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Gene: NPM1 |
Gene summary for NPM1 |
Gene summary. |
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 |
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 |
4869 | NPM1 | GSM4909281 | Human | Breast | IDC | 7.77e-05 | -1.82e-01 | 0.21 |
4869 | NPM1 | GSM4909282 | Human | Breast | IDC | 2.93e-05 | -1.80e-01 | -0.0288 |
4869 | NPM1 | GSM4909285 | Human | Breast | IDC | 7.39e-03 | 2.13e-01 | 0.21 |
4869 | NPM1 | GSM4909286 | Human | Breast | IDC | 3.15e-34 | -3.24e-01 | 0.1081 |
4869 | NPM1 | GSM4909290 | Human | Breast | IDC | 1.20e-19 | -5.92e-01 | 0.2096 |
4869 | NPM1 | GSM4909291 | Human | Breast | IDC | 9.11e-10 | -4.49e-01 | 0.1753 |
4869 | NPM1 | GSM4909293 | Human | Breast | IDC | 1.38e-09 | -1.37e-01 | 0.1581 |
4869 | NPM1 | GSM4909294 | Human | Breast | IDC | 3.38e-02 | -1.17e-01 | 0.2022 |
4869 | NPM1 | GSM4909296 | Human | Breast | IDC | 5.23e-15 | -4.93e-01 | 0.1524 |
4869 | NPM1 | GSM4909297 | Human | Breast | IDC | 2.14e-19 | -2.67e-01 | 0.1517 |
4869 | NPM1 | GSM4909301 | Human | Breast | IDC | 3.24e-59 | -9.58e-01 | 0.1577 |
4869 | NPM1 | GSM4909302 | Human | Breast | IDC | 1.01e-07 | -4.02e-01 | 0.1545 |
4869 | NPM1 | GSM4909304 | Human | Breast | IDC | 1.13e-37 | -5.14e-01 | 0.1636 |
4869 | NPM1 | GSM4909306 | Human | Breast | IDC | 2.81e-11 | -3.04e-01 | 0.1564 |
4869 | NPM1 | GSM4909307 | Human | Breast | IDC | 1.92e-09 | -3.35e-01 | 0.1569 |
4869 | NPM1 | GSM4909309 | Human | Breast | IDC | 3.82e-08 | -4.35e-01 | 0.0483 |
4869 | NPM1 | GSM4909311 | Human | Breast | IDC | 5.83e-55 | -7.31e-01 | 0.1534 |
4869 | NPM1 | GSM4909315 | Human | Breast | IDC | 6.29e-08 | -2.89e-01 | 0.21 |
4869 | NPM1 | GSM4909319 | Human | Breast | IDC | 5.20e-77 | -9.68e-01 | 0.1563 |
4869 | NPM1 | GSM4909320 | Human | Breast | IDC | 5.80e-26 | -1.10e+00 | 0.1575 |
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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:00511683 | Colorectum | MSI-H | nuclear export | 24/1319 | 154/18723 | 1.95e-04 | 5.30e-03 | 24 |
GO:19033123 | Colorectum | MSI-H | negative regulation of mRNA metabolic process | 17/1319 | 92/18723 | 2.11e-04 | 5.55e-03 | 17 |
GO:00064013 | Colorectum | MSI-H | RNA catabolic process | 36/1319 | 278/18723 | 2.95e-04 | 7.25e-03 | 36 |
GO:00442703 | Colorectum | MSI-H | cellular nitrogen compound catabolic process | 52/1319 | 451/18723 | 3.09e-04 | 7.50e-03 | 52 |
GO:00320703 | Colorectum | MSI-H | regulation of deoxyribonuclease activity | 5/1319 | 10/18723 | 3.22e-04 | 7.63e-03 | 5 |
GO:00336743 | Colorectum | MSI-H | positive regulation of kinase activity | 53/1319 | 467/18723 | 3.99e-04 | 8.98e-03 | 53 |
GO:00064023 | Colorectum | MSI-H | mRNA catabolic process | 31/1319 | 232/18723 | 4.39e-04 | 9.45e-03 | 31 |
GO:00159313 | Colorectum | MSI-H | nucleobase-containing compound transport | 30/1319 | 222/18723 | 4.45e-04 | 9.50e-03 | 30 |
GO:00346553 | Colorectum | MSI-H | nucleobase-containing compound catabolic process | 47/1319 | 407/18723 | 5.69e-04 | 1.14e-02 | 47 |
GO:00423263 | Colorectum | MSI-H | negative regulation of phosphorylation | 45/1319 | 385/18723 | 5.71e-04 | 1.14e-02 | 45 |
GO:00458603 | Colorectum | MSI-H | positive regulation of protein kinase activity | 45/1319 | 386/18723 | 6.03e-04 | 1.19e-02 | 45 |
GO:00467003 | Colorectum | MSI-H | heterocycle catabolic process | 50/1319 | 445/18723 | 7.21e-04 | 1.37e-02 | 50 |
GO:00434873 | Colorectum | MSI-H | regulation of RNA stability | 24/1319 | 170/18723 | 8.57e-04 | 1.55e-02 | 24 |
GO:00506573 | Colorectum | MSI-H | nucleic acid transport | 23/1319 | 163/18723 | 1.09e-03 | 1.84e-02 | 23 |
GO:00506583 | Colorectum | MSI-H | RNA transport | 23/1319 | 163/18723 | 1.09e-03 | 1.84e-02 | 23 |
GO:00019333 | Colorectum | MSI-H | negative regulation of protein phosphorylation | 40/1319 | 342/18723 | 1.11e-03 | 1.86e-02 | 40 |
GO:00512363 | Colorectum | MSI-H | establishment of RNA localization | 23/1319 | 166/18723 | 1.40e-03 | 2.19e-02 | 23 |
GO:20010203 | Colorectum | MSI-H | regulation of response to DNA damage stimulus | 28/1319 | 219/18723 | 1.60e-03 | 2.39e-02 | 28 |
GO:00434883 | Colorectum | MSI-H | regulation of mRNA stability | 22/1319 | 158/18723 | 1.65e-03 | 2.44e-02 | 22 |
GO:00194393 | Colorectum | MSI-H | aromatic compound catabolic process | 50/1319 | 467/18723 | 2.04e-03 | 2.85e-02 | 50 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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 |
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 |
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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