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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ISYNA1 |
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Phenotypic Information for ISYNA1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ISYNA1 |
Familial Cancer Database: ISYNA1 |
* 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_INOSITOL_PHOSPHATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: ISYNA1 |
MedGen: ISYNA1 (Human Medical Genetics with Condition) | |
ClinVar: ISYNA1 | |
Phenotype | MGI: ISYNA1 (International Mouse Phenotyping Consortium) |
PhenomicDB: ISYNA1 |
Mutations for ISYNA1 |
* 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 | ISYNA1 | chr19 | 18546210 | 18546230 | WDR87 | chr19 | 38390134 | 38390154 |
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 ISYNA1 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 |
AA368753 | ISYNA1 | 1 | 160 | 19 | 18547190 | 18547553 | CSH2 | 158 | 317 | 17 | 61950608 | 61951036 | |
AW962615 | ISYNA1 | 1 | 159 | 19 | 18547190 | 18547552 | CSH1 | 157 | 509 | 17 | 61973091 | 61973933 | |
BF945926 | ISYNA1 | 8 | 153 | 19 | 18546212 | 18546438 | NCDN | 150 | 229 | 1 | 36032076 | 36032155 |
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=17) | (# total SNVs=15) |
(# total SNVs=1) | (# 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 |
chr19:18546678-18546678 | p.L343L | 3 |
chr19:18547022-18547022 | p.A265A | 2 |
chr19:18547246-18547246 | p.A218V | 2 |
chr19:18546115-18546115 | p.A478V | 2 |
chr19:18546841-18546841 | p.? | 1 |
chr19:18547253-18547253 | p.S216T | 1 |
chr19:18546132-18546132 | p.G472G | 1 |
chr19:18547813-18547813 | p.M129L | 1 |
chr19:18546855-18546855 | p.G321D | 1 |
chr19:18547265-18547265 | p.R212* | 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 |   |   | 6 |   |   | 4 |   |   |   |   | 3 |   | 1 | 1 |   | 3 | 4 |   | 6 |
# mutation | 2 |   |   | 6 |   |   | 4 |   |   |   |   | 3 |   | 1 | 1 |   | 3 | 5 |   | 6 |
nonsynonymous SNV | 1 |   |   | 4 |   |   | 2 |   |   |   |   | 2 |   | 1 |   |   |   | 2 |   | 2 |
synonymous SNV | 1 |   |   | 2 |   |   | 2 |   |   |   |   | 1 |   |   | 1 |   | 3 | 3 |   | 4 |
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 |
chr19:18546942 | p.T244T,ISYNA1 | 1 |
chr19:18547813 | p.S16S,ISYNA1 | 1 |
chr19:18546161 | p.V202M,ISYNA1 | 1 |
chr19:18547041 | p.I14I,ISYNA1 | 1 |
chr19:18547828 | p.I201I,ISYNA1 | 1 |
chr19:18546466 | p.M1L,ISYNA1 | 1 |
chr19:18547215 | p.I201V,ISYNA1 | 1 |
chr19:18548556 | p.S70G,ISYNA1 | 1 |
chr19:18546587 | p.T198N,ISYNA1 | 1 |
chr19:18547239 | p.S45S | 1 |
Other DBs for Point Mutations |
Copy Number for ISYNA1 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 ISYNA1 |
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 |
ATG4D,C16orf13,C19orf53,CCDC124,COPE,ECI1,DDX49, E4F1,FKBP8,GPX4,ISYNA1,LSM4,NME4,NR2F6, QTRT1,RFXANK,RHPN1,SUGP1,SSBP4,UBA52,WDR83 | CEP131,SYNE4,C2orf81,CACFD1,DAK,FBXW9,ISYNA1, ITGA3,LOC92659,LPAR2,LSR,MED16,NAT14,P4HTM, PAFAH1B3,PKP3,PRRG2,SYTL1,TRIM28,WDR34,XYLT2 | ||||
C1QTNF8,C4orf51,CA7,CCL26,CRYBA4,GJA3,HELT, ISYNA1,KRT3,LAG3,NXPH4,TINCR,PPM1K,PRAMEF6, PRB1,PRB2,PRR4,RXFP2,TRIM69,PRSS58,WDR11 | ACTBL2,CCL18,CHIT1,DEFB4A,DUOX1,FAM74A1,FAM92A1P2, FLJ25758,HS3ST2,HTRA4,ISYNA1,KRT6B,KRTAP13-1,LY6D, MMP10,PRAMEF12,RBMXL3,SLC13A4,TM4SF19,TRIM42,XKRY2 |
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 ISYNA1 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB01907 | inositol-3-phosphate synthase 1 | experimental | Nicotinamide-Adenine-Dinucleotide |
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Cross referenced IDs for ISYNA1 |
* 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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