Cancer Cell Metabolism Gene Database

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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 GALNT7
Basic gene info.Gene symbolGALNT7
Gene namepolypeptide N-acetylgalactosaminyltransferase 7
SynonymsGALNAC-T7|GalNAcT7
CytomapUCSC genome browser: 4q31.1
Genomic locationchr4 :174089903-174245118
Type of geneprotein-coding
RefGenesNM_017423.2,
Ensembl idENSG00000109586
DescriptionN-acetylgalactosaminyltransferase 7UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)polypeptide GalNAc transferase 7pp-GaNTase 7protein-UDP acetylg
Modification date20141207
dbXrefs MIM : 605005
HGNC : HGNC
Ensembl : ENSG00000109586
HPRD : 10386
Vega : OTTHUMG00000160817
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT7
BioGPS: 51809
Gene Expression Atlas: ENSG00000109586
The Human Protein Atlas: ENSG00000109586
PathwayNCI Pathway Interaction Database: GALNT7
KEGG: GALNT7
REACTOME: GALNT7
ConsensusPathDB
Pathway Commons: GALNT7
MetabolismMetaCyc: GALNT7
HUMANCyc: GALNT7
RegulationEnsembl's Regulation: ENSG00000109586
miRBase: chr4 :174,089,903-174,245,118
TargetScan: NM_017423
cisRED: ENSG00000109586
ContextiHOP: GALNT7
cancer metabolism search in PubMed: GALNT7
UCL Cancer Institute: GALNT7
Assigned class in ccmGDBC

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Phenotypic Information for GALNT7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT7
Familial Cancer Database: GALNT7
* 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
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GALNT7
MedGen: GALNT7 (Human Medical Genetics with Condition)
ClinVar: GALNT7
PhenotypeMGI: GALNT7 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT7

Mutations for GALNT7
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryGALNT7chr4174148953174148973GALNT7chr4174149168174149188
pancreasGALNT7chr4174121120174121140GALNT7chr4174122694174122714
pancreasGALNT7chr4174129045174129065GALNT7chr4174130717174130737
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 GALNT7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ004985GALNT71321514174137341174137360COL1A214355279404300794047144

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 # 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)

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=58)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr4:174090004-174090004p.G6G4
chr4:174216610-174216610p.R273Q3
chr4:174169388-174169388p.R128R3
chr4:174213410-174213410p.D247N3
chr4:174235124-174235124p.V469M2
chr4:174169569-174169569p.V189I2
chr4:174223217-174223217p.G390R2
chr4:174235151-174235151p.D478H2
chr4:174235223-174235223p.R502*2
chr4:174169386-174169386p.R128C2

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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
# sample13 81   5 161   5229
# mutation13 81   5 171   6228
nonsynonymous SNV12 6    5  5    5 18
synonymous SNV 1 21     121   121 
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
chr4:174213410p.D247N3
chr4:174216610p.R273Q2
chr4:174238797p.R284Q2
chr4:174216643p.E541K2
chr4:174169386p.E141Q1
chr4:174235281p.K363R1
chr4:174219442p.D547Y1
chr4:174169415p.I183N1
chr4:174216618p.T368T1
chr4:174219443p.R628C1

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 GALNT7 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 GALNT7

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

ALDH6A1,ATP8B1,SMIM14,C9orf152,C9orf91,CCDC160,CD46,
EDEM3,EIF2AK3,ENTPD3,FOXA1,GALNT7,KIAA1244,LRRC31,
LRRFIP1,MIA3,SEC16A,SEC62,SETD7,SLC44A4,TMEM87B
ALCAM,ARSD,ATP8B1,CCDC160,CORO2A,EPT1,GALNT3,
GALNT7,HOOK1,MAP7,MARVELD2,MYO5B,OCLN,PPM1H,
RBM47,SHROOM3,SLC38A1,STRBP,TEX9,TMEM87B,TOM1L1

AGR2,ANG,ATP2A3,ATP8B1,SMIM14,CAMK2D,CAPN9,
CD55,CREB3L1,GALNT3,GALNT7,MLPH,MRAP2,REG4,
RNASE4,SIDT1,SRD5A3,ST3GAL4,TC2N,UAP1,ZBTB7C
ACVR1B,ADAM10,AHCYL2,BCL2L11,CDH1,DSG2,EPB41L4B,
GALNT12,GALNT7,LGR4,LIMA1,NCEH1,PIGG,PLD1,
PPAPDC2,PPM1B,RAVER2,SH3BGRL2,SNX30,SYTL2,TMEM87B
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 GALNT7
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
DB01033UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)approvedMercaptopurine
DB00563UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)approvedMethotrexate


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Cross referenced IDs for GALNT7
* 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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