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Gene: NHP2 |
Gene summary for NHP2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NHP2 | Gene ID | 55651 |
Gene name | NHP2 ribonucleoprotein | |
Gene Alias | DKCB2 | |
Cytomap | 5q35.3 | |
Gene Type | protein-coding | GO ID | GO:0000154 | UniProtAcc | J3QSY4 |
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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 |
55651 | NHP2 | GSM4909281 | Human | Breast | IDC | 4.89e-04 | 3.15e-01 | 0.21 |
55651 | NHP2 | GSM4909286 | Human | Breast | IDC | 2.63e-03 | -1.26e-02 | 0.1081 |
55651 | NHP2 | GSM4909293 | Human | Breast | IDC | 3.77e-05 | 2.79e-01 | 0.1581 |
55651 | NHP2 | GSM4909294 | Human | Breast | IDC | 4.85e-05 | 2.74e-02 | 0.2022 |
55651 | NHP2 | GSM4909296 | Human | Breast | IDC | 3.92e-21 | 3.20e-01 | 0.1524 |
55651 | NHP2 | GSM4909297 | Human | Breast | IDC | 5.39e-19 | -1.58e-02 | 0.1517 |
55651 | NHP2 | GSM4909298 | Human | Breast | IDC | 4.40e-22 | 5.33e-01 | 0.1551 |
55651 | NHP2 | GSM4909301 | Human | Breast | IDC | 1.45e-30 | 5.64e-01 | 0.1577 |
55651 | NHP2 | GSM4909304 | Human | Breast | IDC | 4.21e-12 | 4.66e-01 | 0.1636 |
55651 | NHP2 | GSM4909306 | Human | Breast | IDC | 7.95e-12 | 4.00e-01 | 0.1564 |
55651 | NHP2 | GSM4909307 | Human | Breast | IDC | 1.75e-19 | 5.12e-01 | 0.1569 |
55651 | NHP2 | GSM4909308 | Human | Breast | IDC | 2.01e-20 | 5.24e-01 | 0.158 |
55651 | NHP2 | GSM4909309 | Human | Breast | IDC | 6.19e-05 | 1.94e-01 | 0.0483 |
55651 | NHP2 | GSM4909311 | Human | Breast | IDC | 3.36e-48 | 2.87e-02 | 0.1534 |
55651 | NHP2 | GSM4909312 | Human | Breast | IDC | 1.46e-13 | 1.67e-01 | 0.1552 |
55651 | NHP2 | GSM4909316 | Human | Breast | IDC | 2.44e-03 | 1.95e-01 | 0.21 |
55651 | NHP2 | GSM4909317 | Human | Breast | IDC | 3.47e-05 | 3.19e-01 | 0.1355 |
55651 | NHP2 | GSM4909318 | Human | Breast | IDC | 2.86e-08 | 5.13e-01 | 0.2031 |
55651 | NHP2 | GSM4909319 | Human | Breast | IDC | 7.31e-61 | 2.31e-02 | 0.1563 |
55651 | NHP2 | GSM4909320 | Human | Breast | IDC | 1.39e-22 | 5.97e-01 | 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 |
Thyroid | PTC | |
Thyroid | goiters | |
Thyroid | ATC |
∗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: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:00422739 | Breast | Precancer | ribosomal large subunit biogenesis | 22/1080 | 72/18723 | 5.03e-11 | 5.61e-09 | 22 |
GO:00063646 | Breast | Precancer | rRNA processing | 35/1080 | 225/18723 | 7.90e-08 | 4.60e-06 | 35 |
GO:00160726 | Breast | Precancer | rRNA metabolic process | 36/1080 | 236/18723 | 8.59e-08 | 4.84e-06 | 36 |
GO:00108338 | Breast | Precancer | telomere maintenance via telomere lengthening | 15/1080 | 81/18723 | 5.31e-05 | 1.11e-03 | 15 |
GO:00007238 | Breast | Precancer | telomere maintenance | 20/1080 | 131/18723 | 6.10e-05 | 1.25e-03 | 20 |
GO:00344705 | Breast | Precancer | ncRNA processing | 42/1080 | 395/18723 | 9.91e-05 | 1.83e-03 | 42 |
GO:19048743 | Breast | Precancer | positive regulation of telomerase RNA localization to Cajal body | 6/1080 | 15/18723 | 1.16e-04 | 2.08e-03 | 6 |
GO:00070047 | Breast | Precancer | telomere maintenance via telomerase | 13/1080 | 69/18723 | 1.37e-04 | 2.38e-03 | 13 |
GO:00062786 | Breast | Precancer | RNA-dependent DNA biosynthetic process | 13/1080 | 75/18723 | 3.27e-04 | 4.64e-03 | 13 |
GO:19048723 | Breast | Precancer | regulation of telomerase RNA localization to Cajal body | 6/1080 | 18/18723 | 3.70e-04 | 5.04e-03 | 6 |
GO:00906703 | Breast | Precancer | RNA localization to Cajal body | 6/1080 | 19/18723 | 5.14e-04 | 6.65e-03 | 6 |
GO:00906713 | Breast | Precancer | telomerase RNA localization to Cajal body | 6/1080 | 19/18723 | 5.14e-04 | 6.65e-03 | 6 |
GO:00906723 | Breast | Precancer | telomerase RNA localization | 6/1080 | 19/18723 | 5.14e-04 | 6.65e-03 | 6 |
GO:00906853 | Breast | Precancer | RNA localization to nucleus | 6/1080 | 19/18723 | 5.14e-04 | 6.65e-03 | 6 |
GO:00322003 | Breast | Precancer | telomere organization | 20/1080 | 159/18723 | 8.45e-04 | 9.82e-03 | 20 |
GO:00004703 | Breast | Precancer | maturation of LSU-rRNA | 7/1080 | 28/18723 | 8.46e-04 | 9.82e-03 | 7 |
GO:00346604 | Breast | Precancer | ncRNA metabolic process | 45/1080 | 485/18723 | 1.15e-03 | 1.26e-02 | 45 |
GO:00064039 | Breast | Precancer | RNA localization | 23/1080 | 201/18723 | 1.34e-03 | 1.41e-02 | 23 |
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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 |
NHP2 | deletion | Frame_Shift_Del | novel | c.99delN | p.Ile34SerfsTer22 | p.I34Sfs*22 | Q9NX24 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
NHP2 | SNV | Missense_Mutation | c.235A>G | p.Met79Val | p.M79V | Q9NX24 | protein_coding | tolerated(1) | benign(0) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NHP2 | SNV | Missense_Mutation | c.418N>A | p.Asp140Asn | p.D140N | Q9NX24 | protein_coding | tolerated(0.11) | benign(0.007) | TCGA-CI-6619-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
NHP2 | SNV | Missense_Mutation | c.242N>C | p.Leu81Ser | p.L81S | Q9NX24 | protein_coding | deleterious(0) | possibly_damaging(0.773) | TCGA-B5-A11G-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NHP2 | SNV | Missense_Mutation | rs752392516 | c.364N>T | p.Arg122Cys | p.R122C | Q9NX24 | protein_coding | deleterious(0) | probably_damaging(0.931) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
NHP2 | SNV | Missense_Mutation | novel | c.404N>G | p.Tyr135Cys | p.Y135C | Q9NX24 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
NHP2 | SNV | Missense_Mutation | novel | c.43G>T | p.Ala15Ser | p.A15S | Q9NX24 | protein_coding | tolerated(0.51) | benign(0.018) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NHP2 | SNV | Missense_Mutation | c.177G>C | p.Gln59His | p.Q59H | Q9NX24 | protein_coding | tolerated(0.41) | possibly_damaging(0.77) | TCGA-55-6979-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
NHP2 | SNV | Missense_Mutation | c.418N>A | p.Asp140Asn | p.D140N | Q9NX24 | protein_coding | tolerated(0.11) | benign(0.007) | TCGA-L9-A8F4-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
NHP2 | SNV | Missense_Mutation | novel | c.259C>G | p.Pro87Ala | p.P87A | Q9NX24 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-34-2609-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | gemcitabine | PD |
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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 |
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