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Gene: BRAP |
Gene summary for BRAP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BRAP | Gene ID | 8315 |
| Gene name | BRCA1 associated protein | |
| Gene Alias | BRAP2 | |
| Cytomap | 12q24.12 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q59H81 |
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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 |
| 8315 | BRAP | LZE4T | Human | Esophagus | ESCC | 5.30e-04 | 7.72e-02 | 0.0811 |
| 8315 | BRAP | LZE20T | Human | Esophagus | ESCC | 6.89e-08 | 1.97e-01 | 0.0662 |
| 8315 | BRAP | LZE24T | Human | Esophagus | ESCC | 1.08e-04 | 2.31e-01 | 0.0596 |
| 8315 | BRAP | P1T-E | Human | Esophagus | ESCC | 2.71e-11 | 3.77e-01 | 0.0875 |
| 8315 | BRAP | P2T-E | Human | Esophagus | ESCC | 1.02e-27 | 5.06e-01 | 0.1177 |
| 8315 | BRAP | P4T-E | Human | Esophagus | ESCC | 9.83e-12 | 3.27e-01 | 0.1323 |
| 8315 | BRAP | P5T-E | Human | Esophagus | ESCC | 4.99e-09 | 1.98e-01 | 0.1327 |
| 8315 | BRAP | P8T-E | Human | Esophagus | ESCC | 8.34e-16 | 2.39e-01 | 0.0889 |
| 8315 | BRAP | P9T-E | Human | Esophagus | ESCC | 5.05e-12 | 1.41e-01 | 0.1131 |
| 8315 | BRAP | P10T-E | Human | Esophagus | ESCC | 2.22e-16 | 1.97e-01 | 0.116 |
| 8315 | BRAP | P11T-E | Human | Esophagus | ESCC | 3.26e-16 | 4.84e-01 | 0.1426 |
| 8315 | BRAP | P12T-E | Human | Esophagus | ESCC | 2.33e-10 | 1.93e-01 | 0.1122 |
| 8315 | BRAP | P15T-E | Human | Esophagus | ESCC | 5.19e-25 | 3.12e-01 | 0.1149 |
| 8315 | BRAP | P16T-E | Human | Esophagus | ESCC | 5.65e-14 | 2.54e-01 | 0.1153 |
| 8315 | BRAP | P17T-E | Human | Esophagus | ESCC | 1.50e-04 | 2.00e-01 | 0.1278 |
| 8315 | BRAP | P19T-E | Human | Esophagus | ESCC | 1.58e-03 | 4.91e-01 | 0.1662 |
| 8315 | BRAP | P20T-E | Human | Esophagus | ESCC | 2.05e-17 | 3.63e-01 | 0.1124 |
| 8315 | BRAP | P21T-E | Human | Esophagus | ESCC | 2.62e-21 | 3.19e-01 | 0.1617 |
| 8315 | BRAP | P22T-E | Human | Esophagus | ESCC | 1.31e-17 | 2.14e-01 | 0.1236 |
| 8315 | BRAP | P23T-E | Human | Esophagus | ESCC | 7.74e-20 | 4.37e-01 | 0.108 |
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| 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 |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:000726510 | Esophagus | ESCC | Ras protein signal transduction | 201/8552 | 337/18723 | 1.44e-07 | 2.30e-06 | 201 |
| GO:00072659 | Oral cavity | OSCC | Ras protein signal transduction | 185/7305 | 337/18723 | 1.95e-09 | 4.60e-08 | 185 |
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| 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 |
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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. |
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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 |
| BRAP | SNV | Missense_Mutation | novel | c.128C>T | p.Ser43Leu | p.S43L | Q7Z569 | protein_coding | tolerated(0.31) | benign(0) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| BRAP | SNV | Missense_Mutation | c.100N>A | p.Glu34Lys | p.E34K | Q7Z569 | protein_coding | tolerated(0.3) | benign(0.025) | TCGA-A7-A26E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD | |
| BRAP | SNV | Missense_Mutation | c.889N>A | p.Asp297Asn | p.D297N | Q7Z569 | protein_coding | tolerated(0.05) | possibly_damaging(0.58) | TCGA-AC-A3BB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | CR | |
| BRAP | SNV | Missense_Mutation | novel | c.1127N>A | p.Arg376Gln | p.R376Q | Q7Z569 | protein_coding | deleterious(0) | probably_damaging(0.914) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| BRAP | SNV | Missense_Mutation | c.94T>G | p.Ser32Ala | p.S32A | Q7Z569 | protein_coding | tolerated(0.09) | benign(0.025) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BRAP | SNV | Missense_Mutation | novel | c.1220A>C | p.Glu407Ala | p.E407A | Q7Z569 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-B6-A2IU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| BRAP | insertion | Nonsense_Mutation | novel | c.109_110insCCTGCCTCGGCCTCCCAAAGTGCTGGAATTACAGGT | p.Lys37delinsThrCysLeuGlyLeuProLysCysTrpAsnTyrArgTer | p.K37delinsTCLGLPKCWNYR* | Q7Z569 | protein_coding | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| BRAP | insertion | Nonsense_Mutation | novel | c.246_247insTAAGTACTCAAAAGC | p.Asp82_Glu83insTer | p.D82_E83ins* | Q7Z569 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| BRAP | insertion | In_Frame_Ins | novel | c.245-1_245insCTAATTGTAAAAGTCATA | p.Asp82delinsAlaAsnCysLysSerHisAsn | p.D82delinsANCKSHN | Q7Z569 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| BRAP | SNV | Missense_Mutation | c.476N>A | p.Arg159His | p.R159H | Q7Z569 | protein_coding | deleterious(0) | benign(0.396) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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 |
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