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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for XRN2 |
Basic gene info. | Gene symbol | XRN2 |
Gene name | 5'-3' exoribonuclease 2 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 20p11.2-p11.1 | |
Genomic location | chr20 :21283941-21370463 | |
Type of gene | protein-coding | |
RefGenes | NM_012255.3, | |
Ensembl id | ENSG00000088930 | |
Description | DHP proteinDhm1-like protein (mouse homolog) | |
Modification date | 20141207 | |
dbXrefs | MIM : 608851 | |
HGNC : HGNC | ||
Ensembl : ENSG00000088930 | ||
HPRD : 10309 | ||
Vega : OTTHUMG00000032025 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_XRN2 | |
BioGPS: 22803 | ||
Gene Expression Atlas: ENSG00000088930 | ||
The Human Protein Atlas: ENSG00000088930 | ||
Pathway | NCI Pathway Interaction Database: XRN2 | |
KEGG: XRN2 | ||
REACTOME: XRN2 | ||
ConsensusPathDB | ||
Pathway Commons: XRN2 | ||
Metabolism | MetaCyc: XRN2 | |
HUMANCyc: XRN2 | ||
Regulation | Ensembl's Regulation: ENSG00000088930 | |
miRBase: chr20 :21,283,941-21,370,463 | ||
TargetScan: NM_012255 | ||
cisRED: ENSG00000088930 | ||
Context | iHOP: XRN2 | |
cancer metabolism search in PubMed: XRN2 | ||
UCL Cancer Institute: XRN2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for XRN2(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: XRN2 |
Familial Cancer Database: XRN2 |
* 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/ |
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REACTOME_METABOLISM_OF_PROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: XRN2 |
MedGen: XRN2 (Human Medical Genetics with Condition) | |
ClinVar: XRN2 | |
Phenotype | MGI: XRN2 (International Mouse Phenotyping Consortium) |
PhenomicDB: XRN2 |
Mutations for XRN2 |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | XRN2 | chr20 | 21296317 | 21296337 | XRN2 | chr20 | 21299139 | 21299159 |
pancreas | XRN2 | chr20 | 21301630 | 21301650 | XRN2 | chr20 | 21292803 | 21292823 |
pancreas | XRN2 | chr20 | 21308520 | 21308540 | XRN2 | chr20 | 21309134 | 21309154 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows XRN2 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 |
BG004570 | XRN2 | 8 | 163 | 20 | 21311260 | 21312271 | EEF1D | 159 | 283 | 8 | 144674315 | 144674439 | |
BP273629 | FAM172A | 1 | 408 | 5 | 93018889 | 93019294 | XRN2 | 409 | 573 | 20 | 21309207 | 21311181 | |
BQ683058 | WASF3 | 12 | 227 | 13 | 27261627 | 27261841 | XRN2 | 227 | 963 | 20 | 21346298 | 21370268 | |
BF356570 | TARDBP | 16 | 95 | 1 | 11082473 | 11082553 | XRN2 | 91 | 387 | 20 | 21314397 | 21315172 | |
AI917076 | GPRC5A | 2 | 305 | 12 | 13066290 | 13066593 | XRN2 | 301 | 474 | 20 | 21322504 | 21322677 | |
BF947784 | XRN2 | 39 | 443 | 20 | 21308509 | 21308913 | TCERG1 | 440 | 633 | 5 | 145843511 | 145843704 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=70) | (# total SNVs=30) |
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(# total SNVs=1) | (# total SNVs=0) |
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* 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 |
chr20:21312958-21312958 | p.P246P | 5 |
chr20:21306923-21306923 | p.E28K | 3 |
chr20:21312985-21312985 | p.F255F | 2 |
chr20:21309203-21309203 | p.R108C | 2 |
chr20:21328891-21328891 | p.P591P | 2 |
chr20:21328996-21328996 | p.Q597Q | 2 |
chr20:21309225-21309225 | p.R115H | 2 |
chr20:21329006-21329006 | p.V601I | 2 |
chr20:21327166-21327166 | p.W548L | 2 |
chr20:21327175-21327175 | p.R551I | 2 |
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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 | 4 | 3 | 2 | 8 | 2 |   | 5 |   | 7 |   |   | 6 | 3 | 1 |   |   | 6 | 11 | 1 | 18 |
# mutation | 4 | 3 | 2 | 8 | 2 |   | 5 |   | 7 |   |   | 6 | 3 | 1 |   |   | 7 | 14 | 1 | 29 |
nonsynonymous SNV | 3 | 3 | 2 | 6 | 1 |   | 4 |   | 6 |   |   | 6 | 2 | 1 |   |   | 4 | 12 | 1 | 18 |
synonymous SNV | 1 |   |   | 2 | 1 |   | 1 |   | 1 |   |   |   | 1 |   |   |   | 3 | 2 |   | 11 |
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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* 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 |
chr20:21312958 | p.P246P | 3 |
chr20:21327175 | p.R551K | 3 |
chr20:21312985 | p.P591P | 2 |
chr20:21309203 | p.F255L | 2 |
chr20:21328891 | p.R108C | 2 |
chr20:21336744 | p.H567N | 1 |
chr20:21306950 | p.G687E | 1 |
chr20:21314629 | p.Q905H | 1 |
chr20:21346285 | p.S39N | 1 |
chr20:21309266 | p.A200V | 1 |
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* 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. |
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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 XRN2 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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APC,ATRN,SLX4IP,CRNKL1,CSNK2A1,CSNK2A3,DHX9, DPP8,ESF1,GTF2H3,ITCH,PPP4R2,RBBP9,RBM12, SEC23B,SRFBP1,TGFBRAP1,TSTD2,TTC37,XRN2,ZNF81 | ACTL6A,ADNP,CASK,DCLRE1A,DHX15,DHX9,LRBA, OCLN,PRPF40A,PTPRK,RBBP4,SAMD12,SMARCA5,SNX30, TEX9,NDC1,TOP2B,XRCC5,XRN2,ZNF268,ZNF28 |
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ANKEF1,DZANK1,APMAP,MGME1,CRNKL1,CSNK2A1,CSNK2A3, CSRP2BP,ESF1,GINS1,NAA20,NANP,POLR3F,RALGAPA2, RBBP9,SEC23B,SNRPB2,SNX5,TASP1,TRMT6,XRN2 | DPH6,C12orf45,CACYBP,CCT4,COPS4,DAP3,DDX47, DNAJB9,EIF3M,HSPA13,MRPL1,MRPL39,MRPS28,RB1, RGS18,SSR3,STAM,STRAP,TSN,WDR12,XRN2 |
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* 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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Pharmacological Information for XRN2 |
There's no related Drug. |
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Cross referenced IDs for XRN2 |
* 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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