|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC16A4 |
Top |
Phenotypic Information for SLC16A4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SLC16A4 |
Familial Cancer Database: SLC16A4 |
* 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 | |
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
Mutations for SLC16A4 |
* 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 SLC16A4 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=27) | (# total SNVs=12) |
(# total SNVs=3) | (# total SNVs=4) |
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 |
chr1:110921584-110921584 | p.S307S | 4 |
chr1:110924344-110924344 | p.T98T | 3 |
chr1:110925495-110925496 | p.W61fs*22 | 2 |
chr1:110925496-110925497 | p.W61fs*22 | 2 |
chr1:110921715-110921715 | p.N264H | 2 |
chr1:110921782-110921782 | p.T241T | 2 |
chr1:110921490-110921490 | p.L339F | 1 |
chr1:110921820-110921820 | p.C229S | 1 |
chr1:110906422-110906422 | p.P477L | 1 |
chr1:110923731-110923732 | p.A133fs*40 | 1 |
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 |   | 2 |   | 11 |   |   | 1 |   | 3 |   |   | 1 | 2 | 3 |   | 1 | 2 | 7 |   | 2 |
# mutation |   | 2 |   | 8 |   |   | 1 |   | 3 |   |   | 1 | 2 | 3 |   | 1 | 2 | 7 |   | 2 |
nonsynonymous SNV |   | 2 |   | 6 |   |   | 1 |   | 1 |   |   | 1 | 2 | 2 |   | 1 | 2 | 2 |   | 2 |
synonymous SNV |   |   |   | 2 |   |   |   |   | 2 |   |   |   |   | 1 |   |   |   | 5 |   |   |
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 |
chr1:110921584 | p.S197S,SLC16A4 | 4 |
chr1:110921593 | p.L282I,SLC16A4 | 1 |
chr1:110923659 | p.A73G,SLC16A4 | 1 |
chr1:110906469 | p.L47L,SLC16A4 | 1 |
chr1:110921598 | p.I242M,SLC16A4 | 1 |
chr1:110923660 | p.L47P,SLC16A4 | 1 |
chr1:110919607 | p.S240S,SLC16A4 | 1 |
chr1:110921737 | p.Y29N,SLC16A4 | 1 |
chr1:110923715 | p.G60S,SLC16A4 | 1 |
chr1:110919614 | p.S197C,SLC16A4 | 1 |
Other DBs for Point Mutations |
Copy Number for SLC16A4 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 SLC16A4 |
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 |
ALPK1,KIAA0825,CCPG1,DIXDC1,FNDC3A,HFE,HNMT, MEIS3P1,MR1,PDE11A,PJA2,PLSCR4,POLK,PRDM5, RBM43,SH3D19,SLC16A4,SLC24A1,TBC1D19,TLR3,TRIM6 | ABI2,AFAP1L2,ATL1,B3GALNT1,RHNO1,VWA9,CDS1, CMTM6,GNB5,GRAMD1C,LZTFL1,NEBL,PARD6G,PLS1, PRNP,SERPINB5,SLC16A4,TMEM231,TRAPPC2,TSPYL4,TTC8 | ||||
ALDH3B1,LINC00520,C1orf94,CAPN11,CCNG2,DAO,DHRS9, EMP1,FAM132A,IDS,FAM214B,MYPN,PIP4K2C,RRAS, SLC16A4,TANK,TSPAN31,UGT1A4,UGT1A5,VSIG1,YPEL5 | ANGPTL4,ARHGDIG,CDR2L,CYBRD1,DFNA5,DSG3,KIFC3, LRAT,PHYHIPL,PMP22,RHOBTB2,SEC14L2,SFRP5,SFXN3, SLC16A4,SUSD2,TEKT3,TIAM2,TM4SF4,TMEM25,TNFSF15 |
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 SLC16A4 |
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 |
DB00119 | solute carrier family 16, member 4 (monocarboxylic acid transporter 5) | approved; nutraceutical | Pyruvic acid |
Top |
Cross referenced IDs for SLC16A4 |
* 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 @ |