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Gene: NRBF2 |
Gene summary for NRBF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NRBF2 | Gene ID | 29982 |
| Gene name | nuclear receptor binding factor 2 | |
| Gene Alias | COPR | |
| Cytomap | 10q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006793 | UniProtAcc | Q96F24 |
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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 |
| 29982 | NRBF2 | LZE4T | Human | Esophagus | ESCC | 1.92e-16 | 5.26e-01 | 0.0811 |
| 29982 | NRBF2 | LZE7T | Human | Esophagus | ESCC | 9.78e-07 | 2.95e-01 | 0.0667 |
| 29982 | NRBF2 | LZE8T | Human | Esophagus | ESCC | 4.98e-14 | 2.92e-01 | 0.067 |
| 29982 | NRBF2 | LZE20T | Human | Esophagus | ESCC | 8.63e-07 | 2.08e-01 | 0.0662 |
| 29982 | NRBF2 | LZE22T | Human | Esophagus | ESCC | 1.06e-06 | 4.10e-01 | 0.068 |
| 29982 | NRBF2 | LZE24T | Human | Esophagus | ESCC | 5.29e-29 | 7.24e-01 | 0.0596 |
| 29982 | NRBF2 | LZE21T | Human | Esophagus | ESCC | 2.72e-02 | 1.73e-01 | 0.0655 |
| 29982 | NRBF2 | LZE6T | Human | Esophagus | ESCC | 6.71e-05 | 3.47e-01 | 0.0845 |
| 29982 | NRBF2 | P1T-E | Human | Esophagus | ESCC | 7.37e-10 | 6.46e-01 | 0.0875 |
| 29982 | NRBF2 | P2T-E | Human | Esophagus | ESCC | 8.84e-31 | 6.09e-01 | 0.1177 |
| 29982 | NRBF2 | P4T-E | Human | Esophagus | ESCC | 1.76e-27 | 6.24e-01 | 0.1323 |
| 29982 | NRBF2 | P5T-E | Human | Esophagus | ESCC | 3.42e-24 | 5.96e-01 | 0.1327 |
| 29982 | NRBF2 | P8T-E | Human | Esophagus | ESCC | 5.42e-21 | 4.94e-01 | 0.0889 |
| 29982 | NRBF2 | P9T-E | Human | Esophagus | ESCC | 2.48e-11 | 3.26e-01 | 0.1131 |
| 29982 | NRBF2 | P10T-E | Human | Esophagus | ESCC | 4.90e-23 | 3.66e-01 | 0.116 |
| 29982 | NRBF2 | P11T-E | Human | Esophagus | ESCC | 6.29e-19 | 7.89e-01 | 0.1426 |
| 29982 | NRBF2 | P12T-E | Human | Esophagus | ESCC | 1.48e-40 | 7.10e-01 | 0.1122 |
| 29982 | NRBF2 | P15T-E | Human | Esophagus | ESCC | 7.52e-29 | 5.98e-01 | 0.1149 |
| 29982 | NRBF2 | P16T-E | Human | Esophagus | ESCC | 6.37e-26 | 6.04e-01 | 0.1153 |
| 29982 | NRBF2 | P17T-E | Human | Esophagus | ESCC | 1.80e-05 | 3.65e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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 | ||
| 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:0034976111 | Esophagus | ESCC | response to endoplasmic reticulum stress | 192/8552 | 256/18723 | 7.15e-22 | 1.30e-19 | 192 |
| GO:00349767 | Liver | Cirrhotic | response to endoplasmic reticulum stress | 130/4634 | 256/18723 | 1.72e-19 | 3.86e-17 | 130 |
| GO:003497612 | Liver | HCC | response to endoplasmic reticulum stress | 189/7958 | 256/18723 | 1.43e-24 | 4.06e-22 | 189 |
| GO:003497620 | Oral cavity | OSCC | response to endoplasmic reticulum stress | 178/7305 | 256/18723 | 2.59e-23 | 6.06e-21 | 178 |
| GO:0034976110 | Oral cavity | LP | response to endoplasmic reticulum stress | 133/4623 | 256/18723 | 3.84e-21 | 9.24e-19 | 133 |
| GO:003497626 | Skin | AK | response to endoplasmic reticulum stress | 46/1910 | 256/18723 | 9.99e-05 | 1.33e-03 | 46 |
| GO:0034976112 | Skin | cSCC | response to endoplasmic reticulum stress | 128/4864 | 256/18723 | 1.16e-16 | 1.17e-14 | 128 |
| GO:0034976113 | Thyroid | PTC | response to endoplasmic reticulum stress | 161/5968 | 256/18723 | 1.14e-24 | 3.27e-22 | 161 |
| GO:003497633 | Thyroid | ATC | response to endoplasmic reticulum stress | 167/6293 | 256/18723 | 2.62e-25 | 1.03e-22 | 167 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa05010210 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0501038 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0501736 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa0501614 | Liver | Cirrhotic | Huntington disease | 172/2530 | 306/8465 | 1.65e-22 | 1.10e-20 | 6.77e-21 | 172 |
| hsa0501414 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| hsa0502214 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
| hsa0501014 | Liver | Cirrhotic | Alzheimer disease | 180/2530 | 384/8465 | 5.52e-13 | 1.36e-11 | 8.36e-12 | 180 |
| hsa0501710 | Liver | Cirrhotic | Spinocerebellar ataxia | 66/2530 | 143/8465 | 2.58e-05 | 2.15e-04 | 1.32e-04 | 66 |
| hsa041406 | Liver | Cirrhotic | Autophagy - animal | 65/2530 | 141/8465 | 3.10e-05 | 2.47e-04 | 1.52e-04 | 65 |
| hsa0501615 | Liver | Cirrhotic | Huntington disease | 172/2530 | 306/8465 | 1.65e-22 | 1.10e-20 | 6.77e-21 | 172 |
| hsa0501415 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| Page: 1 2 3 |
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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 |
| NRBF2 | SNV | Missense_Mutation | novel | c.295N>G | p.Gln99Glu | p.Q99E | Q96F24 | protein_coding | tolerated(0.07) | benign(0.397) | TCGA-AC-A3QP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| NRBF2 | SNV | Missense_Mutation | novel | c.495N>C | p.Lys165Asn | p.K165N | Q96F24 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NRBF2 | SNV | Missense_Mutation | novel | c.386A>C | p.Glu129Ala | p.E129A | Q96F24 | protein_coding | tolerated(0.12) | benign(0.017) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| NRBF2 | SNV | Missense_Mutation | rs745822881 | c.82G>A | p.Glu28Lys | p.E28K | Q96F24 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NRBF2 | SNV | Missense_Mutation | c.392N>G | p.Gln131Arg | p.Q131R | Q96F24 | protein_coding | tolerated(0.56) | benign(0.003) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD | |
| NRBF2 | SNV | Missense_Mutation | c.182N>T | p.Arg61Met | p.R61M | Q96F24 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| NRBF2 | SNV | Missense_Mutation | c.656N>T | p.Ala219Val | p.A219V | Q96F24 | protein_coding | deleterious(0.04) | benign(0.422) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NRBF2 | SNV | Missense_Mutation | c.4N>A | p.Glu2Lys | p.E2K | Q96F24 | protein_coding | deleterious(0) | benign(0.172) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NRBF2 | SNV | Missense_Mutation | novel | c.487N>A | p.Asp163Asn | p.D163N | Q96F24 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NRBF2 | SNV | Missense_Mutation | c.686N>A | p.Ser229Asn | p.S229N | Q96F24 | protein_coding | tolerated(0.26) | benign(0.009) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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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