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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HCCS |
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Phenotypic Information for HCCS(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: HCCS |
Familial Cancer Database: HCCS |
* 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 | |
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: HCCS |
MedGen: HCCS (Human Medical Genetics with Condition) | |
ClinVar: HCCS | |
Phenotype | MGI: HCCS (International Mouse Phenotyping Consortium) |
PhenomicDB: HCCS |
Mutations for HCCS |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HCCS 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 |
BF857908 | HCCS | 25 | 187 | X | 11130199 | 11133036 | IQSEC1 | 179 | 501 | 3 | 13020548 | 13020870 |
Other DBs for Structural Variants |
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Copy 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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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=15) | (# total SNVs=4) |
(# total SNVs=0) | (# 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 |
chr23:11139095-11139095 | p.R197Q | 2 |
chr23:11135392-11135392 | p.P86P | 1 |
chr23:11139773-11139773 | p.R217H | 1 |
chr23:11132993-11132993 | p.E47* | 1 |
chr23:11135417-11135417 | p.D95H | 1 |
chr23:11139860-11139860 | p.R246H | 1 |
chr23:11132998-11132998 | p.K48N | 1 |
chr23:11135463-11135463 | p.P110L | 1 |
chr23:11139874-11139874 | p.S251T | 1 |
chr23:11133033-11133033 | p.A60V | 1 |
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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 | 2 | 1 |   | 6 | 1 |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 2 | 2 | 1 | 1 |
# mutation | 2 | 1 |   | 6 | 1 |   | 1 |   | 1 |   |   | 2 |   |   |   |   | 2 | 2 | 1 | 1 |
nonsynonymous SNV | 2 |   |   | 4 | 1 |   | 1 |   | 1 |   |   | 1 |   |   |   |   | 1 | 1 | 1 | 1 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   |   |
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 |
chrX:11139773 | p.R217H,HCCS | 2 |
chrX:11136711 | p.K48N,HCCS | 1 |
chrX:11132998 | p.G232V,HCCS | 1 |
chrX:11136729 | p.A60V,HCCS | 1 |
chrX:11133033 | p.R246H,HCCS | 1 |
chrX:11139095 | p.C66C,HCCS | 1 |
chrX:11133052 | p.S251T,HCCS | 1 |
chrX:11139756 | p.P67T,HCCS | 1 |
chrX:11133053 | p.R265H,HCCS | 1 |
chrX:11139765 | p.R69R,HCCS | 1 |
Other DBs for Point Mutations |
Copy Number for HCCS 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 HCCS |
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 |
ARSD,B4GALNT1,CCT5,CDK4,DYRK2,EPR1,FANCB, FUCA2,GEMIN8,GJA10,HCCS,MARCH11,METTL7B,MOSPD2, OR9K2,PIGA,PIR,SYNGR2,TK1,TRIM55,USP36 | ACYP2,BTBD1,CAP2,CFL2,CISD1,COQ3,COX5A, CUTC,CYCS,EPM2A,FEZ2,FKBP3,GRSF1,GYG1, HCCS,KPNA3,MRPL15,MYL12A,NDUFB3,VDAC1,VDAC3 |
APOO,ATP6AP2,CXorf40A,ELK1,FTSJ1,HCCS,MCTS1, MSL3,PDHA1,PDZD11,PIGA,PRDX4,PRPS2,PSMD10, RP2,SCML1,SLC25A5,SMS,UBE2A,UXT,VBP1 | ABI1,ARPC5,ATP5B,BAK1,COX5A,CXorf40A,DBI, GHITM,HCCS,HN1,IMPA1,MAD2L1BP,MYL12A,OSTF1, PLEKHF2,TDRD7,TMSB4XP8,TPMT,UBE2A,UBE2D2,VAMP8 |
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 HCCS |
There's no related Drug. |
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Cross referenced IDs for HCCS |
* 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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