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 MIF
Basic gene info.Gene symbolMIF
Gene namemacrophage migration inhibitory factor (glycosylation-inhibiting factor)
SynonymsGIF|GLIF|MMIF
CytomapUCSC genome browser: 22q11.23
Genomic locationchr22 :24236564-24237409
Type of geneprotein-coding
RefGenesNM_002415.1,
Ensembl idENSG00000240972
DescriptionL-dopachrome isomeraseL-dopachrome tautomerasemacrophage migration inhibitory factorphenylpyruvate tautomerase
Modification date20141207
dbXrefs MIM : 153620
HGNC : HGNC
HPRD : 01091
ProteinUniProt: P14174
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MIF
BioGPS: 4282
Gene Expression Atlas: ENSG00000240972
The Human Protein Atlas: ENSG00000240972
PathwayNCI Pathway Interaction Database: MIF
KEGG: MIF
REACTOME: MIF
ConsensusPathDB
Pathway Commons: MIF
MetabolismMetaCyc: MIF
HUMANCyc: MIF
RegulationEnsembl's Regulation: ENSG00000240972
miRBase: chr22 :24,236,564-24,237,409
TargetScan: NM_002415
cisRED: ENSG00000240972
ContextiHOP: MIF
cancer metabolism search in PubMed: MIF
UCL Cancer Institute: MIF
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MIF in cancer cell metabolism1. Choi J, Jung W-H, Koo JS (2013) Metabolism-related proteins are differentially expressed according to the molecular subtype of invasive breast cancer defined by surrogate immunohistochemistry. Pathobiology 80: 41-52. go to article

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Phenotypic Information for MIF(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MIF
Familial Cancer Database: MIF
* 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_TYROSINE_METABOLISM
KEGG_PHENYLALANINE_METABOLISM

check002.gifOthers
OMIM 153620; gene.
604302; phenotype.
Orphanet 85414; Systemic-onset juvenile idiopathic arthritis.
DiseaseKEGG Disease: MIF
MedGen: MIF (Human Medical Genetics with Condition)
ClinVar: MIF
PhenotypeMGI: MIF (International Mouse Phenotyping Consortium)
PhenomicDB: MIF

Mutations for MIF
* 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 MIF related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=3)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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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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
chr22:24236984-24236984p.D45V2
chr22:24236667-24236667p.P2P1
chr22:24236713-24236713p.G18W1
chr22:24237238-24237238p.N98I1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1                1  
# mutation1                1  
nonsynonymous SNV                 1  
synonymous SNV1                   
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
chr22:24236667p.P2P1
chr22:24236713p.G18W1

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 MIF 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 MIF

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

ADAT3,C19orf60,C1orf86,CCDC124,DDTL,DGCR6L,GLI4,
JOSD2,LSM7,MIF,MRPL23,LINC00116,NDUFA11,NDUFB7,
PGLS,RPS19BP1,SCAND1,THAP7,TSPO,UQCR10,YDJC
ADAT3,AGTRAP,ARRDC1,EMC10,C1orf86,CHPF,CNFN,
CTXN1,EXOSC4,EVA1B,HSPBP1,LMAN2,LSM7,MIF,
MRPS12,NHP2,PPDPF,PTRH1,RHOD,TMEM102,YIPF2

BID,UQCC3,PTRHD1,DDT,DDTL,MIF,MRPL12,
MRPL27,MRPL54,MTFP1,NDUFA6,POLR2F,SCO2,SF3B5,
THAP7,PAM16,TRAPPC5,TSPO,TXN2,UQCR10,YDJC
C17orf49,CLPP,COPE,DDOST,DHRS13,EIF5A,HAUS7,
LAGE3,NAA38,MIF,MRPL37,MRPS34,MTG1,PAFAH1B3,
PIH1D1,PSMB3,RNASEH2A,RUVBL2,TK1,TMEM11,TSPO
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 MIF
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P14174; -.
ChemistryChEMBL CHEMBL2111430; -.
Organism-specific databasesPharmGKB PA30819; -.
Organism-specific databasesCTD 4282; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01880macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental3,4-Dihydroxycinnamic Acid
DB02728macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental7-Hydroxy-2-Oxo-Chromene-3-Carboxylic Acid Ethyl Ester
DB04272macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimentalCitric Acid
DB07718macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental3-(4-HYDROXY-PHENYL)PYRUVIC ACID
DB07888macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental3-(4-HYDROXYPHENYL)-4,5-DIHYDRO-5-ISOXAZOLE-ACETIC ACID METHYL ESTER
DB08333macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME
DB08334macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental3-FLUORO-4-HYDROXYBENZALDEHYDE O-(CYCLOHEXYLCARBONYL)OXIME
DB08335macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental4-HYDROXYBENZALDEHYDE O-(3,3-DIMETHYLBUTANOYL)OXIME
DB08765macrophage migration inhibitory factor (glycosylation-inhibiting factor)experimental6-HYDROXY-1,3-BENZOTHIAZOLE-2-SULFONAMIDE


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Cross referenced IDs for MIF
* 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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