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 HDC
Basic gene info.Gene symbolHDC
Gene namehistidine decarboxylase
Synonyms-
CytomapUCSC genome browser: 15q21.2
Genomic locationchr15 :50534145-50558162
Type of geneprotein-coding
RefGenesNM_002112.3,
Ensembl idENSG00000140287
Description-
Modification date20141207
dbXrefs MIM : 142704
HGNC : HGNC
Ensembl : ENSG00000140287
HPRD : 00817
Vega : OTTHUMG00000131644
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HDC
BioGPS: 3067
Gene Expression Atlas: ENSG00000140287
The Human Protein Atlas: ENSG00000140287
PathwayNCI Pathway Interaction Database: HDC
KEGG: HDC
REACTOME: HDC
ConsensusPathDB
Pathway Commons: HDC
MetabolismMetaCyc: HDC
HUMANCyc: HDC
RegulationEnsembl's Regulation: ENSG00000140287
miRBase: chr15 :50,534,145-50,558,162
TargetScan: NM_002112
cisRED: ENSG00000140287
ContextiHOP: HDC
cancer metabolism search in PubMed: HDC
UCL Cancer Institute: HDC
Assigned class in ccmGDBC

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

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

Mutations for HDC
* 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 HDC 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=71)
Stat. for Synonymous SNVs
(# total SNVs=17)
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
chr15:50544965-50544965p.R265H3
chr15:50535170-50535170p.E426K3
chr15:50555448-50555448p.R63Q2
chr15:50535348-50535348p.R412C2
chr15:50544942-50544942p.D273N2
chr15:50534514-50534514p.E644D2
chr15:50535044-50535044p.R468*2
chr15:50534666-50534666p.A594T2
chr15:50534519-50534519p.P643S2
chr15:50540510-50540510p.R358C2

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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
# sample2 1144 2    972  258 9
# mutation2 1174 2    1082  2712 9
nonsynonymous SNV2 1123 2    861  189 8
synonymous SNV   51      221  93 1
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
chr15:50555448p.R63Q3
chr15:50534698p.V639I2
chr15:50534531p.E426K2
chr15:50535170p.D273N2
chr15:50544942p.R583H2
chr15:50546735p.R468Q1
chr15:50534694p.S354G1
chr15:50540453p.T247T1
chr15:50544822p.T149M1
chr15:50550644p.L565L1

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 HDC 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 HDC

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

AKR7A2P1,APLP1,C9orf135,CADPS,CRYGC,DKFZP434H168,FAM107B,
FGF12,FLJ46111,GRIA1,GRIN1,HAO2,HDC,KIRREL3,
NDP,SFXN1,SLC18A2,TAGLN3,TMEM196,TPH2,TWISTNB
BASP1,C16orf54,GCSAML,C1orf186,CMA1,CPA3,CSF2RB,
CTSG,ERVFRD-1,HDC,IL18R1,IL2RA,IL5RA,MAS1L,
MRGPRX2,MS4A2,RGS13,SAMSN1,SIGLEC6,SLC18A2,TPSAB1

A2M,ATP8B4,C10orf128,GCSAML,C1orf186,CPA3,CTSG,
ERVFRD-1,FGF7,FLI1,GATA1,HDC,MAP3K12,MEOX1,
MS4A2,PDE7B,SIGLEC6,SIGLEC17P,SLC18A2,TPSAB1,TPSB2
ACTL7A,ATP6V1C2,C1orf186,CDK15,CHIT1,CPA3,CTSG,
EMR2,HDC,HS3ST2,ISYNA1,ITGAX,MS4A2,PIK3R6,
RRP7B,SIGLEC6,SIGLEC17P,SYNDIG1,TNFRSF4,TPSAB1,TPSB2
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 HDC
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114histidine decarboxylasenutraceuticalPyridoxal Phosphate
DB00117histidine decarboxylaseapproved; nutraceuticalL-Histidine
DB00667histidine decarboxylaseapprovedHistamine Phosphate


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Cross referenced IDs for HDC
* 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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