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Gene: NOL3 |
Gene summary for NOL3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NOL3 | Gene ID | 8996 |
| Gene name | nucleolar protein 3 | |
| Gene Alias | ARC | |
| Cytomap | 16q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | O60936 |
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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 |
| 8996 | NOL3 | GSM4909291 | Human | Breast | IDC | 6.77e-06 | 3.74e-01 | 0.1753 |
| 8996 | NOL3 | GSM4909296 | Human | Breast | IDC | 3.20e-05 | 2.85e-01 | 0.1524 |
| 8996 | NOL3 | GSM4909311 | Human | Breast | IDC | 8.04e-07 | 4.59e-02 | 0.1534 |
| 8996 | NOL3 | GSM4909315 | Human | Breast | IDC | 7.07e-20 | 5.64e-01 | 0.21 |
| 8996 | NOL3 | GSM4909316 | Human | Breast | IDC | 2.12e-08 | 5.93e-01 | 0.21 |
| 8996 | NOL3 | GSM4909319 | Human | Breast | IDC | 1.27e-07 | 7.76e-02 | 0.1563 |
| 8996 | NOL3 | GSM4909321 | Human | Breast | IDC | 4.22e-23 | 6.18e-01 | 0.1559 |
| 8996 | NOL3 | brca3 | Human | Breast | Precancer | 2.98e-09 | 2.94e-01 | -0.0263 |
| 8996 | NOL3 | DCIS2 | Human | Breast | DCIS | 3.91e-37 | 1.58e-01 | 0.0085 |
| 8996 | NOL3 | LZE4T | Human | Esophagus | ESCC | 1.66e-17 | 5.18e-01 | 0.0811 |
| 8996 | NOL3 | LZE5T | Human | Esophagus | ESCC | 4.79e-04 | 4.39e-01 | 0.0514 |
| 8996 | NOL3 | LZE7T | Human | Esophagus | ESCC | 3.06e-09 | 5.68e-01 | 0.0667 |
| 8996 | NOL3 | LZE8T | Human | Esophagus | ESCC | 1.16e-05 | 2.24e-01 | 0.067 |
| 8996 | NOL3 | LZE20T | Human | Esophagus | ESCC | 1.80e-07 | 2.80e-01 | 0.0662 |
| 8996 | NOL3 | LZE22D1 | Human | Esophagus | HGIN | 2.26e-05 | 2.40e-01 | 0.0595 |
| 8996 | NOL3 | LZE24T | Human | Esophagus | ESCC | 7.21e-04 | 1.26e-01 | 0.0596 |
| 8996 | NOL3 | LZE21T | Human | Esophagus | ESCC | 2.22e-03 | 2.93e-01 | 0.0655 |
| 8996 | NOL3 | P1T-E | Human | Esophagus | ESCC | 2.49e-15 | 5.62e-01 | 0.0875 |
| 8996 | NOL3 | P2T-E | Human | Esophagus | ESCC | 7.69e-11 | 2.73e-01 | 0.1177 |
| 8996 | NOL3 | P4T-E | Human | Esophagus | ESCC | 2.52e-33 | 7.94e-01 | 0.1323 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:009055917 | Skin | cSCC | regulation of membrane permeability | 35/4864 | 78/18723 | 2.32e-04 | 1.91e-03 | 35 |
| GO:001082317 | Skin | cSCC | negative regulation of mitochondrion organization | 24/4864 | 49/18723 | 4.54e-04 | 3.47e-03 | 24 |
| GO:0071453111 | Skin | cSCC | cellular response to oxygen levels | 66/4864 | 177/18723 | 5.79e-04 | 4.21e-03 | 66 |
| GO:001095125 | Skin | cSCC | negative regulation of endopeptidase activity | 89/4864 | 252/18723 | 6.05e-04 | 4.38e-03 | 89 |
| GO:001046626 | Skin | cSCC | negative regulation of peptidase activity | 91/4864 | 262/18723 | 9.73e-04 | 6.58e-03 | 91 |
| GO:003461226 | Skin | cSCC | response to tumor necrosis factor | 88/4864 | 253/18723 | 1.11e-03 | 7.31e-03 | 88 |
| GO:190217617 | Skin | cSCC | negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway | 12/4864 | 20/18723 | 1.34e-03 | 8.54e-03 | 12 |
| GO:00164858 | Skin | cSCC | protein processing | 79/4864 | 225/18723 | 1.43e-03 | 9.02e-03 | 79 |
| GO:003320915 | Skin | cSCC | tumor necrosis factor-mediated signaling pathway | 39/4864 | 99/18723 | 2.33e-03 | 1.36e-02 | 39 |
| GO:007135625 | Skin | cSCC | cellular response to tumor necrosis factor | 79/4864 | 229/18723 | 2.48e-03 | 1.42e-02 | 79 |
| GO:007145617 | Skin | cSCC | cellular response to hypoxia | 55/4864 | 151/18723 | 2.88e-03 | 1.61e-02 | 55 |
| GO:200123727 | Skin | cSCC | negative regulation of extrinsic apoptotic signaling pathway | 38/4864 | 97/18723 | 2.95e-03 | 1.64e-02 | 38 |
| GO:0036294111 | Skin | cSCC | cellular response to decreased oxygen levels | 58/4864 | 161/18723 | 3.00e-03 | 1.66e-02 | 58 |
| GO:00063765 | Skin | cSCC | mRNA splice site selection | 22/4864 | 49/18723 | 3.18e-03 | 1.74e-02 | 22 |
| GO:00380616 | Skin | cSCC | NIK/NF-kappaB signaling | 52/4864 | 143/18723 | 3.83e-03 | 2.05e-02 | 52 |
| GO:1903201110 | Skin | cSCC | regulation of oxidative stress-induced cell death | 30/4864 | 74/18723 | 4.32e-03 | 2.27e-02 | 30 |
| GO:19012225 | Skin | cSCC | regulation of NIK/NF-kappaB signaling | 42/4864 | 112/18723 | 4.71e-03 | 2.40e-02 | 42 |
| GO:005123527 | Skin | cSCC | maintenance of location | 106/4864 | 327/18723 | 5.17e-03 | 2.61e-02 | 106 |
| GO:19021087 | Skin | cSCC | regulation of mitochondrial membrane permeability involved in apoptotic process | 20/4864 | 45/18723 | 5.54e-03 | 2.74e-02 | 20 |
| GO:00607596 | Skin | cSCC | regulation of response to cytokine stimulus | 57/4864 | 162/18723 | 5.77e-03 | 2.85e-02 | 57 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| NOL3 | SNV | Missense_Mutation | c.343N>C | p.Asp115His | p.D115H | O60936 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.966) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NOL3 | SNV | Missense_Mutation | novel | c.60N>C | p.Gln20His | p.Q20H | O60936 | protein_coding | benign(0.187) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| NOL3 | SNV | Missense_Mutation | novel | c.604G>A | p.Glu202Lys | p.E202K | O60936 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.516) | TCGA-XS-A8TJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| NOL3 | SNV | Missense_Mutation | novel | c.299N>T | p.Gly100Val | p.G100V | O60936 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.991) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NOL3 | SNV | Missense_Mutation | rs528140604 | c.635N>T | p.Pro212Leu | p.P212L | O60936 | protein_coding | tolerated_low_confidence(0.31) | benign(0) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| NOL3 | insertion | Frame_Shift_Ins | novel | c.190_191insC | p.Gly64AlafsTer52 | p.G64Afs*52 | O60936 | protein_coding | TCGA-AP-A0LH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | PD | ||
| NOL3 | SNV | Missense_Mutation | novel | c.796G>A | p.Glu266Lys | p.E266K | O60936 | protein_coding | deleterious_low_confidence(0) | benign(0.042) | TCGA-CV-7097-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| NOL3 | SNV | Missense_Mutation | c.514N>A | p.Pro172Thr | p.P172T | O60936 | protein_coding | tolerated_low_confidence(0.08) | benign(0.025) | TCGA-D7-A4YY-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | SD | |
| NOL3 | SNV | Missense_Mutation | rs547594151 | c.259G>A | p.Ala87Thr | p.A87T | O60936 | protein_coding | tolerated_low_confidence(0.25) | benign(0.196) | TCGA-HU-A4G8-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD |
| Page: 1 |
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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 |
| Page: 1 |
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