Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 UGT2B28
Basic gene info.Gene symbolUGT2B28
Gene nameUDP glucuronosyltransferase 2 family, polypeptide B28
Synonyms-
CytomapUCSC genome browser: 4q13.2
Genomic locationchr4 :70146216-70160768
Type of geneprotein-coding
RefGenesNM_001207004.1,
NM_053039.1,
Ensembl idENSG00000135226
DescriptionUDP glycosyltransferase 2 family, polypeptide B28UDP-glucuronosyltransferase 2B28UDPGT 2B28
Modification date20141207
dbXrefs MIM : 606497
HGNC : HGNC
Ensembl : ENSG00000135226
HPRD : 05931
Vega : OTTHUMG00000129401
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UGT2B28
BioGPS: 54490
Gene Expression Atlas: ENSG00000135226
The Human Protein Atlas: ENSG00000135226
PathwayNCI Pathway Interaction Database: UGT2B28
KEGG: UGT2B28
REACTOME: UGT2B28
ConsensusPathDB
Pathway Commons: UGT2B28
MetabolismMetaCyc: UGT2B28
HUMANCyc: UGT2B28
RegulationEnsembl's Regulation: ENSG00000135226
miRBase: chr4 :70,146,216-70,160,768
TargetScan: NM_001207004
cisRED: ENSG00000135226
ContextiHOP: UGT2B28
cancer metabolism search in PubMed: UGT2B28
UCL Cancer Institute: UGT2B28
Assigned class in ccmGDBC

Top
Phenotypic Information for UGT2B28(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UGT2B28
Familial Cancer Database: UGT2B28
* 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_ASCORBATE_AND_ALDARATE_METABOLISM
KEGG_STARCH_AND_SUCROSE_METABOLISM
KEGG_RETINOL_METABOLISM
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_CYTOCHROME_P450
KEGG_DRUG_METABOLISM_OTHER_ENZYMES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: UGT2B28
MedGen: UGT2B28 (Human Medical Genetics with Condition)
ClinVar: UGT2B28
PhenotypeMGI: UGT2B28 (International Mouse Phenotyping Consortium)
PhenomicDB: UGT2B28

Mutations for UGT2B28
* 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 UGT2B28 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

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample  1              
GAIN (# sample)                 
LOSS (# sample)  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)

Top
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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=78)
Stat. for Synonymous SNVs
(# total SNVs=26)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr4:70152481-70152481p.E294E5
chr4:70146681-70146681p.P155S4
chr4:70160509-70160509p.K524N3
chr4:70156380-70156380p.G387G3
chr4:70146230-70146230p.K4K3
chr4:70156481-70156481p.S421L3
chr4:70146620-70146620p.K134N3
chr4:70148376-70148376p.P289H3
chr4:70146759-70146759p.E181K2
chr4:70156375-70156375p.H386Y2

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 96 3 3  166   339111
# mutation21 115 3 3  176   328111
nonsynonymous SNV21 94 1 2  124   236 11
synonymous SNV   21 2 1  52   921 
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])

Top
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
chr4:70152481p.E294E,UGT2B284
chr4:70146620p.K134N,UGT2B283
chr4:70155432p.L74L,UGT2B282
chr4:70160509p.K524N2
chr4:70146396p.T351I2
chr4:70156391p.P289H,UGT2B282
chr4:70160257p.D99N,UGT2B282
chr4:70146759p.E181K,UGT2B282
chr4:70146440p.S421L2
chr4:70146570p.S110L,UGT2B282

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 UGT2B28 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]

Top
Gene Expression for UGT2B28

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ACSM1,ADH1C,ALOX15B,C15orf43,CHRNA2,CLDN8,GGT1,
GGT3P,ISX,LST-3TM12,MPV17L,PNLIPRP3,SCP2,SERHL2,
SERHL,SLC38A4,SLCO1B1,SPINK8,SRD5A1,SULT1C3,UGT2B28
ADAM2,AWAT2,B3GAT1,C6orf223,CPB2,DHRS2,HIST1H4H,
HPGD,HSD3B1,HSD3B2,MPV17L,PNLIPRP3,PPEF1,MSMO1,
SERHL2,SERHL,SRD5A1,TARP,UGT2B10,UGT2B11,UGT2B28

AMPH,ARR3,CDH4,CNGA3,CYLC1,ELOVL2,FAM181B,
GAD2,GSTA1,MYCN,MYCNOS,NNAT,P2RY4,PON1,
PRSS53,SCARNA20,SERPINA12,SYNGR4,UGT2B11,UGT2B28,ZNF385B
ACBD4,ACY1,AKR1C3,AKR7A3,BPHL,C11orf80,C5orf47,
CCDC17,FAM3B,GLYCTK,HCG9,HSD17B3,LIN7A,MYL5,
RBKS,RELL2,SCRN2,SLC16A5,SLC25A34,UCKL1,UGT2B28
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for UGT2B28


There's no related Drug.
Top
Cross referenced IDs for UGT2B28
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas