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Gene: NBDY |
Gene summary for NBDY |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NBDY | Gene ID | 550643 |
| Gene name | negative regulator of P-body association | |
| Gene Alias | LINC01420 | |
| Cytomap | Xp11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000956 | UniProtAcc | A0A0U1RRE5 |
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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 |
| 550643 | NBDY | GSM4909281 | Human | Breast | IDC | 7.62e-45 | 8.72e-01 | 0.21 |
| 550643 | NBDY | GSM4909282 | Human | Breast | IDC | 5.18e-10 | 4.71e-01 | -0.0288 |
| 550643 | NBDY | GSM4909286 | Human | Breast | IDC | 1.09e-02 | 6.86e-02 | 0.1081 |
| 550643 | NBDY | GSM4909293 | Human | Breast | IDC | 1.14e-13 | 4.07e-01 | 0.1581 |
| 550643 | NBDY | GSM4909298 | Human | Breast | IDC | 2.77e-03 | 2.14e-01 | 0.1551 |
| 550643 | NBDY | GSM4909302 | Human | Breast | IDC | 7.75e-08 | 3.95e-01 | 0.1545 |
| 550643 | NBDY | GSM4909305 | Human | Breast | IDC | 1.23e-02 | 2.84e-01 | 0.0436 |
| 550643 | NBDY | GSM4909306 | Human | Breast | IDC | 1.55e-26 | 6.41e-01 | 0.1564 |
| 550643 | NBDY | GSM4909307 | Human | Breast | IDC | 8.21e-06 | 3.30e-01 | 0.1569 |
| 550643 | NBDY | GSM4909308 | Human | Breast | IDC | 4.30e-23 | 5.27e-01 | 0.158 |
| 550643 | NBDY | GSM4909311 | Human | Breast | IDC | 6.55e-05 | -1.39e-01 | 0.1534 |
| 550643 | NBDY | GSM4909315 | Human | Breast | IDC | 2.77e-05 | 3.58e-01 | 0.21 |
| 550643 | NBDY | GSM4909319 | Human | Breast | IDC | 5.97e-11 | 4.80e-02 | 0.1563 |
| 550643 | NBDY | GSM4909321 | Human | Breast | IDC | 1.85e-05 | 2.84e-01 | 0.1559 |
| 550643 | NBDY | brca1 | Human | Breast | Precancer | 3.85e-08 | -2.13e-01 | -0.0338 |
| 550643 | NBDY | brca2 | Human | Breast | Precancer | 3.85e-08 | -2.13e-01 | -0.024 |
| 550643 | NBDY | brca3 | Human | Breast | Precancer | 8.23e-09 | -2.13e-01 | -0.0263 |
| 550643 | NBDY | brca10 | Human | Breast | Precancer | 7.56e-06 | 3.34e-01 | -0.0029 |
| 550643 | NBDY | NCCBC5 | Human | Breast | DCIS | 1.90e-03 | 1.88e-01 | 0.2046 |
| 550643 | NBDY | DCIS2 | Human | Breast | DCIS | 1.73e-75 | 3.53e-01 | 0.0085 |
| Page: 1 2 3 |
| 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 | ||
| 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:00064028 | Breast | Precancer | mRNA catabolic process | 31/1080 | 232/18723 | 1.12e-05 | 2.93e-04 | 31 |
| GO:00064018 | Breast | Precancer | RNA catabolic process | 34/1080 | 278/18723 | 2.88e-05 | 6.39e-04 | 34 |
| GO:00346558 | Breast | Precancer | nucleobase-containing compound catabolic process | 42/1080 | 407/18723 | 1.91e-04 | 3.06e-03 | 42 |
| GO:00467007 | Breast | Precancer | heterocycle catabolic process | 44/1080 | 445/18723 | 3.49e-04 | 4.88e-03 | 44 |
| GO:00442708 | Breast | Precancer | cellular nitrogen compound catabolic process | 44/1080 | 451/18723 | 4.64e-04 | 6.12e-03 | 44 |
| GO:00009566 | Breast | Precancer | nuclear-transcribed mRNA catabolic process | 16/1080 | 112/18723 | 6.87e-04 | 8.36e-03 | 16 |
| GO:00194397 | Breast | Precancer | aromatic compound catabolic process | 44/1080 | 467/18723 | 9.55e-04 | 1.07e-02 | 44 |
| GO:19013617 | Breast | Precancer | organic cyclic compound catabolic process | 45/1080 | 495/18723 | 1.73e-03 | 1.74e-02 | 45 |
| GO:000640113 | Breast | IDC | RNA catabolic process | 38/1434 | 278/18723 | 3.54e-04 | 5.16e-03 | 38 |
| GO:000640213 | Breast | IDC | mRNA catabolic process | 33/1434 | 232/18723 | 4.12e-04 | 5.66e-03 | 33 |
| GO:000095613 | Breast | IDC | nuclear-transcribed mRNA catabolic process | 18/1434 | 112/18723 | 2.09e-03 | 1.96e-02 | 18 |
| GO:190136112 | Breast | IDC | organic cyclic compound catabolic process | 56/1434 | 495/18723 | 2.12e-03 | 1.99e-02 | 56 |
| GO:004670012 | Breast | IDC | heterocycle catabolic process | 51/1434 | 445/18723 | 2.51e-03 | 2.25e-02 | 51 |
| GO:003465513 | Breast | IDC | nucleobase-containing compound catabolic process | 47/1434 | 407/18723 | 3.12e-03 | 2.63e-02 | 47 |
| GO:004427012 | Breast | IDC | cellular nitrogen compound catabolic process | 50/1434 | 451/18723 | 5.29e-03 | 3.93e-02 | 50 |
| GO:001943912 | Breast | IDC | aromatic compound catabolic process | 51/1434 | 467/18723 | 6.54e-03 | 4.59e-02 | 51 |
| GO:000640123 | Breast | DCIS | RNA catabolic process | 38/1390 | 278/18723 | 1.91e-04 | 3.08e-03 | 38 |
| GO:000640223 | Breast | DCIS | mRNA catabolic process | 33/1390 | 232/18723 | 2.35e-04 | 3.70e-03 | 33 |
| GO:000095622 | Breast | DCIS | nuclear-transcribed mRNA catabolic process | 18/1390 | 112/18723 | 1.48e-03 | 1.50e-02 | 18 |
| GO:003465522 | Breast | DCIS | nucleobase-containing compound catabolic process | 47/1390 | 407/18723 | 1.69e-03 | 1.68e-02 | 47 |
| Page: 1 2 3 4 |
| 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 |
| NBDY | SNV | Missense_Mutation | novel | c.7N>T | p.Asp3Tyr | p.D3Y | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.937) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NBDY | SNV | Missense_Mutation | novel | c.125N>C | p.Asn42Thr | p.N42T | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| NBDY | SNV | Missense_Mutation | novel | c.97C>T | p.Arg33Cys | p.R33C | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.833) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NBDY | SNV | Missense_Mutation | novel | c.98N>A | p.Arg33His | p.R33H | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.711) | TCGA-EY-A1GF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
| Page: 1 |
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