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Gene: NPM1 |
Gene summary for NPM1 |
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Gene information | Species | Human | Gene symbol | NPM1 | Gene ID | 4869 |
Gene name | nucleophosmin 1 | |
Gene Alias | B23 | |
Cytomap | 5q35.1 | |
Gene Type | protein-coding | GO ID | GO:0000054 | UniProtAcc | A0A140VJQ2 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
4869 | NPM1 | EEC-subject2 | Human | Endometrium | EEC | 1.71e-48 | -7.30e-01 | -0.2607 |
4869 | NPM1 | EEC-subject3 | Human | Endometrium | EEC | 1.61e-22 | -4.61e-01 | -0.2525 |
4869 | NPM1 | EEC-subject4 | Human | Endometrium | EEC | 3.32e-14 | -4.08e-01 | -0.2571 |
4869 | NPM1 | EEC-subject5 | Human | Endometrium | EEC | 5.24e-15 | -4.03e-01 | -0.249 |
4869 | NPM1 | GSM5276934 | Human | Endometrium | EEC | 1.39e-14 | 1.95e-01 | -0.0913 |
4869 | NPM1 | GSM5276937 | Human | Endometrium | EEC | 1.04e-23 | 3.09e-01 | -0.0897 |
4869 | NPM1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 7.82e-55 | -1.14e+00 | -0.1869 |
4869 | NPM1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 7.93e-60 | -1.28e+00 | -0.1875 |
4869 | NPM1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 3.48e-63 | -1.23e+00 | -0.1883 |
4869 | NPM1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.54e-78 | -1.21e+00 | -0.1934 |
4869 | NPM1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 3.36e-80 | -1.22e+00 | -0.1917 |
4869 | NPM1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 5.50e-76 | -1.22e+00 | -0.1916 |
4869 | NPM1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.51e-12 | -3.49e-01 | -0.1269 |
4869 | NPM1 | LZE11D | Human | Esophagus | HGIN | 4.34e-06 | -1.05e+00 | -0.005 |
4869 | NPM1 | LZE2T | Human | Esophagus | ESCC | 4.09e-34 | 2.07e+00 | 0.082 |
4869 | NPM1 | LZE3D | Human | Esophagus | HGIN | 5.13e-43 | 1.78e+00 | 0.0668 |
4869 | NPM1 | LZE4T | Human | Esophagus | ESCC | 1.15e-16 | 1.09e+00 | 0.0811 |
4869 | NPM1 | LZE5T | Human | Esophagus | ESCC | 2.07e-04 | 6.32e-01 | 0.0514 |
4869 | NPM1 | LZE7T | Human | Esophagus | ESCC | 4.73e-21 | 1.58e+00 | 0.0667 |
4869 | NPM1 | LZE8T | Human | Esophagus | ESCC | 2.59e-09 | 1.41e+00 | 0.067 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
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∗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 |
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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). |
Page: 1 2 3 4 5 6 7 8 9 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
GO:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
GO:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
GO:00434849 | Breast | Precancer | regulation of RNA splicing | 34/1080 | 148/18723 | 2.66e-12 | 4.75e-10 | 34 |
GO:00064138 | Breast | Precancer | translational initiation | 30/1080 | 118/18723 | 3.23e-12 | 5.58e-10 | 30 |
GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
GO:00422739 | Breast | Precancer | ribosomal large subunit biogenesis | 22/1080 | 72/18723 | 5.03e-11 | 5.61e-09 | 22 |
GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
GO:00480249 | Breast | Precancer | regulation of mRNA splicing, via spliceosome | 22/1080 | 101/18723 | 5.29e-08 | 3.18e-06 | 22 |
GO:00064466 | Breast | Precancer | regulation of translational initiation | 19/1080 | 79/18723 | 7.99e-08 | 4.60e-06 | 19 |
GO:00313969 | Breast | Precancer | regulation of protein ubiquitination | 33/1080 | 210/18723 | 1.45e-07 | 7.82e-06 | 33 |
GO:19017969 | Breast | Precancer | regulation of signal transduction by p53 class mediator | 19/1080 | 93/18723 | 1.20e-06 | 4.60e-05 | 19 |
GO:19033118 | Breast | Precancer | regulation of mRNA metabolic process | 38/1080 | 288/18723 | 1.63e-06 | 5.97e-05 | 38 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
NPM1 | SNV | Missense_Mutation | c.553N>A | p.Glu185Lys | p.E185K | P06748 | protein_coding | tolerated(0.12) | possibly_damaging(0.458) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NPM1 | SNV | Missense_Mutation | novel | c.503N>G | p.Asp168Gly | p.D168G | P06748 | protein_coding | tolerated(0.11) | benign(0.061) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NPM1 | SNV | Missense_Mutation | c.7N>T | p.Asp3Tyr | p.D3Y | P06748 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
NPM1 | SNV | Missense_Mutation | c.81A>T | p.Lys27Asn | p.K27N | P06748 | protein_coding | deleterious(0.02) | benign(0.425) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
NPM1 | SNV | Missense_Mutation | novel | c.478G>C | p.Ala160Pro | p.A160P | P06748 | protein_coding | deleterious(0.03) | possibly_damaging(0.892) | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NPM1 | SNV | Missense_Mutation | rs376742289 | c.586N>G | p.Ile196Val | p.I196V | P06748 | protein_coding | tolerated(0.65) | benign(0.001) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NPM1 | SNV | Missense_Mutation | novel | c.607A>C | p.Asn203His | p.N203H | P06748 | protein_coding | deleterious(0.04) | benign(0.063) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NPM1 | insertion | Frame_Shift_Ins | novel | c.477_478insACCA | p.Ala160ThrfsTer3 | p.A160Tfs*3 | P06748 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
NPM1 | SNV | Missense_Mutation | novel | c.717N>C | p.Lys239Asn | p.K239N | P06748 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NPM1 | SNV | Missense_Mutation | c.296N>C | p.Val99Ala | p.V99A | P06748 | protein_coding | deleterious(0.05) | benign(0.272) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | Crizotinib | CRIZOTINIB | 27009859,25749034,24509625,18089725,25421750 | |
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | IPP-204106 | |||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | N/A | 19047294,26586702,16109776,26676635,26239249,25281355,24573385,25713434 | ||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | AZD3463 | 27009859 | ||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | Deguelin | DEGUELIN | 25348016,25242579 | |
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | Venetoclax | VENETOCLAX | ||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | EPZ004777 | 27535106 | ||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | MI-503 | 27535106 | ||
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | TRETINOIN | TRETINOIN | 19965647,21719597 | |
4869 | NPM1 | CLINICALLY ACTIONABLE, DNA REPAIR, DRUGGABLE GENOME, DRUG RESISTANCE | Midostaurin | MIDOSTAURIN |
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