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Gene: BMS1 |
Gene summary for BMS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BMS1 | Gene ID | 9790 |
| Gene name | BMS1 ribosome biogenesis factor | |
| Gene Alias | ACC | |
| Cytomap | 10q11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000462 | UniProtAcc | Q14692 |
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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 |
| 9790 | BMS1 | LZE4T | Human | Esophagus | ESCC | 3.44e-14 | 4.76e-01 | 0.0811 |
| 9790 | BMS1 | LZE8T | Human | Esophagus | ESCC | 2.54e-03 | 1.58e-01 | 0.067 |
| 9790 | BMS1 | LZE24T | Human | Esophagus | ESCC | 7.38e-08 | 2.56e-01 | 0.0596 |
| 9790 | BMS1 | P1T-E | Human | Esophagus | ESCC | 3.03e-03 | 1.92e-01 | 0.0875 |
| 9790 | BMS1 | P2T-E | Human | Esophagus | ESCC | 1.99e-20 | 3.71e-01 | 0.1177 |
| 9790 | BMS1 | P4T-E | Human | Esophagus | ESCC | 2.51e-10 | 3.35e-01 | 0.1323 |
| 9790 | BMS1 | P5T-E | Human | Esophagus | ESCC | 3.67e-15 | 2.87e-01 | 0.1327 |
| 9790 | BMS1 | P8T-E | Human | Esophagus | ESCC | 4.69e-18 | 2.07e-01 | 0.0889 |
| 9790 | BMS1 | P9T-E | Human | Esophagus | ESCC | 8.40e-07 | 9.64e-02 | 0.1131 |
| 9790 | BMS1 | P10T-E | Human | Esophagus | ESCC | 2.34e-12 | 1.29e-01 | 0.116 |
| 9790 | BMS1 | P11T-E | Human | Esophagus | ESCC | 1.90e-12 | 5.10e-01 | 0.1426 |
| 9790 | BMS1 | P12T-E | Human | Esophagus | ESCC | 2.73e-29 | 6.66e-01 | 0.1122 |
| 9790 | BMS1 | P15T-E | Human | Esophagus | ESCC | 5.76e-12 | 3.48e-01 | 0.1149 |
| 9790 | BMS1 | P16T-E | Human | Esophagus | ESCC | 1.08e-18 | 2.34e-01 | 0.1153 |
| 9790 | BMS1 | P17T-E | Human | Esophagus | ESCC | 2.41e-04 | 3.57e-01 | 0.1278 |
| 9790 | BMS1 | P19T-E | Human | Esophagus | ESCC | 3.91e-02 | 3.19e-01 | 0.1662 |
| 9790 | BMS1 | P20T-E | Human | Esophagus | ESCC | 7.59e-07 | 1.76e-01 | 0.1124 |
| 9790 | BMS1 | P21T-E | Human | Esophagus | ESCC | 1.44e-23 | 5.54e-01 | 0.1617 |
| 9790 | BMS1 | P22T-E | Human | Esophagus | ESCC | 1.11e-14 | 1.90e-01 | 0.1236 |
| 9790 | BMS1 | P23T-E | Human | Esophagus | ESCC | 8.91e-23 | 6.77e-01 | 0.108 |
| 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:00062602 | Cervix | CC | DNA replication | 48/2311 | 260/18723 | 2.70e-03 | 1.85e-02 | 48 |
| GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00304904 | Esophagus | ESCC | maturation of SSU-rRNA | 45/8552 | 50/18723 | 5.07e-11 | 1.63e-09 | 45 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00004623 | Esophagus | ESCC | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 32/8552 | 37/18723 | 2.96e-07 | 4.23e-06 | 32 |
| GO:00004693 | Esophagus | ESCC | cleavage involved in rRNA processing | 24/8552 | 27/18723 | 3.48e-06 | 3.84e-05 | 24 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:00004783 | Esophagus | ESCC | endonucleolytic cleavage involved in rRNA processing | 14/8552 | 15/18723 | 1.47e-04 | 9.85e-04 | 14 |
| GO:00004793 | Esophagus | ESCC | endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 14/8552 | 15/18723 | 1.47e-04 | 9.85e-04 | 14 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| BMS1 | SNV | Missense_Mutation | novel | c.1600G>C | p.Glu534Gln | p.E534Q | Q14692 | protein_coding | tolerated(0.11) | benign(0.261) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| BMS1 | SNV | Missense_Mutation | rs764660270 | c.787G>A | p.Asp263Asn | p.D263N | Q14692 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| BMS1 | SNV | Missense_Mutation | c.1033G>T | p.Val345Leu | p.V345L | Q14692 | protein_coding | tolerated(0.38) | benign(0.038) | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | CR | ||
| BMS1 | SNV | Missense_Mutation | c.1823A>T | p.Glu608Val | p.E608V | Q14692 | protein_coding | tolerated(0.1) | benign(0.036) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BMS1 | SNV | Missense_Mutation | c.3692T>A | p.Leu1231Gln | p.L1231Q | Q14692 | protein_coding | tolerated(0.61) | benign(0.005) | TCGA-D8-A143-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| BMS1 | SNV | Missense_Mutation | c.559N>C | p.Asp187His | p.D187H | Q14692 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BMS1 | insertion | Frame_Shift_Ins | novel | c.2205_2206insCGTGCAGGAGCACAGGAGCCCCACACATGTAGAGCAAT | p.Phe737AlafsTer24 | p.F737Afs*24 | Q14692 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| BMS1 | insertion | Nonsense_Mutation | novel | c.1925_1926insTGTGAAGATATTTCCGTTTAGCAATTATTTGGATGGGGCCAGAAGTTAGC | p.Glu642AspfsTer17 | p.E642Dfs*17 | Q14692 | protein_coding | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD | ||
| BMS1 | SNV | Missense_Mutation | novel | c.1375G>A | p.Gly459Ser | p.G459S | Q14692 | protein_coding | tolerated(0.36) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| BMS1 | SNV | Missense_Mutation | novel | c.2863C>T | p.Pro955Ser | p.P955S | Q14692 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | 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 12 13 14 15 |
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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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