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Gene: BOP1 |
Gene summary for BOP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BOP1 | Gene ID | 23246 |
| Gene name | BOP1 ribosomal biogenesis factor | |
| Gene Alias | BOP1 | |
| Cytomap | 8q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0000027 | UniProtAcc | Q14137 |
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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 |
| 23246 | BOP1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 9.37e-08 | 3.24e-01 | -0.059 |
| 23246 | BOP1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.62e-05 | 2.89e-01 | 0.096 |
| 23246 | BOP1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.98e-08 | 2.81e-01 | 0.0674 |
| 23246 | BOP1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.23e-02 | 3.02e-01 | 0.0588 |
| 23246 | BOP1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.64e-37 | 8.95e-01 | 0.3859 |
| 23246 | BOP1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.27e-15 | 4.71e-01 | 0.3005 |
| 23246 | BOP1 | CRC-3-11773 | Human | Colorectum | CRC | 2.12e-14 | 5.85e-01 | 0.2564 |
| 23246 | BOP1 | LZE20T | Human | Esophagus | ESCC | 2.13e-04 | 2.29e-01 | 0.0662 |
| 23246 | BOP1 | LZE22T | Human | Esophagus | ESCC | 1.57e-06 | 4.58e-01 | 0.068 |
| 23246 | BOP1 | LZE24T | Human | Esophagus | ESCC | 7.15e-21 | 5.66e-01 | 0.0596 |
| 23246 | BOP1 | LZE21T | Human | Esophagus | ESCC | 9.05e-05 | 4.96e-01 | 0.0655 |
| 23246 | BOP1 | P1T-E | Human | Esophagus | ESCC | 8.48e-05 | 2.99e-01 | 0.0875 |
| 23246 | BOP1 | P2T-E | Human | Esophagus | ESCC | 3.48e-27 | 5.64e-01 | 0.1177 |
| 23246 | BOP1 | P4T-E | Human | Esophagus | ESCC | 6.35e-23 | 5.97e-01 | 0.1323 |
| 23246 | BOP1 | P5T-E | Human | Esophagus | ESCC | 7.53e-37 | 7.40e-01 | 0.1327 |
| 23246 | BOP1 | P8T-E | Human | Esophagus | ESCC | 7.24e-10 | 2.25e-01 | 0.0889 |
| 23246 | BOP1 | P9T-E | Human | Esophagus | ESCC | 4.34e-24 | 6.70e-01 | 0.1131 |
| 23246 | BOP1 | P10T-E | Human | Esophagus | ESCC | 1.53e-22 | 4.07e-01 | 0.116 |
| 23246 | BOP1 | P11T-E | Human | Esophagus | ESCC | 3.55e-09 | 5.06e-01 | 0.1426 |
| 23246 | BOP1 | P12T-E | Human | Esophagus | ESCC | 1.47e-43 | 9.53e-01 | 0.1122 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| 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:0022618 | Colorectum | AD | ribonucleoprotein complex assembly | 92/3918 | 220/18723 | 1.49e-12 | 2.60e-10 | 92 |
| GO:0071826 | Colorectum | AD | ribonucleoprotein complex subunit organization | 94/3918 | 227/18723 | 1.70e-12 | 2.87e-10 | 94 |
| GO:0022613 | Colorectum | AD | ribonucleoprotein complex biogenesis | 151/3918 | 463/18723 | 1.96e-09 | 1.39e-07 | 151 |
| GO:0072331 | Colorectum | AD | signal transduction by p53 class mediator | 58/3918 | 163/18723 | 1.04e-05 | 2.40e-04 | 58 |
| GO:0042255 | Colorectum | AD | ribosome assembly | 28/3918 | 61/18723 | 1.08e-05 | 2.47e-04 | 28 |
| GO:1901796 | Colorectum | AD | regulation of signal transduction by p53 class mediator | 36/3918 | 93/18723 | 6.58e-05 | 1.07e-03 | 36 |
| GO:0042273 | Colorectum | AD | ribosomal large subunit biogenesis | 28/3918 | 72/18723 | 3.74e-04 | 4.31e-03 | 28 |
| GO:0042254 | Colorectum | AD | ribosome biogenesis | 84/3918 | 299/18723 | 1.82e-03 | 1.50e-02 | 84 |
| GO:0000027 | Colorectum | AD | ribosomal large subunit assembly | 12/3918 | 27/18723 | 5.07e-03 | 3.38e-02 | 12 |
| GO:00718262 | Colorectum | MSS | ribonucleoprotein complex subunit organization | 90/3467 | 227/18723 | 6.88e-14 | 1.78e-11 | 90 |
| GO:00226182 | Colorectum | MSS | ribonucleoprotein complex assembly | 88/3467 | 220/18723 | 7.12e-14 | 1.78e-11 | 88 |
| GO:00226132 | Colorectum | MSS | ribonucleoprotein complex biogenesis | 144/3467 | 463/18723 | 2.76e-11 | 3.67e-09 | 144 |
| GO:00422552 | Colorectum | MSS | ribosome assembly | 26/3467 | 61/18723 | 1.15e-05 | 2.71e-04 | 26 |
| GO:00422732 | Colorectum | MSS | ribosomal large subunit biogenesis | 28/3467 | 72/18723 | 4.16e-05 | 7.83e-04 | 28 |
| GO:00723312 | Colorectum | MSS | signal transduction by p53 class mediator | 49/3467 | 163/18723 | 2.30e-04 | 3.19e-03 | 49 |
| GO:00422542 | Colorectum | MSS | ribosome biogenesis | 79/3467 | 299/18723 | 4.32e-04 | 5.23e-03 | 79 |
| GO:19017962 | Colorectum | MSS | regulation of signal transduction by p53 class mediator | 30/3467 | 93/18723 | 1.03e-03 | 1.02e-02 | 30 |
| GO:0000470 | Colorectum | MSS | maturation of LSU-rRNA | 12/3467 | 28/18723 | 2.53e-03 | 2.02e-02 | 12 |
| GO:0006364 | Colorectum | MSS | rRNA processing | 58/3467 | 225/18723 | 4.17e-03 | 3.03e-02 | 58 |
| GO:0016072 | Colorectum | MSS | rRNA metabolic process | 60/3467 | 236/18723 | 5.01e-03 | 3.46e-02 | 60 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| BOP1 | SNV | Missense_Mutation | novel | c.2015N>C | p.His672Pro | p.H672P | Q14137 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A1FW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| BOP1 | SNV | Missense_Mutation | rs782512248 | c.226N>A | p.Glu76Lys | p.E76K | Q14137 | protein_coding | tolerated(0.33) | benign(0.019) | TCGA-AR-A0TZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Doxorubicin | PD |
| BOP1 | SNV | Missense_Mutation | novel | c.2015N>C | p.His672Pro | p.H672P | Q14137 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AR-A1AT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD |
| BOP1 | SNV | Missense_Mutation | novel | c.760N>A | p.Glu254Lys | p.E254K | Q14137 | protein_coding | tolerated(0.75) | benign(0.012) | TCGA-D8-A73U-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| BOP1 | insertion | Frame_Shift_Ins | novel | c.445_446insC | p.His149ProfsTer20 | p.H149Pfs*20 | Q14137 | protein_coding | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| BOP1 | insertion | In_Frame_Ins | novel | c.146_147insAGATTATGGACAACTACGTTACCCCTTCTTGAGTTT | p.Asp49delinsGluAspTyrGlyGlnLeuArgTyrProPheLeuSerPhe | p.D49delinsEDYGQLRYPFLSF | Q14137 | protein_coding | TCGA-BH-A0HB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| BOP1 | SNV | Missense_Mutation | novel | c.473N>A | p.Arg158His | p.R158H | Q14137 | protein_coding | deleterious(0) | probably_damaging(0.939) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| BOP1 | SNV | Missense_Mutation | novel | c.811N>T | p.Arg271Cys | p.R271C | Q14137 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-C5-A1BJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| BOP1 | SNV | Missense_Mutation | novel | c.1733G>T | p.Ser578Ile | p.S578I | Q14137 | protein_coding | deleterious(0.03) | benign(0.325) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| BOP1 | SNV | Missense_Mutation | novel | c.1399G>A | p.Ala467Thr | p.A467T | Q14137 | protein_coding | tolerated(0.51) | benign(0.003) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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