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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SLC25A2 |
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Phenotypic Information for SLC25A2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: SLC25A2 |
Familial Cancer Database: SLC25A2 |
* 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_AMINO_ACIDS_AND_DERIVATIVES |
Mutations for SLC25A2 |
* 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 SLC25A2 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 |
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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=48) | (# total SNVs=11) |
(# total SNVs=2) | (# total SNVs=3) |
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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 |
chr5:140683389-140683389 | p.A15V | 4 |
chr5:140683302-140683303 | p.Y44fs*1 | 3 |
chr5:140683342-140683342 | p.D31N | 3 |
chr5:140683204-140683204 | p.E77K | 2 |
chr5:140682884-140682884 | p.G183G | 2 |
chr5:140682677-140682677 | p.T252T | 2 |
chr5:140683343-140683343 | p.F30F | 2 |
chr5:140683268-140683268 | p.Y55Y | 2 |
chr5:140682711-140682711 | p.S241F | 2 |
chr5:140683317-140683317 | p.T39M | 2 |
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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 | 3 | 2 |   | 8 | 1 |   | 1 |   | 2 | 1 |   | 6 | 1 | 1 |   | 1 | 7 | 9 |   | 8 |
# mutation | 3 | 2 |   | 8 | 1 |   | 1 |   | 2 | 1 |   | 7 | 2 | 1 |   | 1 | 9 | 10 |   | 11 |
nonsynonymous SNV | 2 | 2 |   | 6 |   |   |   |   | 1 |   |   | 6 | 2 | 1 |   | 1 | 6 | 9 |   | 10 |
synonymous SNV | 1 |   |   | 2 | 1 |   | 1 |   | 1 | 1 |   | 1 |   |   |   |   | 3 | 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 |
chr5:140683343 | p.A15V | 3 |
chr5:140683389 | p.F30F | 3 |
chr5:140683317 | p.T39M | 2 |
chr5:140683342 | p.D31N | 2 |
chr5:140682837 | p.K292N | 1 |
chr5:140683420 | p.L212S | 1 |
chr5:140682557 | p.R93S | 1 |
chr5:140683154 | p.P29P | 1 |
chr5:140682702 | p.R291R | 1 |
chr5:140683297 | p.G208G | 1 |
Other DBs for Point Mutations |
Copy Number for SLC25A2 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 SLC25A2 |
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 |
ANKS4B,BAZ1A,LINC01559,PCNXL4,CHD8,CTAGE5,DTWD2, FANCM,LINC01184,GRIN2B,KIAA0391,MIPOL1,PAX9,POLE2, RALGAPA1,RDH11,REG4,SLC25A21,TRAPPC6B,TTLL5,ZNF253 | ARMC1,NADK2,DCTN4,FAM120C,FAM47E,FBXO9,FRS2, MBTPS2,NRIP1,NT5DC1,PLA2G12A,RAB18,RAD21,TRMT10A, RHOT1,RNF170,SENP2,ARHGEF26,SLC25A21,SRPK2,UBE2W | ||||
ANXA13,CA8,CIB4,CIT,CKAP4,FAM174B,GALNT8, KIF19,MAK,MIPOL1,OPRD1,PCSK1,RAP1GAP,RHBDL3, SLAIN1,SLC25A21,SLC26A9,SPINK4,SSTR1,STXBP1,UGT2B4 | ARL4D,C16orf45,CAB39L,CES1,CFL2,FBXO17,MORN5, MSRB3,MXRA7,NT5DC3,NUDT10,NUDT11,PDLIM3,PDLIM4, PTPLA,RASL12,RASSF8,SLC25A21,SOX15,ST3GAL3,TSPAN2 |
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 SLC25A2 |
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 |
DB00129 | solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 2 | approved; nutraceutical | L-Ornithine |
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Cross referenced IDs for SLC25A2 |
* 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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