TissGeneSummary for NEDD1 |
Gene summary |
Basic gene information | Gene symbol | NEDD1 |
Gene name | neural precursor cell expressed, developmentally down-regulated 1 | |
Synonyms | GCP-WD|TUBGCP7 | |
Cytomap | UCSC genome browser: 12q23.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001135175.1, NM_001135176.1,NM_001135177.1,NM_152905.3, | |
Description | NEDD-1neural precursor cell expressed developmentally down-regulated protein 1protein NEDD1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 600372 | |
HGNC : HGNC | ||
Ensembl : ENSG00000139350 | ||
HPRD : 02655 | ||
Vega : OTTHUMG00000170604 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NEDD1 | |
BioGPS: 121441 | ||
Pathway | NCI Pathway Interaction Database: NEDD1 | |
KEGG: NEDD1 | ||
REACTOME: NEDD1 | ||
Pathway Commons: NEDD1 | ||
Context | iHOP: NEDD1 | |
ligand binding site mutation search in PubMed: NEDD1 | ||
UCL Cancer Institute: NEDD1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | BladderTestis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | BLCATGCT | |
Reference showing the relevant tissue of NEDD1 | ||
Description by TissGene annotations | Have significant anti-correlated miRNA TissgsLTS |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
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TissGeneExp for NEDD1 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
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TissGene-miRNA for NEDD1 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
ACC | hsa-miR-200b-3p | MIMAT0000318 | 0.011 | -0.32 | 78 |
ACC | hsa-miR-200b-3p | MIMAT0000318 | 0.011 | -0.32 | 78 |
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TissGeneMut for NEDD1 |
TissGeneSNV for NEDD1 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.R230I | READ | 2 |
p.S568L | BLCA | 1 |
p.N162K | LUAD | 1 |
p.L251V | HNSC | 1 |
p.H623Y | HNSC | 1 |
p.L353V | BLCA | 1 |
p.Q393H | LUAD | 1 |
p.S475Y | LIHC | 1 |
p.F410L | SKCM | 1 |
p.S108L | SKCM | 1 |
p.S21C | HNSC | 1 |
p.A351P | LIHC | 1 |
p.T606M | UCEC | 1 |
p.S555F | ACC | 1 |
p.S338F | SKCM | 1 |
p.A582V | COAD | 1 |
p.V204L | OV | 1 |
p.R166Q | COAD | 1 |
p.H290Y | LUAD | 1 |
p.S548F | ACC | 1 |
p.G137V | SKCM | 1 |
p.S309G | PRAD | 1 |
p.A214S | UCEC | 1 |
p.S564Y | UCEC | 1 |
p.R276Q | UCEC | 1 |
p.R597S | UCEC | 1 |
p.E628D | HNSC | 1 |
p.S510T | COAD | 1 |
p.D573N | READ | 1 |
p.E386K | SKCM | 1 |
p.L99F | LUSC | 1 |
p.G11R | COAD | 1 |
p.Y170H | HNSC | 1 |
p.S566L | SKCM | 1 |
p.Y234N | MESO | 1 |
p.D33H | KIRC | 1 |
p.R662I | STAD | 1 |
p.H146N | OV | 1 |
p.S586F | SKCM | 1 |
p.R590C | SKCM | 1 |
p.G339R | HNSC | 1 |
p.P197S | SKCM | 1 |
p.M631I | UCEC | 1 |
p.S637* | BLCA | 1 |
p.N613I | STAD | 1 |
p.D228H | LUAD | 1 |
p.R657* | UCEC | 1 |
p.D26H | KIRC | 1 |
p.G333E | LUAD | 1 |
p.H608R | ACC | 1 |
p.P412T | LUAD | 1 |
p.N193S | LUAD | 1 |
p.A52T | STAD | 1 |
p.V187A | LUAD | 1 |
p.T380R | COAD | 1 |
p.S468Y | LIHC | 1 |
p.A508T | COAD | 1 |
p.E492* | HNSC | 1 |
p.A346V | HNSC | 1 |
p.P197L | SKCM | 1 |
p.R655I | STAD | 1 |
p.N620I | STAD | 1 |
p.D400N | BLCA | 1 |
p.A6T | PAAD | 1 |
p.S557F | HNSC | 1 |
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TissGeneCNV for NEDD1 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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TissGeneFusions for NEDD1 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
Chimerdb3.0 | ChiTaRs | NA | BF332108 | CCDC90A-NEDD1 | chr6:13789346 | chr12:97342426 | |
Chimerdb3.0 | FusionScan | SARC | TCGA-DX-A3M1-01A | NEDD1-TMTC2 | Out-of-Frame | chr12:97331171 | chr12:83358802 |
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TissGeneNet for NEDD1 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
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TissGeneProg for NEDD1 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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TissGeneClin for NEDD1 |
TissGeneDrug for NEDD1 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for NEDD1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0024623 | Malignant neoplasm of stomach | 1 | BeFree |
umls:C0027627 | Neoplasm Metastasis | 1 | BeFree |
umls:C0699791 | Stomach Carcinoma | 1 | BeFree |