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 symbolMTHFD1L
Gene namemethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like
SynonymsFTHFSDC1|MTC1THFS|dJ292B18.2
CytomapUCSC genome browser: 6q25.1
Genomic locationchr6 :151186814-151220136
Type of geneprotein-coding
RefGenesNM_001242767.1,
NM_001242768.1,NM_001242769.1,NM_015440.4,
Ensembl idENSG00000120254
Description10-formyl-THF synthetaseformyltetrahydrofolate synthetase domain containing 1monofunctional C1-tetrahydrofolate synthase, mitochondrial
Modification date20141207
dbXrefs MIM : 611427
HGNC : HGNC
Ensembl : ENSG00000120254
HPRD : 09967
Vega : OTTHUMG00000015828
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFD1L
BioGPS: 25902
Gene Expression Atlas: ENSG00000120254
The Human Protein Atlas: ENSG00000120254
PathwayNCI Pathway Interaction Database: MTHFD1L
KEGG: MTHFD1L
REACTOME: MTHFD1L
ConsensusPathDB
Pathway Commons: MTHFD1L
MetabolismMetaCyc: MTHFD1L
HUMANCyc: MTHFD1L
RegulationEnsembl's Regulation: ENSG00000120254
miRBase: chr6 :151,186,814-151,220,136
TargetScan: NM_001242767
cisRED: ENSG00000120254
ContextiHOP: MTHFD1L
cancer metabolism search in PubMed: MTHFD1L
UCL Cancer Institute: MTHFD1L
Assigned class in ccmGDBC

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Phenotypic Information for MTHFD1L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MTHFD1L
MedGen: MTHFD1L (Human Medical Genetics with Condition)
ClinVar: MTHFD1L
PhenotypeMGI: MTHFD1L (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTHFD1L related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA764935MTHFD1L12376151300887151301123MTHFD1L2373376151311062151311164
AI311578MTHFD1L41136151220027151220136RNU5E-111348458054850080550879
BP339812IMP31409157593209475932561MTHFD1L4065826151281493151293131
AA829961MTHFD1L12376151300887151301123MTHFD1L2374746151310926151311164
AA811452MTHFD1L12376151300887151301123MTHFD1L2374976151310903151311164
AF190155MTHFD1L118156151328155151329970MTHFD1L180322806151324685151325162
AW976998MTHFD1L12276151300887151301113MTHFD1L2274266151310965151311164
AA815116MTHFD1L12376151300887151301123MTHFD1L2374746151310926151311164

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 # sample1                
GAIN (# sample)1                
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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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=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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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
chr6:151281413-151281413p.A602A3
chr6:151239797-151239797p.R326Q3
chr6:151187018-151187018p.G20G2
chr6:151247259-151247259p.D362N2
chr6:151258063-151258063p.T460T2
chr6:151198960-151198960p.E139K2
chr6:151203912-151203912p.I144I2
chr6:151334956-151334956p.E769D2
chr6:151265691-151265691p.D504N2
chr6:151243371-151243371p.R339C2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 152 3 3  822  29111
# mutation14 152 3 3  822  29115
nonsynonymous SNV14 12  3 2  622  15115
synonymous SNV   32   1  2    14  
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
chr6:151270259p.T461T,MTHFD1L2
chr6:151258063p.S246S,MTHFD1L2
chr6:151239797p.D505Y,MTHFD1L2
chr6:151281413p.R327Q,MTHFD1L2
chr6:151243371p.R340C,MTHFD1L2
chr6:151247259p.D363N,MTHFD1L2
chr6:151265691p.T573T,MTHFD1L2
chr6:151209072p.A603A,MTHFD1L2
chr6:151197269p.L619P,MTHFD1L1
chr6:151293131p.E770D,MTHFD1L1

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 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

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

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
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 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



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