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 MTHFD1L

Basic gene info.	Gene symbol	MTHFD1L
	Gene name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like
	Synonyms	FTHFSDC1\|MTC1THFS\|dJ292B18.2
	Cytomap	UCSC genome browser: 6q25.1
	Genomic location	chr6 :151186814-151220136
	Type of gene	protein-coding
	RefGenes	NM_001242767.1, NM_001242768.1,NM_001242769.1,NM_015440.4,
	Ensembl id	ENSG00000120254
	Description	10-formyl-THF synthetaseformyltetrahydrofolate synthetase domain containing 1monofunctional C1-tetrahydrofolate synthase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 611427
	HGNC : HGNC
	Ensembl : ENSG00000120254
	HPRD : 09967
	Vega : OTTHUMG00000015828
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTHFD1L
	BioGPS: 25902
	Gene Expression Atlas: ENSG00000120254
	The Human Protein Atlas: ENSG00000120254
Pathway	NCI Pathway Interaction Database: MTHFD1L
	KEGG: MTHFD1L
	REACTOME: MTHFD1L
	ConsensusPathDB
	Pathway Commons: MTHFD1L
Metabolism	MetaCyc: MTHFD1L
	HUMANCyc: MTHFD1L
Regulation	Ensembl's Regulation: ENSG00000120254
	miRBase: chr6 :151,186,814-151,220,136
	TargetScan: NM_001242767
	cisRED: ENSG00000120254
Context	iHOP: MTHFD1L
	cancer metabolism search in PubMed: MTHFD1L
	UCL Cancer Institute: MTHFD1L
Assigned class in ccmGDB	C

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Phenotypic Information for MTHFD1L(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MTHFD1L
	Familial Cancer Database: MTHFD1L

* 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_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: MTHFD1L
	MedGen: MTHFD1L (Human Medical Genetics with Condition)
	ClinVar: MTHFD1L
Phenotype	MGI: MTHFD1L (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MTHFD1L

Mutations for MTHFD1L

* 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 MTHFD1L 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
AA764935	MTHFD1L	1	237	6	151300887	151301123	MTHFD1L	237	337	6	151311062	151311164
AI311578	MTHFD1L	4	113	6	151220027	151220136	RNU5E-1	113	484	5	80548500	80550879
BP339812	IMP3	1	409	15	75932094	75932561	MTHFD1L	406	582	6	151281493	151293131
AA829961	MTHFD1L	1	237	6	151300887	151301123	MTHFD1L	237	474	6	151310926	151311164
AA811452	MTHFD1L	1	237	6	151300887	151301123	MTHFD1L	237	497	6	151310903	151311164
AF190155	MTHFD1L	1	1815	6	151328155	151329970	MTHFD1L	1803	2280	6	151324685	151325162
AW976998	MTHFD1L	1	227	6	151300887	151301113	MTHFD1L	227	426	6	151310965	151311164
AA815116	MTHFD1L	1	237	6	151300887	151301123	MTHFD1L	237	474	6	151310926	151311164

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=67)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=1)	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
chr6:151281413-151281413	p.A602A	3
chr6:151239797-151239797	p.R326Q	3
chr6:151243371-151243371	p.R339C	2
chr6:151187018-151187018	p.G20G	2
chr6:151247259-151247259	p.D362N	2
chr6:151258063-151258063	p.T460T	2
chr6:151198960-151198960	p.E139K	2
chr6:151203912-151203912	p.I144I	2
chr6:151334956-151334956	p.E769D	2
chr6:151265691-151265691	p.D504N	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	1	4		15	2		3		3			8	2	2			2	9	1	11
# mutation	1	4		15	2		3		3			8	2	2			2	9	1	15
nonsynonymous SNV	1	4		12			3		2			6	2	2			1	5	1	15
synonymous SNV				3	2				1			2					1	4

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
chr6:151209072	p.T461T,MTHFD1L	2
chr6:151270259	p.S246S,MTHFD1L	2
chr6:151258063	p.D505Y,MTHFD1L	2
chr6:151239797	p.R327Q,MTHFD1L	2
chr6:151281413	p.R340C,MTHFD1L	2
chr6:151243371	p.D363N,MTHFD1L	2
chr6:151247259	p.T573T,MTHFD1L	2
chr6:151265691	p.A603A,MTHFD1L	2
chr6:151334921	p.M626I,MTHFD1L	1
chr6:151247379	p.E816Q,MTHFD1L	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 MTHFD1L 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 MTHFD1L

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


AMD1,ANKS6,CDC20,CTPS1,EXO5,COLGALT1,HMGA1, IFRD1,MPP6,MTHFD1L,NIP7,NUP93,PABPC4,PLEKHG1, PPP1R14C,PSAT1,TBPL1,ULBP1,YARS,YBX1,ZFP69B	ADORA3,C1RL,CASP4,EXOG,FAM20A,FAM57A,IFI16, LOC541471,LYN,MTHFD1L,MYD88,OSMR,RASSF2,SAMSN1, SELPLG,SLCO2B1,SULF2,TMEM173,TPM4,TUBA1B,UBASH3B

CAD,CCDC86,CDCA5,CTPS1,EFTUD2,LMNB2,MCM4, MTHFD1L,NCAPD3,NCL,NLE1,NOLC1,POLR1A,SLC7A5, SSRP1,STC2,TCP1,TRAP1,XPO5,XPOT,YARS	CALR,CRELD2,DNAJC10,GARS,HM13,HSP90B1,HSPA5, HYOU1,IARS,IPO4,LRP8,MANF,MARS,MCM6, MTHFD1L,PDIA4,PKM,RUVBL1,SLC38A5,SRM,YARS

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 MTHFD1L

There's no related Drug.

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Cross referenced IDs for MTHFD1L

* 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