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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GRHL1 |
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Phenotypic Information for GRHL1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GRHL1 |
Familial Cancer Database: GRHL1 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GRHL1 |
MedGen: GRHL1 (Human Medical Genetics with Condition) | |
ClinVar: GRHL1 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | GRHL1 | chr2 | 10114019 | 10114039 | GRHL1 | chr2 | 10103889 | 10103909 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GRHL1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
BE693592 | GOLGA4 | 9 | 269 | 3 | 37368943 | 37369203 | GRHL1 | 264 | 337 | 2 | 10136337 | 10136410 | |
BE144212 | ARL17A | 45 | 327 | 17 | 197735 | 198201 | GRHL1 | 323 | 647 | 2 | 10141544 | 10141871 | |
BG013794 | C6orf62 | 1 | 172 | 6 | 24705832 | 24706008 | GRHL1 | 162 | 322 | 2 | 10102599 | 10104113 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=32) | (# total SNVs=13) |
(# total SNVs=2) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr2:10126330-10126330 | p.V208I | 3 |
chr2:10136458-10136458 | p.R347* | 3 |
chr2:10139098-10139098 | p.S372S | 2 |
chr2:10130834-10130834 | p.R238Q | 2 |
chr2:10101455-10101455 | p.S23S | 2 |
chr2:10140793-10140793 | p.E416D | 2 |
chr2:10130855-10130855 | p.R245Q | 2 |
chr2:10101458-10101458 | p.I24I | 2 |
chr2:10104169-10104169 | p.R112* | 2 |
chr2:10140800-10140800 | p.S421fs*6 | 2 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 3 | 2 |   | 5 | 1 |   | 5 |   | 1 | 1 |   | 6 | 1 | 1 |   |   | 10 | 7 |   | 7 |
# mutation | 3 | 2 |   | 8 | 1 |   | 5 |   | 1 | 1 |   | 8 | 1 | 1 |   |   | 11 | 8 |   | 8 |
nonsynonymous SNV | 2 | 2 |   | 4 | 1 |   | 5 |   | 1 | 1 |   | 6 | 1 | 1 |   |   | 7 | 7 |   | 6 |
synonymous SNV | 1 |   |   | 4 |   |   |   |   |   |   |   | 2 |   |   |   |   | 4 | 1 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr2:10101455 | p.D187N | 2 |
chr2:10130834 | p.P518S | 2 |
chr2:10136059 | p.V221I | 2 |
chr2:10101557 | p.R427Q | 2 |
chr2:10139116 | p.H294P | 1 |
chr2:10102598 | p.P462P | 1 |
chr2:10126264 | p.S77S | 1 |
chr2:10132241 | p.R327G | 1 |
chr2:10101237 | p.L472F | 1 |
chr2:10140759 | p.R111I | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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