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 SLC44A1

Basic gene info.	Gene symbol	SLC44A1
	Gene name	solute carrier family 44 (choline transporter), member 1
	Synonyms	CD92\|CDW92\|CHTL1\|CTL1
	Cytomap	UCSC genome browser: 9q31.2
	Genomic location	chr9 :108006928-108153682
	Type of gene	protein-coding
	RefGenes	NM_022109.2, NM_001286730.1,NM_080546.4,
	Ensembl id	ENSG00000070214
	Description	CDW92 antigencholine transporter-like protein 1solute carrier family 44, member 1
	Modification date	20141207
dbXrefs	MIM : 606105
	HGNC : HGNC
	Ensembl : ENSG00000070214
	HPRD : 16197
	Vega : OTTHUMG00000020421
Protein	UniProt: Q8WWI5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SLC44A1
	BioGPS: 23446
	Gene Expression Atlas: ENSG00000070214
	The Human Protein Atlas: ENSG00000070214
Pathway	NCI Pathway Interaction Database: SLC44A1
	KEGG: SLC44A1
	REACTOME: SLC44A1
	ConsensusPathDB
	Pathway Commons: SLC44A1
Metabolism	MetaCyc: SLC44A1
	HUMANCyc: SLC44A1
Regulation	Ensembl's Regulation: ENSG00000070214
	miRBase: chr9 :108,006,928-108,153,682
	TargetScan: NM_022109
	cisRED: ENSG00000070214
Context	iHOP: SLC44A1
	cancer metabolism search in PubMed: SLC44A1
	UCL Cancer Institute: SLC44A1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for SLC44A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SLC44A1
	Familial Cancer Database: SLC44A1

* 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	606105; gene.
Orphanet
Disease	KEGG Disease: SLC44A1
	MedGen: SLC44A1 (Human Medical Genetics with Condition)
	ClinVar: SLC44A1
Phenotype	MGI: SLC44A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SLC44A1

Mutations for SLC44A1

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	SLC44A1	chr9	108007269	108007289	RCAN2	chr6	46452129	46452149

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 SLC44A1 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
CD050630	NOTCH2	22	271	1	120612011	120612259	SLC44A1	264	480	9	108007210	108007437
BX504871	SLC44A1	1	148	9	108132314	108132461	KDM2A	132	233	11	67025031	67025132
C02459	SLC44A1	1	146	9	108152447	108152591	SLC44A1	140	348	9	108153184	108153392

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=51)	Stat. for Synonymous SNVs (# total SNVs=12)

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
chr9:108097968-108097968	p.A132T	4
chr9:108127819-108127819	p.R437C	3
chr9:108123483-108123483	p.V258L	2
chr9:108127850-108127850	p.S447C	2
chr9:108097969-108097969	p.A132V	2
chr9:108118629-108118629	p.E213*	2
chr9:108120671-108120671	p.V239V	2
chr9:108136923-108136923	p.T513T	2
chr9:108136937-108136937	p.A518V	1
chr9:108061534-108061534	p.R24C	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		2	1	14	1		2		1			7	1	2			7	6		8
# mutation		2	1	14	1		2		1			9	1	2			7	7		8
nonsynonymous SNV		2		10	1		2		1			7	1	2			5	4		6
synonymous SNV			1	4								2					2	3		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
chr9:108136923	p.R437C,SLC44A1	2
chr9:108123571	p.S447C,SLC44A1	2
chr9:108127819	p.R457Q,SLC44A1	2
chr9:108127850	p.A132V,SLC44A1	2
chr9:108127880	p.R287L,SLC44A1	2
chr9:108097969	p.T513T,SLC44A1	2
chr9:108061569	p.R528Q,SLC44A1	1
chr9:108126837	p.R57I,SLC44A1	1
chr9:108110667	p.A185V,SLC44A1	1
chr9:108128681	p.V366F,SLC44A1	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 SLC44A1 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 SLC44A1

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


ANO6,ARHGEF12,TMEM245,INIP,FAM120A,FAM120AOS,FAM172A, FKTN,INPP4B,KIAA0430,MAP3K1,MARCH8,MEGF9,MFAP3, RAB14,SLC44A1,SPIN1,SPTLC1,TSTD2,ZNF484,ZNF510	AFTPH,APH1B,CMTM6,DKFZP586I1420,ERBB4,ESR1,HHAT, IQCH,LOC344595,MGAT4A,MYO6,JADE3,RAB6C,RERG, SLC44A1,TMEM30B,TSPAN5,TSPYL4,TTC30B,UBP1,ZNRF2

FAM206A,C9orf85,CCDC28A,CD164,EPB41L4B,ERP44,FAM120AOS, GALNT12,LRRC19,LRRC31,NIPSNAP3A,OSTF1,PDCL,PPP6C, RAB14,SH3BGRL2,SLC35B3,SLC35D2,SLC44A1,SPTLC1,STX19	AHCYL2,ATP8B1,MCU,DSG2,ENTPD5,EPB41L4B,EPCAM, FBXO34,GPR39,LGR4,PPARG,PPM1B,RASSF6,SH3BGRL2, SLC35A3,SLC35B3,SLC44A1,TMEM170A,TMPRSS4,UGT8,XK

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 SLC44A1

There's no related Drug.

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Cross referenced IDs for SLC44A1

* 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