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Gene: NRDE2 |
Gene summary for NRDE2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NRDE2 | Gene ID | 55051 |
| Gene name | NRDE-2, necessary for RNA interference, domain containing | |
| Gene Alias | C14orf102 | |
| Cytomap | 14q32.11 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | Q9H7Z3 |
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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 |
| 55051 | NRDE2 | LZE7T | Human | Esophagus | ESCC | 5.28e-04 | 1.40e-01 | 0.0667 |
| 55051 | NRDE2 | LZE20T | Human | Esophagus | ESCC | 7.59e-05 | 2.16e-01 | 0.0662 |
| 55051 | NRDE2 | LZE24T | Human | Esophagus | ESCC | 1.32e-05 | 1.09e-01 | 0.0596 |
| 55051 | NRDE2 | LZE21T | Human | Esophagus | ESCC | 2.85e-02 | 3.11e-01 | 0.0655 |
| 55051 | NRDE2 | P1T-E | Human | Esophagus | ESCC | 2.51e-02 | 2.04e-01 | 0.0875 |
| 55051 | NRDE2 | P2T-E | Human | Esophagus | ESCC | 2.03e-13 | 1.79e-01 | 0.1177 |
| 55051 | NRDE2 | P4T-E | Human | Esophagus | ESCC | 1.23e-13 | 1.93e-01 | 0.1323 |
| 55051 | NRDE2 | P5T-E | Human | Esophagus | ESCC | 6.02e-18 | 9.76e-02 | 0.1327 |
| 55051 | NRDE2 | P8T-E | Human | Esophagus | ESCC | 3.32e-18 | 3.05e-01 | 0.0889 |
| 55051 | NRDE2 | P9T-E | Human | Esophagus | ESCC | 1.61e-04 | 1.60e-01 | 0.1131 |
| 55051 | NRDE2 | P10T-E | Human | Esophagus | ESCC | 5.01e-54 | 7.99e-01 | 0.116 |
| 55051 | NRDE2 | P11T-E | Human | Esophagus | ESCC | 5.90e-08 | 2.81e-01 | 0.1426 |
| 55051 | NRDE2 | P12T-E | Human | Esophagus | ESCC | 1.06e-19 | 4.02e-01 | 0.1122 |
| 55051 | NRDE2 | P15T-E | Human | Esophagus | ESCC | 5.52e-23 | 4.35e-01 | 0.1149 |
| 55051 | NRDE2 | P16T-E | Human | Esophagus | ESCC | 5.06e-14 | 2.18e-01 | 0.1153 |
| 55051 | NRDE2 | P17T-E | Human | Esophagus | ESCC | 1.02e-02 | 1.83e-01 | 0.1278 |
| 55051 | NRDE2 | P20T-E | Human | Esophagus | ESCC | 1.34e-09 | 2.24e-01 | 0.1124 |
| 55051 | NRDE2 | P21T-E | Human | Esophagus | ESCC | 1.27e-11 | 1.18e-01 | 0.1617 |
| 55051 | NRDE2 | P22T-E | Human | Esophagus | ESCC | 7.46e-13 | 1.27e-01 | 0.1236 |
| 55051 | NRDE2 | P23T-E | Human | Esophagus | ESCC | 1.31e-13 | 1.80e-01 | 0.108 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0006913110 | Esophagus | ESCC | nucleocytoplasmic transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0051169110 | Esophagus | ESCC | nuclear transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0006403110 | Esophagus | ESCC | RNA localization | 166/8552 | 201/18723 | 1.95e-27 | 6.18e-25 | 166 |
| GO:003238618 | Esophagus | ESCC | regulation of intracellular transport | 243/8552 | 337/18723 | 3.20e-23 | 7.25e-21 | 243 |
| GO:0006401110 | Esophagus | ESCC | RNA catabolic process | 204/8552 | 278/18723 | 3.39e-21 | 5.66e-19 | 204 |
| GO:005123617 | Esophagus | ESCC | establishment of RNA localization | 134/8552 | 166/18723 | 1.23e-20 | 1.81e-18 | 134 |
| GO:0051168110 | Esophagus | ESCC | nuclear export | 126/8552 | 154/18723 | 1.88e-20 | 2.65e-18 | 126 |
| GO:005065717 | Esophagus | ESCC | nucleic acid transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:005065817 | Esophagus | ESCC | RNA transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:0032388110 | Esophagus | ESCC | positive regulation of intracellular transport | 152/8552 | 202/18723 | 7.89e-18 | 7.36e-16 | 152 |
| GO:001593117 | Esophagus | ESCC | nucleobase-containing compound transport | 162/8552 | 222/18723 | 9.87e-17 | 7.93e-15 | 162 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:0046822110 | Esophagus | ESCC | regulation of nucleocytoplasmic transport | 88/8552 | 106/18723 | 1.88e-15 | 1.19e-13 | 88 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:000640512 | Esophagus | ESCC | RNA export from nucleus | 68/8552 | 84/18723 | 2.99e-11 | 1.01e-09 | 68 |
| GO:0009895111 | Esophagus | ESCC | negative regulation of catabolic process | 201/8552 | 320/18723 | 3.88e-10 | 1.05e-08 | 201 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
| NRDE2 | SNV | Missense_Mutation | c.1088T>C | p.Leu363Pro | p.L363P | Q9H7Z3 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-AN-A0XN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| NRDE2 | SNV | Missense_Mutation | c.457N>C | p.Glu153Gln | p.E153Q | Q9H7Z3 | protein_coding | deleterious(0.01) | possibly_damaging(0.69) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| NRDE2 | SNV | Missense_Mutation | c.2039N>A | p.Phe680Tyr | p.F680Y | Q9H7Z3 | protein_coding | tolerated(0.89) | benign(0.001) | TCGA-BH-A0B5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR | |
| NRDE2 | SNV | Missense_Mutation | rs78302825 | c.3448C>T | p.Arg1150Trp | p.R1150W | Q9H7Z3 | protein_coding | deleterious(0) | probably_damaging(0.952) | TCGA-BH-A0BL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| NRDE2 | SNV | Missense_Mutation | c.1792N>C | p.Asp598His | p.D598H | Q9H7Z3 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| NRDE2 | SNV | Missense_Mutation | c.337G>A | p.Asp113Asn | p.D113N | Q9H7Z3 | protein_coding | tolerated(0.18) | benign(0.379) | TCGA-E2-A1L7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| NRDE2 | SNV | Missense_Mutation | rs368842771 | c.1585N>T | p.Arg529Trp | p.R529W | Q9H7Z3 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E9-A5UO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NRDE2 | insertion | Nonsense_Mutation | novel | c.430_431insTTCAATAAGTATTAGTTGAATAAATGAATCCAAAAGTAC | p.Asp144delinsValGlnTerValLeuValGluTerMetAsnProLysValHis | p.D144delinsVQ*VLVE*MNPKVH | Q9H7Z3 | protein_coding | TCGA-A7-A0CG-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| NRDE2 | insertion | In_Frame_Ins | novel | c.2676_2677insGCTGGCCCCTCTGCGAGAGGCACTCTCACAGGCTTTAAA | p.Ser892_Asn893insAlaGlyProSerAlaArgGlyThrLeuThrGlyPheLys | p.S892_N893insAGPSARGTLTGFK | Q9H7Z3 | protein_coding | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| NRDE2 | SNV | Missense_Mutation | rs771864754 | c.2141N>A | p.Arg714His | p.R714H | Q9H7Z3 | protein_coding | tolerated(0.17) | benign(0.011) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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