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 symbolMTHFD2L
Gene namemethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like
Synonyms-
CytomapUCSC genome browser: 4q13.3
Genomic locationchr4 :75023828-75168814
Type of geneprotein-coding
RefGenesNM_001144978.1,
NM_001004346.2,
Ensembl idENSG00000163738
DescriptionMTHFD2-likeNADP-dependent methylenetetrahydrofolate dehydrogenase 2-like proteinprobable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2
Modification date20141207
dbXrefs MIM : 614047
HGNC : HGNC
Ensembl : ENSG00000163738
HPRD : 17608
Vega : OTTHUMG00000157135
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFD2L
BioGPS: 441024
Gene Expression Atlas: ENSG00000163738
The Human Protein Atlas: ENSG00000163738
PathwayNCI Pathway Interaction Database: MTHFD2L
KEGG: MTHFD2L
REACTOME: MTHFD2L
ConsensusPathDB
Pathway Commons: MTHFD2L
MetabolismMetaCyc: MTHFD2L
HUMANCyc: MTHFD2L
RegulationEnsembl's Regulation: ENSG00000163738
miRBase: chr4 :75,023,828-75,168,814
TargetScan: NM_001144978
cisRED: ENSG00000163738
ContextiHOP: MTHFD2L
cancer metabolism search in PubMed: MTHFD2L
UCL Cancer Institute: MTHFD2L
Assigned class in ccmGDBC

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Phenotypic Information for MTHFD2L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MTHFD2L
MedGen: MTHFD2L (Human Medical Genetics with Condition)
ClinVar: MTHFD2L
PhenotypeMGI: MTHFD2L (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryMTHFD2Lchr47504485675044876chr47199796271997982
ovaryMTHFD2Lchr47507145875071478chr46740935967409379
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTHFD2L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU155734LGALS11507223807166338075809MTHFD2L49351547502313775023161
AK023167ZDHHC203260132203319322033450MTHFD2L261213847506551175168812
AX794778ZDHHC203260132203319322033450MTHFD2L261213847506551175168812

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2 1   5 2 3      
GAIN (# sample)2 1       2      
LOSS (# sample)      5 2 1      
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr4:75167509-75167509p.I287fs*>33
chr4:75040332-75040332p.S27G2
chr4:75065603-75065603p.D124N2
chr4:75065526-75065526p.R98Q1
chr4:75091075-75091075p.H199Y1
chr4:75040299-75040299p.W16R1
chr4:75065528-75065528p.T99A1
chr4:75091079-75091079p.T200M1
chr4:75040300-75040300p.W16L1
chr4:75167517-75167517p.I287I1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1 61      111  5215
# mutation 1 51      121  5215
nonsynonymous SNV   51      121  4213
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr4:75040332p.S85G2
chr4:75065601p.W74R1
chr4:75167517p.V285A1
chr4:75040299p.W74L1
chr4:75065631p.G289D1
chr4:75040300p.G78G1
chr4:75065637p.V297V1
chr4:75040313p.P321S1
chr4:75091075p.S85I1
chr4:75091079p.L334F1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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