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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GALC |
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Phenotypic Information for GALC(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: GALC |
Familial Cancer Database: GALC |
* 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/ |
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KEGG_SPHINGOLIPID_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: GALC |
MedGen: GALC (Human Medical Genetics with Condition) | |
ClinVar: GALC | |
Phenotype | MGI: GALC (International Mouse Phenotyping Consortium) |
PhenomicDB: GALC |
Mutations for GALC |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | GALC | chr14 | 88401403 | 88401423 | chr14 | 92235144 | 92235164 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GALC 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 |
DA803568 | WDR74 | 2 | 110 | 11 | 62609173 | 62609281 | GALC | 111 | 566 | 14 | 88450801 | 88459517 | |
U77631 | RAPGEF6 | 40 | 177 | 5 | 130883800 | 130928129 | GALC | 165 | 461 | 14 | 88458648 | 88458945 | |
BQ292312 | GSN | 14 | 237 | 9 | 124053312 | 124053530 | GALC | 229 | 383 | 14 | 88400470 | 88400624 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   | 1 |   | 1 |   | 1 |   |   |   |   | 1 |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 1 |   | 1 |   |   |   |   |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=43) | (# total SNVs=15) |
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(# total SNVs=0) | (# total SNVs=1) |
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* 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 |
chr14:88459448-88459448 | p.A21P | 3 |
chr14:88442730-88442730 | p.E242K | 3 |
chr14:88459434-88459434 | p.G25G | 3 |
chr14:88459499-88459499 | p.W4R | 2 |
chr14:88450880-88450880 | p.? | 2 |
chr14:88401080-88401080 | p.R685H | 2 |
chr14:88454828-88454828 | p.R79G | 2 |
chr14:88401110-88401110 | p.Q675P | 2 |
chr14:88407888-88407888 | p.I562T | 2 |
chr14:88454857-88454857 | p.R69Q | 2 |
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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 | 4 |   | 1 | 5 | 2 |   | 3 |   | 1 |   |   | 5 | 4 |   |   | 1 | 5 | 5 |   | 10 |
# mutation | 4 |   | 1 | 6 | 2 |   | 3 |   | 1 |   |   | 4 | 4 |   |   | 1 | 6 | 6 |   | 10 |
nonsynonymous SNV | 2 |   |   | 5 |   |   | 1 |   |   |   |   | 4 | 2 |   |   |   | 3 | 5 |   | 7 |
synonymous SNV | 2 |   | 1 | 1 | 2 |   | 2 |   | 1 |   |   |   | 2 |   |   | 1 | 3 | 1 |   | 3 |
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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* 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 |
chr14:88450795 | p.V152V,GALC | 2 |
chr14:88401080 | p.R662H,GALC | 2 |
chr14:88434718 | p.G300R,GALC | 2 |
chr14:88442730 | p.R267H,GALC | 2 |
chr14:88431915 | p.E219K,GALC | 2 |
chr14:88411957 | p.E208G,GALC | 1 |
chr14:88454828 | p.L31L,GALC | 1 |
chr14:88431916 | p.F441L,GALC | 1 |
chr14:88411975 | p.L206L,GALC | 1 |
chr14:88459326 | p.G25G,GALC | 1 |
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* 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. |
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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 GALC |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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ALDH6A1,ARID4A,ATG2B,BTBD7,KIAA0825,CTSO,DICER1, ELF1,GALC,GOLGA5,NEK9,PJA2,RPS6KA5,SEL1L, SLC39A9,STAM2,TMEM87B,TRIP11,TTC8,ZC3H14,ZFYVE1 | ACAP2,CASC4,EXOC1,FAM8A1,FAR1,FCHO2,GABPA, GALC,GNA13,MIER1,PAPD4,PRKAA1,RASA1,SEPT10, SLC35A5,SPTLC1,TBC1D15,TM9SF3,TMEM30A,UBL3,VAMP4 |
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AP4S1,ACKR4___CX3CR1,CHIC1,CHURC1,FAM179B,FCF1,GALC, GOLGA5,LACTB2,LPCAT3,MBIP,NR1H4,PLBD1,PSEN1, SEC23A,SLC16A2,SPATA7,TINF2,TM9SF1,TMEM117,VIPAS39 | A1CF,ABCA5,CLCN5,CTH,GALC,GOLIM4,GUCY2C, CERS6,MOGAT2,PPARGC1A,RNF128,SIDT2,SLC30A4,SMPD3, SSTR1,TMEM181,TNFRSF10D,USP37,VIL1,ZNF664,ZNF711 |
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* 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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Pharmacological Information for GALC |
There's no related Drug. |
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Cross referenced IDs for GALC |
* 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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