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 MTHFD2L

Basic gene info.	Gene symbol	MTHFD2L
	Gene name	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like
	Synonyms	-
	Cytomap	UCSC genome browser: 4q13.3
	Genomic location	chr4 :75023828-75168814
	Type of gene	protein-coding
	RefGenes	NM_001144978.1, NM_001004346.2,
	Ensembl id	ENSG00000163738
	Description	MTHFD2-likeNADP-dependent methylenetetrahydrofolate dehydrogenase 2-like proteinprobable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2
	Modification date	20141207
dbXrefs	MIM : 614047
	HGNC : HGNC
	Ensembl : ENSG00000163738
	HPRD : 17608
	Vega : OTTHUMG00000157135
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTHFD2L
	BioGPS: 441024
	Gene Expression Atlas: ENSG00000163738
	The Human Protein Atlas: ENSG00000163738
Pathway	NCI Pathway Interaction Database: MTHFD2L
	KEGG: MTHFD2L
	REACTOME: MTHFD2L
	ConsensusPathDB
	Pathway Commons: MTHFD2L
Metabolism	MetaCyc: MTHFD2L
	HUMANCyc: MTHFD2L
Regulation	Ensembl's Regulation: ENSG00000163738
	miRBase: chr4 :75,023,828-75,168,814
	TargetScan: NM_001144978
	cisRED: ENSG00000163738
Context	iHOP: MTHFD2L
	cancer metabolism search in PubMed: MTHFD2L
	UCL Cancer Institute: MTHFD2L
Assigned class in ccmGDB	C

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Phenotypic Information for MTHFD2L(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MTHFD2L
	Familial Cancer Database: MTHFD2L

* 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: MTHFD2L
	MedGen: MTHFD2L (Human Medical Genetics with Condition)
	ClinVar: MTHFD2L
Phenotype	MGI: MTHFD2L (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MTHFD2L

Mutations for MTHFD2L

* 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
ovary	MTHFD2L	chr4	75044856	75044876		chr4	71997962	71997982
ovary	MTHFD2L	chr4	75071458	75071478		chr4	67409359	67409379

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 MTHFD2L 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
BU155734	LGALS1	1	507	22	38071663	38075809	MTHFD2L	493	515	4	75023137	75023161
AK023167	ZDHHC20	3	260	13	22033193	22033450	MTHFD2L	261	2138	4	75065511	75168812
AX794778	ZDHHC20	3	260	13	22033193	22033450	MTHFD2L	261	2138	4	75065511	75168812

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=20)	Stat. for Synonymous SNVs (# total SNVs=4)

Stat. for Deletions (# total SNVs=3)	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
chr4:75167509-75167509	p.I287fs*>3	3
chr4:75040332-75040332	p.S27G	2
chr4:75065603-75065603	p.D124N	2
chr4:75147154-75147154	p.L215S	1
chr4:75040303-75040303	p.V17G	1
chr4:75065564-75065564	p.D111Y	1
chr4:75147190-75147190	p.V227A	1
chr4:75040313-75040313	p.G20G	1
chr4:75065573-75065573	p.H114Y	1
chr4:75147202-75147202	p.G231D	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		6	1							1	1	1			5	2	1	5
# mutation		1		5	1							1	2	1			5	2	1	5
nonsynonymous SNV				5	1							1	2	1			4	2	1	3
synonymous SNV		1															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
chr4:75040332	p.S85G	2
chr4:75091079	p.G142S	1
chr4:75040333	p.I345I	1
chr4:75091091	p.T157A	1
chr4:75041093	p.N160D	1
chr4:75147190	p.A163V	1
chr4:75065528	p.H172Y	1
chr4:75147202	p.L181P	1
chr4:75065537	p.A191V	1
chr4:75147227	p.A193V	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 MTHFD2L 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 MTHFD2L

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


C11orf71,COA5,FAM200B,GRSF1,DANCR,LOC100303728,LOC147727, LOC202781,LOC400027,LOC400752,LOC401588,MRPL1,MTHFD2L,RCHY1, RUFY3,SDAD1,SNHG10,TCTE3,THAP6,THAP9,UTP3	ACTR6,AP1AR,VCPKMT,C5orf28,CAAP1,CLDN12,CSNK1A1, EEF1E1,KIAA0895,LZTFL1,LAMTOR3,MTHFD2L,NUP35,NUPL2, ORC4,POT1,PRSS16,SRSF6,SVIP,TMEM161B,ZBED5

ATP5L,C14orf142,COMMD8,COX18,DCK,DANCR,MTHFD2L, MYEOV2,NDUFB1,NUDCD2,NUP54,ORC4,PACRGL,PHF5A, RCHY1,SDHD,SNRPG,TIMM8B,TMEM126B,TOMM22,UQCR10	BRIX1,DTD2,KATNBL1,C5orf28,TRAPPC13,CCDC58,TRMT13, MRPL1,MRPL32,MRPL50,MTERF3,MTHFD2L,NUPL2,OTUD6B, PAK1IP1,PRMT3,PTRH2,RCN2,TRMT10C,TAF9,TRUB1

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 MTHFD2L

There's no related Drug.

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Cross referenced IDs for MTHFD2L

* 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