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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPS21 |
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Phenotypic Information for RPS21(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPS21 |
Familial Cancer Database: RPS21 |
* 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 | |
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: RPS21 |
MedGen: RPS21 (Human Medical Genetics with Condition) | |
ClinVar: RPS21 | |
Phenotype | MGI: RPS21 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPS21 |
Mutations for RPS21 |
* 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 RPS21 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 |
AV751221 | RPS21 | 17 | 276 | 20 | 60962666 | 60963578 | XIST | 275 | 412 | X | 73069526 | 73069668 | |
BC036946 | ANKRD52 | 12 | 3464 | 12 | 56635489 | 56646649 | RPS21 | 3456 | 3777 | 20 | 60962379 | 60963576 | |
BP251502 | RPS21 | 1 | 399 | 20 | 60962115 | 60963573 | LRBA | 382 | 403 | 4 | 151616176 | 151616197 | |
AI275065 | RPS21 | 3 | 97 | 20 | 60963482 | 60963576 | PIAS3 | 93 | 345 | 1 | 145578462 | 145578714 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 |   |   |   |   | 1 |   |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
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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=4) | (# 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 |
chr20:60963410-60963410 | p.I78F | 1 |
chr20:60963412-60963412 | p.I78I | 1 |
chr20:60963413-60963413 | p.V79F | 1 |
chr20:60962424-60962424 | p.D10D | 1 |
chr20:60962678-60962678 | p.N21S | 1 |
chr20:60962688-60962688 | p.I24I | 1 |
chr20:60962906-60962906 | p.K41T | 1 |
chr20:60963367-60963367 | p.G63G | 1 |
chr20:60963374-60963374 | p.D66H | 1 |
chr20:60963378-60963395 | p.D67_L72delDSILRL | 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 |   | 1 |   |   | 1 |   | 1 |   |   |   |   |   | 1 |   |   |   |   |   |   | 2 |
# mutation |   | 1 |   |   | 1 |   | 1 |   |   |   |   |   | 1 |   |   |   |   |   |   | 2 |
nonsynonymous SNV |   |   |   |   | 1 |   | 1 |   |   |   |   |   | 1 |   |   |   |   |   |   | 1 |
synonymous SNV |   | 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 |
chr20:60962906 | p.K41T | 1 |
chr20:60963374 | p.D66H | 1 |
chr20:60963388 | p.L70L | 1 |
chr20:60963404 | p.D76N | 1 |
chr20:60963410 | p.I78F | 1 |
chr20:60963412 | p.I78I | 1 |
Other DBs for Point Mutations |
Copy Number for RPS21 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 RPS21 |
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 |
ADRM1,UQCC3,LSM7,MRPS26,NDUFA11,NDUFB7,POLR2I, RPL13,RPL18A,RPL27A,RPL28,RPL35,RPL36,RPL37A, RPLP2,RPS10,RPS19,RPS21,RPS9,SNRPD2,UBA52 | RPL10,RPL13,RPL13A,RPL14,RPL18,RPL18A,RPL19, RPL28,RPL29,RPL32,RPL35,RPL36,RPL37,RPS10, RPS14,RPS16,RPS19,RPS21,RPS2,RPS8,RPSAP58 |
AHCY,ATP5E,ATP5J2,C11orf31,C8orf59,CHCHD2,COMMD7, EEF1B2,MYEOV2,PDRG1,PFDN4,PSMA7,ROMO1,RPS10, RPS14,RPS15A,RPS18,RPS21,RPS3,RPS7,UBL5 | ABT1,EEF1B2,MRPL54,PHB2,RPL18A,RPL32,RPL35, RPLP1,RPS10,RPS11,RPS13,RPS14,RPS18,RPS21, RPS3,RPS3A,RPS5,RPS6,RPS8,SNRPD2,UXT |
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 RPS21 |
There's no related Drug. |
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Cross referenced IDs for RPS21 |
* 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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