|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for F9 |
Top |
Phenotypic Information for F9(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: F9 |
Familial Cancer Database: F9 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||
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_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: F9 |
MedGen: F9 (Human Medical Genetics with Condition) | |
ClinVar: F9 | |
Phenotype | MGI: F9 (International Mouse Phenotyping Consortium) |
PhenomicDB: F9 |
Mutations for F9 |
* 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 F9 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 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=95) | (# total SNVs=25) |
(# total SNVs=0) | (# total SNVs=0) |
Top |
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 |
chr23:138643994-138643994 | p.R384* | 5 |
chr23:138633258-138633258 | p.T186T | 4 |
chr23:138623283-138623283 | p.K109R | 3 |
chr23:138630596-138630596 | p.S156T | 3 |
chr23:138644029-138644029 | p.F395L | 3 |
chr23:138642945-138642945 | p.V257I | 2 |
chr23:138633376-138633376 | p.R226R | 2 |
chr23:138619310-138619310 | p.V77A | 2 |
chr23:138643870-138643870 | p.T342T | 2 |
chr23:138644105-138644105 | p.G421R | 2 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 |   | 1 |   | 20 | 3 |   | 5 |   | 2 |   |   | 12 | 7 | 1 |   |   | 8 | 5 |   | 9 |
# mutation |   | 1 |   | 16 | 3 |   | 5 |   | 2 |   |   | 15 | 7 | 1 |   |   | 9 | 5 |   | 8 |
nonsynonymous SNV |   | 1 |   | 12 | 2 |   | 5 |   | 2 |   |   | 12 | 5 | 1 |   |   | 7 | 4 |   | 7 |
synonymous SNV |   |   |   | 4 | 1 |   |   |   |   |   |   | 3 | 2 |   |   |   | 2 | 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]) |
Top |
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:138623283 | p.K109R | 3 |
chrX:138643737 | p.S156P | 2 |
chrX:138643813 | p.G280S | 2 |
chrX:138644029 | p.F395L | 2 |
chrX:138633258 | p.R298Q | 2 |
chrX:138643014 | p.E323E | 2 |
chrX:138630596 | p.T186T | 2 |
chrX:138619203 | p.I256I | 1 |
chrX:138633338 | p.L372I | 1 |
chrX:138623303 | p.F55L | 1 |
Other DBs for Point Mutations |
Copy Number for F9 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] |
Top |
Gene Expression for F9 |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
APCS,APOA2,APOA4,APOC3,ARG1,C8A,C9, CREB3L3,CRP,F2,F9,FABP1,FGF23,HP, ITIH1,MT1B,PLG,SERPINA7,SERPINC1,SLC17A2,TM4SF5 | ACSL3,ADAM2,ALOX15B,APOD,DHRS2,ENPP3,F9, GUSB,HAAO,HIST1H2BG,HIST1H4H,NANOG,NAT2,PPEF1, RNASE12,SERHL2,SERHL,SPINK8,SULT1C3,UGT2B10,UGT2B11 | ||||
AHSG,ALB,APCS,APOA5,APOC3,C8A,C8B, C9,CFHR2,CFHR5,CRP,CYP4A11,F9,FGA, FGG,GDF2,HPX,ITIH1,MBL2,SERPINC1,SPP2 | ALB,APCS,APOA2,C3P1,C8A,CFHR2,CFHR5, CYP4A22,DNAJB8,F13B,F9,FGG,HRG,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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for F9 |
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 |
DB00170 | coagulation factor IX | approved; nutraceutical | Menadione | ||
DB03847 | coagulation factor IX | experimental | Gamma-Carboxy-Glutamic Acid | ||
DB00682 | coagulation factor IX | approved | Warfarin | ||
DB00668 | coagulation factor IX | approved | Epinephrine |
Top |
Cross referenced IDs for F9 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |