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Gene: NME2 |
Gene summary for NME2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NME2 | Gene ID | 4831 |
Gene name | NME/NM23 nucleoside diphosphate kinase 2 | |
Gene Alias | NDKB | |
Cytomap | 17q21.33 | |
Gene Type | protein-coding | GO ID | GO:0001678 | UniProtAcc | P22392 |
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Malignant transformation analysis |
Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
Malignant transformation involving gene list. |
Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
4831 | NME2 | HSIL_HPV_1 | Human | Cervix | HSIL_HPV | 2.01e-04 | 2.87e-01 | 0.0116 |
4831 | NME2 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 2.80e-03 | 2.49e-01 | 0.0208 |
4831 | NME2 | sample1 | Human | Cervix | CC | 2.21e-49 | 1.33e+00 | 0.0959 |
4831 | NME2 | sample3 | Human | Cervix | CC | 5.90e-83 | 1.17e+00 | 0.1387 |
4831 | NME2 | H2 | Human | Cervix | HSIL_HPV | 5.92e-25 | 7.14e-01 | 0.0632 |
4831 | NME2 | L1 | Human | Cervix | CC | 7.66e-39 | 1.17e+00 | 0.0802 |
4831 | NME2 | T1 | Human | Cervix | CC | 2.46e-52 | 1.07e+00 | 0.0918 |
4831 | NME2 | T2 | Human | Cervix | CC | 3.28e-32 | 1.16e+00 | 0.0709 |
4831 | NME2 | T3 | Human | Cervix | CC | 1.21e-80 | 1.16e+00 | 0.1389 |
4831 | NME2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.74e-102 | 1.64e+00 | 0.0155 |
4831 | NME2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.21e-60 | 1.77e+00 | -0.1808 |
4831 | NME2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 5.56e-36 | 1.64e+00 | 0.0216 |
4831 | NME2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.14e-76 | 2.04e+00 | -0.0811 |
4831 | NME2 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.01e-46 | 1.06e+00 | -0.1088 |
4831 | NME2 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.61e-90 | 1.70e+00 | -0.1954 |
4831 | NME2 | HTA11_411_2000001011 | Human | Colorectum | SER | 6.46e-27 | 1.92e+00 | -0.2602 |
4831 | NME2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.45e-19 | 1.66e+00 | -0.2196 |
4831 | NME2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.82e-39 | 1.45e+00 | -0.1207 |
4831 | NME2 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.22e-53 | 1.83e+00 | -0.1526 |
4831 | NME2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.97e-106 | 1.96e+00 | -0.1464 |
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Transcriptomic changes along malignancy continuum. |
∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
Figure of enriched GO biological processes. |
Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | |
Colorectum | SER | |
Colorectum | MSS | |
Colorectum | MSI-H | |
Colorectum | FAP |
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004259310 | Endometrium | AEH | glucose homeostasis | 55/2100 | 258/18723 | 1.87e-06 | 5.74e-05 | 55 |
GO:00713269 | Endometrium | AEH | cellular response to monosaccharide stimulus | 38/2100 | 154/18723 | 1.96e-06 | 5.93e-05 | 38 |
GO:003350010 | Endometrium | AEH | carbohydrate homeostasis | 55/2100 | 259/18723 | 2.12e-06 | 6.31e-05 | 55 |
GO:00506788 | Endometrium | AEH | regulation of epithelial cell proliferation | 73/2100 | 381/18723 | 3.04e-06 | 8.44e-05 | 73 |
GO:003459916 | Endometrium | AEH | cellular response to oxidative stress | 58/2100 | 288/18723 | 6.49e-06 | 1.58e-04 | 58 |
GO:000915016 | Endometrium | AEH | purine ribonucleotide metabolic process | 68/2100 | 368/18723 | 2.26e-05 | 4.35e-04 | 68 |
GO:000913210 | Endometrium | AEH | nucleoside diphosphate metabolic process | 30/2100 | 124/18723 | 3.39e-05 | 6.05e-04 | 30 |
GO:004693910 | Endometrium | AEH | nucleotide phosphorylation | 26/2100 | 101/18723 | 3.57e-05 | 6.26e-04 | 26 |
GO:00506795 | Endometrium | AEH | positive regulation of epithelial cell proliferation | 43/2100 | 207/18723 | 4.55e-05 | 7.61e-04 | 43 |
GO:000616510 | Endometrium | AEH | nucleoside diphosphate phosphorylation | 25/2100 | 99/18723 | 7.05e-05 | 1.08e-03 | 25 |
GO:000616316 | Endometrium | AEH | purine nucleotide metabolic process | 70/2100 | 396/18723 | 7.46e-05 | 1.13e-03 | 70 |
GO:000925910 | Endometrium | AEH | ribonucleotide metabolic process | 68/2100 | 385/18723 | 9.63e-05 | 1.39e-03 | 68 |
GO:001969310 | Endometrium | AEH | ribose phosphate metabolic process | 69/2100 | 396/18723 | 1.31e-04 | 1.79e-03 | 69 |
GO:00308564 | Endometrium | AEH | regulation of epithelial cell differentiation | 33/2100 | 154/18723 | 1.81e-04 | 2.32e-03 | 33 |
GO:007252116 | Endometrium | AEH | purine-containing compound metabolic process | 71/2100 | 416/18723 | 2.01e-04 | 2.54e-03 | 71 |
GO:00109758 | Endometrium | AEH | regulation of neuron projection development | 75/2100 | 445/18723 | 2.01e-04 | 2.54e-03 | 75 |
GO:000915210 | Endometrium | AEH | purine ribonucleotide biosynthetic process | 35/2100 | 169/18723 | 2.36e-04 | 2.84e-03 | 35 |
GO:004343410 | Endometrium | AEH | response to peptide hormone | 70/2100 | 414/18723 | 2.93e-04 | 3.35e-03 | 70 |
GO:190370614 | Endometrium | AEH | regulation of hemopoiesis | 63/2100 | 367/18723 | 3.81e-04 | 4.10e-03 | 63 |
GO:00313468 | Endometrium | AEH | positive regulation of cell projection organization | 61/2100 | 353/18723 | 3.91e-04 | 4.20e-03 | 61 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa012325 | Esophagus | ESCC | Nucleotide metabolism | 59/4205 | 85/8465 | 1.67e-04 | 6.58e-04 | 3.37e-04 | 59 |
hsa012405 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa002405 | Esophagus | ESCC | Pyrimidine metabolism | 41/4205 | 58/8465 | 9.14e-04 | 2.92e-03 | 1.49e-03 | 41 |
hsa0123212 | Esophagus | ESCC | Nucleotide metabolism | 59/4205 | 85/8465 | 1.67e-04 | 6.58e-04 | 3.37e-04 | 59 |
hsa0124012 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa0024012 | Esophagus | ESCC | Pyrimidine metabolism | 41/4205 | 58/8465 | 9.14e-04 | 2.92e-03 | 1.49e-03 | 41 |
hsa01240 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
hsa01232 | Liver | Cirrhotic | Nucleotide metabolism | 39/2530 | 85/8465 | 1.27e-03 | 6.73e-03 | 4.15e-03 | 39 |
hsa00240 | Liver | Cirrhotic | Pyrimidine metabolism | 27/2530 | 58/8465 | 5.31e-03 | 1.88e-02 | 1.16e-02 | 27 |
hsa00983 | Liver | Cirrhotic | Drug metabolism - other enzymes | 34/2530 | 80/8465 | 1.08e-02 | 3.57e-02 | 2.20e-02 | 34 |
hsa012401 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
hsa012321 | Liver | Cirrhotic | Nucleotide metabolism | 39/2530 | 85/8465 | 1.27e-03 | 6.73e-03 | 4.15e-03 | 39 |
hsa002401 | Liver | Cirrhotic | Pyrimidine metabolism | 27/2530 | 58/8465 | 5.31e-03 | 1.88e-02 | 1.16e-02 | 27 |
hsa009831 | Liver | Cirrhotic | Drug metabolism - other enzymes | 34/2530 | 80/8465 | 1.08e-02 | 3.57e-02 | 2.20e-02 | 34 |
hsa012402 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
hsa002402 | Liver | HCC | Pyrimidine metabolism | 44/4020 | 58/8465 | 9.34e-06 | 7.11e-05 | 3.95e-05 | 44 |
hsa012322 | Liver | HCC | Nucleotide metabolism | 59/4020 | 85/8465 | 3.30e-05 | 1.88e-04 | 1.04e-04 | 59 |
hsa009832 | Liver | HCC | Drug metabolism - other enzymes | 54/4020 | 80/8465 | 2.25e-04 | 1.09e-03 | 6.08e-04 | 54 |
hsa012403 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
hsa002403 | Liver | HCC | Pyrimidine metabolism | 44/4020 | 58/8465 | 9.34e-06 | 7.11e-05 | 3.95e-05 | 44 |
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Cell-cell communication analysis |
Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
Annotation of somatic variants for genes involved in malignant transformation |
Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
NME2 | SNV | Missense_Mutation | novel | c.290N>T | p.Ala97Val | p.A97V | P22392 | protein_coding | tolerated(0.17) | benign(0.013) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
NME2 | SNV | Missense_Mutation | rs757730632 | c.247N>A | p.Val83Met | p.V83M | P22392 | protein_coding | deleterious(0.01) | possibly_damaging(0.585) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NME2 | SNV | Missense_Mutation | rs757730632 | c.247N>A | p.Val83Met | p.V83M | P22392 | protein_coding | deleterious(0.01) | possibly_damaging(0.585) | TCGA-BG-A221-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NME2 | SNV | Missense_Mutation | novel | c.335T>G | p.Val112Gly | p.V112G | P22392 | protein_coding | deleterious(0.04) | benign(0.168) | TCGA-BS-A0UA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
NME2 | SNV | Missense_Mutation | novel | c.439N>T | p.His147Tyr | p.H147Y | P22392 | protein_coding | tolerated(0.48) | benign(0) | TCGA-21-5783-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
NME2 | SNV | Missense_Mutation | rs777392074 | c.263G>A | p.Arg88Gln | p.R88Q | P22392 | protein_coding | deleterious(0.02) | benign(0.3) | TCGA-HD-A4C1-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NME2 | SNV | Missense_Mutation | rs377454242 | c.314N>A | p.Arg105His | p.R105H | P22392 | protein_coding | deleterious(0.04) | possibly_damaging(0.786) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
Identification of chemicals and drugs interact with genes involved in malignant transfromation |
(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
4831 | NME2 | KINASE | zidovudine | ZIDOVUDINE | 22960662 | |
4831 | NME2 | KINASE | lamivudine | LAMIVUDINE | ||
4831 | NME2 | KINASE | tenofovir | TENOFOVIR | ||
4831 | NME2 | KINASE | adefovir dipivoxil | |||
4831 | NME2 | KINASE | PROGESTERONE | PROGESTERONE | 15674352 |
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