Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 FHIT
Basic gene info.Gene symbolFHIT
Gene namefragile histidine triad
SynonymsAP3Aase|FRA3B
CytomapUCSC genome browser: 3p14.2
Genomic locationchr3 :59735035-61237133
Type of geneprotein-coding
RefGenesNM_001166243.1,
NM_002012.2,
Ensembl idENSG00000262683
DescriptionAP3A hydrolasebis(5'-adenosyl)-triphosphatasediadenosine 5',5'''-P1,P3-triphosphate hydrolasedinucleosidetriphosphatasetumor suppressor protein
Modification date20141207
dbXrefs MIM : 601153
HGNC : HGNC
Ensembl : ENSG00000189283
HPRD : 03096
Vega : OTTHUMG00000158591
ProteinUniProt: P49789
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FHIT
BioGPS: 2272
Gene Expression Atlas: ENSG00000262683
The Human Protein Atlas: ENSG00000262683
PathwayNCI Pathway Interaction Database: FHIT
KEGG: FHIT
REACTOME: FHIT
ConsensusPathDB
Pathway Commons: FHIT
MetabolismMetaCyc: FHIT
HUMANCyc: FHIT
RegulationEnsembl's Regulation: ENSG00000262683
miRBase: chr3 :59,735,035-61,237,133
TargetScan: NM_001166243
cisRED: ENSG00000262683
ContextiHOP: FHIT
cancer metabolism search in PubMed: FHIT
UCL Cancer Institute: FHIT
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of FHIT in cancer cell metabolism1. O'Keefe LV, Colella A, Dayan S, Chen Q, Choo A, et al. (2011) Drosophila orthologue of WWOX, the chromosomal fragile site FRA16D tumour suppressor gene, functions in aerobic metabolism and regulates reactive oxygen species. Hum Mol Genet 20: 497-509. doi: 10.1093/hmg/ddq495. pmid: 3016910. go to article
2. Watson DG, Tonelli F, Alossaimi M, Williamson L, Chan E, et al. (2013) The roles of sphingosine kinases 1 and 2 in regulating the Warburg effect in prostate cancer cells. Cell Signal 25: 1011-1017. doi: 10.1016/j.cellsig.2013.01.002. pmid: 3595369. go to article

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

check002.gifOthers
OMIM 601153; gene.
Orphanet 151; Familial renal cell carcinoma.
DiseaseKEGG Disease: FHIT
MedGen: FHIT (Human Medical Genetics with Condition)
ClinVar: FHIT
PhenotypeMGI: FHIT (International Mouse Phenotyping Consortium)
PhenomicDB: FHIT

Mutations for FHIT
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastFHITchr36055080260550802CCDC88Cchr149180929791809297
haematopoietic_and_lymphoid_tissueFHITchr36066616160666161FHITchr36066616160666161
haematopoietic_and_lymphoid_tissueFHITchr36110764061107640FHITchr36110764061107640
large_intestineFHITchr35998495359984953FHITchr36001982960019829
large_intestineFHITchr36023831660238316FHITchr36064119360641193
large_intestineFHITchr36025657460256574FHITchr36026126860261268
large_intestineFHITchr36047254860472548FHITchr36075215260752152
large_intestineFHITchr36055794660557946FHITchr36056656560566565
large_intestineFHITchr36065200660652006FHITchr36102473361024733
large_intestineFHITchr36071798460717984FHITchr36102037661020376
large_intestineFHITchr36115415261154152chr36137600761376007
liverFHITchr36013653160136531FHITchr36088459160884591
liverFHITchr36036148860361488FHITchr36043089260430892
liverFHITchr36108008661080086chr36125650261256502
ovaryFHITchr35980428259804302FHITchr35979813459798154
ovaryFHITchr35980428459804304FHITchr35979813459798154
ovaryFHITchr35989609759896117FHITchr36028336260283382
ovaryFHITchr35994121259941232FHITchr36005020860050228
ovaryFHITchr36008137060081390chr36128243761282457
ovaryFHITchr36017770260177722FHITchr36020229060202310
ovaryFHITchr36018019960180219FHITchr36018036460180384
ovaryFHITchr36018148560181505chr3178639250178639270
ovaryFHITchr36023660060236620GMDSchr617939061793926
ovaryFHITchr36024598960246009FHITchr36073348860733508
ovaryFHITchr36030553160305551chr37236613972366159
ovaryFHITchr36031805860318078FHITchr36077627560776295
ovaryFHITchr36031807560318095FHITchr36077627560776295
ovaryFHITchr36035039260350412FHITchr36076643660766456
ovaryFHITchr36038753860387558FHITchr36041059660410616
ovaryFHITchr36048085460480874FHITchr36047898860479008
ovaryFHITchr36077685360776873chr1851236295123649
ovaryFHITchr36078825660788276FHITchr36093418660934206
ovaryFHITchr36078865560788675FHITchr36085746460857484
ovaryFHITchr36079623760796257FHITchr36092848860928508
ovaryFHITchr36083897160838991FHITchr36099328860993308
ovaryFHITchr36084447760844497FHITchr36081043360810453
ovaryFHITchr36096736160967381FHITchr36123040061230420
ovaryFHITchr36114963661149656FGF13chr23137880991137881011
ovaryFHITchr36117171361171733NCALDchr8103063101103063121
pancreasFHITchr35975336759753387FHITchr35995269459952714
pancreasFHITchr35978461659784636FHITchr36043894760438967
pancreasFHITchr35978592659785946FHITchr35993355259933572
pancreasFHITchr35978637359786393FHITchr35989943559899455
pancreasFHITchr35982811159828131FHITchr35985191859851938
pancreasFHITchr35983135959831379FHITchr36002760960027629
pancreasFHITchr35986217359862193FHITchr35991170659911726
pancreasFHITchr35987168059871700FHITchr36020668360206703
pancreasFHITchr35996422359964243FHITchr36012361660123636
pancreasFHITchr35999587459995894FHITchr36026940260269422
pancreasFHITchr35999626959996289FHITchr36033430060334320
pancreasFHITchr35999997159999991FHITchr36109684461096864
pancreasFHITchr36005498760055007FHITchr36019195060191970
pancreasFHITchr36005707360057093FHITchr36019920960199229
pancreasFHITchr36007141160071431FHITchr36008555060085570
pancreasFHITchr36008580560085825FHITchr36021478560214805
pancreasFHITchr36011674660116766FHITchr36011681960116839
pancreasFHITchr36016886960168889FHITchr36019616160196181
pancreasFHITchr36018444660184466FHITchr36022449560224515
pancreasFHITchr36018678960186809FHITchr36034843560348455
pancreasFHITchr36021285260212872FHITchr36025884260258862
pancreasFHITchr36029454860294568FHITchr36035288160352901
pancreasFHITchr36032093860320958FHITchr36059003360590053
pancreasFHITchr36032707660327096FHITchr36056021560560235
pancreasFHITchr36033405460334074FHITchr36053296160532981
pancreasFHITchr36033463760334657FHITchr36035901460359034
pancreasFHITchr36033835060338370FHITchr36056619960566219
pancreasFHITchr36034326260343282FHITchr36067114760671167
pancreasFHITchr36034518160345201FHITchr36033906060339080
pancreasFHITchr36035429760354317FHITchr36039422660394246
pancreasFHITchr36036829860368318FHITchr36045126860451288
pancreasFHITchr36038582860385848FHITchr36040054860400568
pancreasFHITchr36039395260393972FHITchr36047213460472154
pancreasFHITchr36039413060394150FHITchr36049933560499355
pancreasFHITchr36039618260396202FHITchr36044899360449013
pancreasFHITchr36039877960398799FHITchr36044708460447104
pancreasFHITchr36040087260400892FHITchr36053273560532755
pancreasFHITchr36041218960412209FHITchr36058592460585944
pancreasFHITchr36041961160419631FHITchr36102978961029809
pancreasFHITchr36042565460425674FHITchr36042711660427136
pancreasFHITchr36042797760427997FHITchr36053074560530765
pancreasFHITchr36043015760430177FHITchr36043413660434156
pancreasFHITchr36043282060432840FHITchr36043327260433292
pancreasFHITchr36043892360438943FHITchr36049792560497945
pancreasFHITchr36044180060441820FHITchr36056181060561830
pancreasFHITchr36044894160448961FHITchr36045322660453246
pancreasFHITchr36045450360454523FHITchr36049643560496455
pancreasFHITchr36045658260456602FHITchr36052580360525823
pancreasFHITchr36046405760464077FHITchr36058765660587676
pancreasFHITchr36047658960476609FHITchr36048606360486083
pancreasFHITchr36049557160495591FHITchr36051374760513767
pancreasFHITchr36049980160499821FHITchr36061534860615368
pancreasFHITchr36050433360504353FHITchr36054480460544824
pancreasFHITchr36050965760509677FHITchr36061280760612827
pancreasFHITchr36051022560510245FHITchr36059178660591806
pancreasFHITchr36051218460512204FHITchr36060859460608614
pancreasFHITchr36052153260521552FHITchr36059534460595364
pancreasFHITchr36053834960538369FHITchr36053978060539800
pancreasFHITchr36054044860540468FHITchr36054478360544803
pancreasFHITchr36055351260553532FHITchr36063600460636024
pancreasFHITchr36055495360554973FHITchr36053482160534841
pancreasFHITchr36057159360571593FHITchr36059987760599877
pancreasFHITchr36059024460590264FHITchr36073939460739414
pancreasFHITchr36060670560606725TTC28chr222906574729065767
pancreasFHITchr36060940060609420FHITchr36064786560647885
pancreasFHITchr36062684660626866FHITchr36063117460631194
pancreasFHITchr36063509260635112FHITchr36063786560637885
pancreasFHITchr36064955460649574FHITchr36082174760821767
pancreasFHITchr36065711060657130FHITchr36062868060628700
pancreasFHITchr36066598860666008FHITchr36066874060668760
pancreasFHITchr36075422860754248chr37826543978265459
pancreasFHITchr36079073360790753FHITchr36084221960842239
pancreasFHITchr36084055260840572FHITchr36086772160867741
pancreasFHITchr36084606360846083FHITchr36084692960846949
pancreasFHITchr36089051460890534FHITchr36092153060921550
pancreasFHITchr36103662261036642FHITchr36100728561007305
pancreasFHITchr36104216161042181FHITchr36112089061120910
pancreasFHITchr36117484661174866FHITchr36118130261181322
skinFHITchr36013275460132754FHITchr36020454360204543
skinFHITchr36087212560872125FHITchr36101321561013215
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 FHIT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP430864GNAS14179205748442657484792FHIT16918935978443059784450
DB472087FHIT135636080761361237135PEG1034750979429818994298373
DA292821FHIT116035988184259882001MYLK-AS11615513123337558123339383
DB472103FHIT135636080761361237135PEG1034749779429818994298362
DA646434FHIT149236033685860337352UBC48673612125398136125399198
BU726961SLC17A72193194993266449932736FHIT9113436009168460091727
BX951598FHIT135836050727760507634SLC30A635765623244649432446793
CD518664FHIT17736032313960323215RFTN2742852198512770198512981
BF370943FHIT2018336021377260213935PRDM121802179133551986133552034

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 # sample1542162286 3317 18138321
GAIN (# sample)3  22 3 412 12422
LOSS (# sample)124214 283 29 5  6136119
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=18)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr3:59908131-59908131p.V97I2
chr3:59999800-59999800p.T61M2
chr3:59999837-59999837p.D49Y1
chr3:60522690-60522690p.S2S1
chr3:59908129-59908129p.V97V1
chr3:59999845-59999845p.R46H1
chr3:59737979-59737979p.A139A1
chr3:59999858-59999858p.R42W1
chr3:59737980-59737980p.A139V1
chr3:59908137-59908137p.V95L1

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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
# sample 1 11      31  131 6
# mutation 1 11      31  131 6
nonsynonymous SNV 1 11      2   131 4
synonymous SNV           11      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
chr3:59999845p.A24T,FHIT1
chr3:59737980p.S22P,FHIT1
chr3:59999858p.A139V,FHIT1
chr3:59737982p.L17L,FHIT1
chr3:59999869p.E138D,FHIT1
chr3:59737985p.S2S,FHIT1
chr3:60522614p.A137A,FHIT1
chr3:59738022p.F125Y,FHIT1
chr3:60522626p.E115K,FHIT1
chr3:59908077p.V97I,FHIT1

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 FHIT 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 FHIT

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

CFAP69,CACNA1F,CCDC24,CHIA,CLK1,EPOR,FHIT,
HEMK1,KLHDC1,LOC149620,LOC284440,LOC340508,NICN1,PCSK4,
PHF1,PROK1,RBM5,SLC25A45,SUGT1P3,CFAP70,ZNF18
ZFAS1,DTNB,EEF1G,EIF3D,FBL,FHIT,IMPDH2,
NOB1,NONO,NPM1,RPL12,RPL5,RPL6,RPLP0,
RPS18,RPS4X,RPS6,RPS7,RPS8,RPSAP58,SNHG8

ABHD14B,ADAT2,TAMM41,EIF4EBP3,FHIT,GPX2,IMMP2L,
METAP1D,ME3,MRPS25,MTL5,NDUFAF2,PRDX5,QARS,
QTRT1,RPL14,RPL32,RPP40,SUPT3H,TMCO6,ZNF76
VPS51___IFT46,HMGN2P46,CTU1,DUS2,F8A1,FHIT,FOXA1,
FOXD2,FRAT2,FUK,KIF19,KREMEN1,OTUD7A,PABPC1,
PABPC3,PRKCG,RBM10,RPL13AP6,TEC,TIGD5,TMCO4
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 FHIT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P49789; -.
ChemistryChEMBL CHEMBL1795151; -.
Organism-specific databasesPharmGKB PA28140; -.
Organism-specific databasesCTD 2272; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02373fragile histidine triadexperimentalAdenosine Monotungstate
DB04173fragile histidine triadexperimentalFructose
DB04389fragile histidine triadexperimentalAdo-P-Ch2-P-Ps-Ado


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Cross referenced IDs for FHIT
* 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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