC13,NR3C2, PLS1,PTPRH,SLC44A4,STYK1,TJP3,TMEM63B,TSPAN1	CAPN2,CAPN5,CDCP1,CLCN2,CNNM4,GBA,ITM2C, MARK2,OSBPL2,PAK1,PCDH1,PCSK7,PRSS8,RAB19, SCAMP2,SCNN1A,SGPP2,SLC44A4,ST14,TJP3,TMEM63B

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 SLC44A4

There's no related Drug.

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Cross referenced IDs for SLC44A4

* 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