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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NADK |
Basic gene info. | Gene symbol | NADK |
Gene name | NAD kinase | |
Synonyms | dJ283E3.1 | |
Cytomap | UCSC genome browser: 1p36.33 | |
Genomic location | chr1 :1682670-1711508 | |
Type of gene | protein-coding | |
RefGenes | NM_001198993.1, NM_001198994.1,NM_001198995.1,NM_023018.4, | |
Ensembl id | ENSG00000008130 | |
Description | poly(P)/ATP NAD kinase | |
Modification date | 20141207 | |
dbXrefs | MIM : 611616 | |
HGNC : HGNC | ||
Ensembl : ENSG00000008130 | ||
HPRD : 16907 | ||
Vega : OTTHUMG00000000942 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NADK | |
BioGPS: 65220 | ||
Gene Expression Atlas: ENSG00000008130 | ||
The Human Protein Atlas: ENSG00000008130 | ||
Pathway | NCI Pathway Interaction Database: NADK | |
KEGG: NADK | ||
REACTOME: NADK | ||
ConsensusPathDB | ||
Pathway Commons: NADK | ||
Metabolism | MetaCyc: NADK | |
HUMANCyc: NADK | ||
Regulation | Ensembl's Regulation: ENSG00000008130 | |
miRBase: chr1 :1,682,670-1,711,508 | ||
TargetScan: NM_001198993 | ||
cisRED: ENSG00000008130 | ||
Context | iHOP: NADK | |
cancer metabolism search in PubMed: NADK | ||
UCL Cancer Institute: NADK | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for NADK(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: NADK |
Familial Cancer Database: NADK |
* 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 | |
KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: NADK |
MedGen: NADK (Human Medical Genetics with Condition) | |
ClinVar: NADK | |
Phenotype | MGI: NADK (International Mouse Phenotyping Consortium) |
PhenomicDB: NADK |
Mutations for NADK |
* 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 |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | NADK | chr1 | 1707983 | 1708003 | KANK4 | chr1 | 62781915 | 62781935 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NADK 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 |
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) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
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=33) | (# total SNVs=6) |
(# total SNVs=1) | (# total SNVs=2) |
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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 |
chr1:1685554-1685554 | p.T346M | 2 |
chr1:1686040-1686040 | p.N262K | 2 |
chr1:1688745-1688745 | p.I90F | 2 |
chr1:1684472-1684472 | p.P404P | 2 |
chr1:1684347-1684348 | p.E445_G446insE | 2 |
chr1:1686834-1686834 | p.Q223* | 2 |
chr1:1685737-1685737 | p.T310M | 2 |
chr1:1696764-1696764 | p.G28S | 2 |
chr1:1685520-1685520 | p.P357P | 1 |
chr1:1688633-1688633 | p.T127M | 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 | 2 | 1 |   | 8 |   |   | 1 |   |   | 1 |   | 4 | 1 | 1 |   |   | 5 | 10 | 1 | 8 |
# mutation | 2 | 1 |   | 8 |   |   | 1 |   |   | 1 |   | 4 | 1 | 1 |   |   | 5 | 10 | 1 | 9 |
nonsynonymous SNV | 2 | 1 |   | 6 |   |   |   |   |   | 1 |   | 3 | 1 | 1 |   |   | 3 | 5 | 1 | 8 |
synonymous SNV |   |   |   | 2 |   |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 | 5 |   | 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 |
chr1:1685737 | p.T314M,NADK | 2 |
chr1:1685554 | p.T278M,NADK | 2 |
chr1:1686902 | p.V332F,NADK | 1 |
chr1:1685086 | p.Q189R,NADK | 1 |
chr1:1696699 | p.D29N,NADK | 1 |
chr1:1685773 | p.F179I,NADK | 1 |
chr1:1687735 | p.Y21Y,NADK | 1 |
chr1:1685498 | p.G300G,NADK | 1 |
chr1:1696731 | p.L174R,NADK | 1 |
chr1:1685986 | p.K12N,NADK | 1 |
Other DBs for Point Mutations |
Copy Number for NADK 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 NADK |
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 |
ACAP3,ATAD3A,CDK11A,CDK11B,CPSF3L,DNAJC11,DVL1, CPTP,GNB1,LOC148413,LOC401010,LRRC47,MIB2,NADK, NOC2L,PANK4,PLEKHM2,SDF4,SSU72,UBE2J2,WRAP73 | AIFM2,AP1M1,C1QTNF1,COL4A1,COL4A2,EHD2,FURIN, ITPK1,CTIF,LIPE,LRP1,MYO1C,NADK,PALM, PHLDB1,ST6GALNAC6,SURF4,TFE3,TNIP1,TPD52L2,TUSC5 | ||||
ARHGEF16,C1orf159,CDK11B,CPSF3L,CPT2,DHDDS,DVL1, CPTP,GNB1,CEP104,LRRC47,MFN2,MKNK1,NADK, PANK4,RER1,SDF4,SSU72,TNFRSF14,TPRG1L,UBE2J2 | ACSS2,ADAP1,AP1M2,APEX2,ARHGEF16,CAPN5,CLDN7, CRB3,DOK4,ELOVL1,LGALS4,LLGL2,NADK,SHD, SIRT7,SLC44A4,STXBP2,TJP3,TMEM8A,TPRN,TRPC4AP |
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 NADK |
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 |
DB00160 | NAD kinase | approved; nutraceutical | L-Alanine | ||
DB00130 | NAD kinase | approved; nutraceutical; investigational | L-Glutamine | ||
DB00150 | NAD kinase | approved; nutraceutical | L-Tryptophan |
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Cross referenced IDs for NADK |
* 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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