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 GALNT1
Basic gene info.Gene symbolGALNT1
Gene namepolypeptide N-acetylgalactosaminyltransferase 1
SynonymsGALNAC-T1
CytomapUCSC genome browser: 18q12.1
Genomic locationchr18 :33234532-33291798
Type of geneprotein-coding
RefGenesNM_020474.3,
Ensembl idENSG00000141429
DescriptionGalNAc transferase 1UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)polypeptide GalNAc transferase 1pp-GaNTase 1protein-UDP acetylgalactosaminyltr
Modification date20141207
dbXrefs MIM : 602273
HGNC : HGNC
Ensembl : ENSG00000141429
HPRD : 03781
Vega : OTTHUMG00000132567
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GALNT1
BioGPS: 2589
Gene Expression Atlas: ENSG00000141429
The Human Protein Atlas: ENSG00000141429
PathwayNCI Pathway Interaction Database: GALNT1
KEGG: GALNT1
REACTOME: GALNT1
ConsensusPathDB
Pathway Commons: GALNT1
MetabolismMetaCyc: GALNT1
HUMANCyc: GALNT1
RegulationEnsembl's Regulation: ENSG00000141429
miRBase: chr18 :33,234,532-33,291,798
TargetScan: NM_020474
cisRED: ENSG00000141429
ContextiHOP: GALNT1
cancer metabolism search in PubMed: GALNT1
UCL Cancer Institute: GALNT1
Assigned class in ccmGDBC

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Phenotypic Information for GALNT1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GALNT1
Familial Cancer Database: GALNT1
* 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: GALNT1
MedGen: GALNT1 (Human Medical Genetics with Condition)
ClinVar: GALNT1
PhenotypeMGI: GALNT1 (International Mouse Phenotyping Consortium)
PhenomicDB: GALNT1

Mutations for GALNT1
* 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
pancreasGALNT1chr183325268333252703chr183436550534365525
pancreasGALNT1chr183326242133262441TMPRSS15chr211965282719652847
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 GALNT1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG289433GALNT11557183326338733271068NFX155263893334827633348363
W52720GALNT1163183328967733289739GALNT161249183328354533289714
DA662182ZSCAN301122183287009532870216GALNT1121555183326335333269190
AI952718PCYT1B13287X2466819024676354GALNT1281404183327097533271098
AI656193PCYT1B13287X2466819024676354GALNT1281404183327097533271098

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=41)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr18:33263508-33263508p.C212F2
chr18:33283583-33283583p.N503N2
chr18:33270975-33270975p.?2
chr18:33243615-33243615p.H55Y2
chr18:33272189-33272189p.L402V2
chr18:33271056-33271056p.T353T2
chr18:33271142-33271142p.Y382C2
chr18:33272292-33272293p.?2
chr18:33272171-33272171p.I396V2
chr18:33257555-33257555p.G105G2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 42 2 1  3631 45110
# mutation12 42 2 1  3631 45112
nonsynonymous SNV1  31 1 1  3221 44 9
synonymous SNV 2 11 1     41   113
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
chr18:33263508p.T353T2
chr18:33271056p.C212F2
chr18:33257697p.H55Y1
chr18:33269245p.M313I1
chr18:33234753p.T478A1
chr18:33272259p.M75I1
chr18:33263466p.N320S1
chr18:33271038p.C497F1
chr18:33234759p.A93V1
chr18:33282891p.E322D1

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 GALNT1 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 GALNT1

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

CHST2,FSCN1,GALNT18,IL32,IL34,LMNA,LTBR,
MIIP,MMP7,NFKB2,NFKBIE,PRKCDBP,RASSF4,RELB,
RHOG,RPS6KA4,SLC25A22,TIMM44,TMEM39B,TWF2,TYMP
ADRA2C,ARHGAP23,ADM5,ACKR1,TMEM255B,GALNT18,GGT5,
HDAC7,HYAL2,ID3,IFITM3,LPCAT4,MEGF6,MFNG,
NOS3,PPM1F,RASIP1,SEMA6B,SLCO4A1,SPNS2,TMEM173

ADCY1,CLEC2B,DENND5A,FADS1,FADS3,FAM124A,FJX1,
GAL,GALNT18,GPR63,GSTT2,ITPRIPL1,LDLRAD3,LOXL3,
MAP7D3,NCDN,PGBD1,SAAL1,TMEM132A,TRIM65,TTYH2
AKT3,ARHGAP23,C20orf194,DENND5A,FAM65A,GALNT18,GLI3,
LRIG1,NFATC4,NFIX,NPR2,PBX3,PHLDB2,RILPL1,
RUSC2,SHISA4,TBKBP1,TIMP2,TMEM109,ZBTB47,ZFPM2
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 GALNT1


There's no related Drug.
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Cross referenced IDs for GALNT1
* 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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