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 GRHL1
Basic gene info.Gene symbolGRHL1
Gene namegrainyhead-like 1 (Drosophila)
SynonymsLBP32|MGR|NH32|TFCP2L2
CytomapUCSC genome browser: 2p25.1
Genomic locationchr2 :10091791-10142412
Type of geneprotein-coding
RefGenesNM_198182.2,
Ensembl idENSG00000134317
DescriptionLBP protein 32grainyhead-like protein 1 homologmammalian grainyheadtranscription factor CP2-like 2transcription factor LBP-32
Modification date20141207
dbXrefs MIM : 609786
HGNC : HGNC
Ensembl : ENSG00000134317
HPRD : 18176
Vega : OTTHUMG00000151704
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GRHL1
BioGPS: 29841
Gene Expression Atlas: ENSG00000134317
The Human Protein Atlas: ENSG00000134317
PathwayNCI Pathway Interaction Database: GRHL1
KEGG: GRHL1
REACTOME: GRHL1
ConsensusPathDB
Pathway Commons: GRHL1
MetabolismMetaCyc: GRHL1
HUMANCyc: GRHL1
RegulationEnsembl's Regulation: ENSG00000134317
miRBase: chr2 :10,091,791-10,142,412
TargetScan: NM_198182
cisRED: ENSG00000134317
ContextiHOP: GRHL1
cancer metabolism search in PubMed: GRHL1
UCL Cancer Institute: GRHL1
Assigned class in ccmGDBC

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Phenotypic Information for GRHL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GRHL1
Familial Cancer Database: GRHL1
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GRHL1
MedGen: GRHL1 (Human Medical Genetics with Condition)
ClinVar: GRHL1
PhenotypeMGI: GRHL1 (International Mouse Phenotyping Consortium)
PhenomicDB: GRHL1

Mutations for GRHL1
* 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
ovaryGRHL1chr21011401910114039GRHL1chr21010388910103909
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 GRHL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE693592GOLGA4926933736894337369203GRHL126433721013633710136410
BE144212ARL17A4532717197735198201GRHL132364721014154410141871
BG013794C6orf62117262470583224706008GRHL116232221010259910104113

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=2)
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
chr2:10136458-10136458p.R347*3
chr2:10126330-10126330p.V208I3
chr2:10101455-10101455p.S23S2
chr2:10140793-10140793p.E416D2
chr2:10101458-10101458p.I24I2
chr2:10130855-10130855p.R245Q2
chr2:10104169-10104169p.R112*2
chr2:10140800-10140800p.S421fs*62
chr2:10104439-10104439p.R138W2
chr2:10105453-10105453p.I162I2

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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
# sample32 51 5 11 611  107 7
# mutation32 81 5 11 811  118 8
nonsynonymous SNV22 41 5 11 611  77 6
synonymous SNV1  4       2    41 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
chr2:10101455p.V221I2
chr2:10130834p.R427Q2
chr2:10136059p.D187N2
chr2:10101557p.P518S2
chr2:10104149p.V13V1
chr2:10095163p.G220D1
chr2:10130832p.I417I1
chr2:10136041p.L556F1
chr2:10104439p.A47V1
chr2:10095208p.E426E1

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 GRHL1 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 GRHL1

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

ADAM17,ATL2,ATP6V1C2,B3GNT5,BCL11A,CPSF3,FZD7,
GFRA3,GRHL1,GTF3C2,KLF11,NOL10,PDIA6,PELI1,
PPP1CB,PSME4,RNASEH1,TMEM79,USP6NL,YWHAQ,ZNF750
CCL28,CTBP2,DSC2,EHF,ETV6,FAM60A,GRHL1,
KIAA1671,KIAA1804,KIT,METAP1,NEBL,NSUN7,PIK3C2G,
SDR42E1,SHANK2,SUDS3,WWC1,ZNF33B,ZNF667,ZNF750

AFAP1L2,ANGPTL4,ANXA1,BARX2,C18orf25,CDR2L,FAM83A,
GNA15,GRHL1,IKZF2,IL1RN,KCTD1,KLK5,MYOF,
PTPRU,RHBDL2,SERPINB2,SGMS1,SPRR1A,ST6GALNAC2,TACSTD2
APCS,C3P1,C8A,CFHR2,CFHR5,CYP4A22,DNAJB8,
F13B,F9,FGA,FGB,FGG,GRHL1,KIR3DP1,
KRTAP4-11,KRTAP5-3,LECT2,LOC100129935,LINC00160,OR1N1,SLC17A2
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 GRHL1


There's no related Drug.
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Cross referenced IDs for GRHL1
* 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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