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Gene: BRCA1 |
Gene summary for BRCA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BRCA1 | Gene ID | 672 |
| Gene name | BRCA1 DNA repair associated | |
| Gene Alias | BRCAI | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000075 | UniProtAcc | P38398 |
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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 |
| 672 | BRCA1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.76e-02 | 3.19e-01 | -0.1088 |
| 672 | BRCA1 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.03e-16 | 4.99e-01 | -0.1954 |
| 672 | BRCA1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.85e-02 | 3.24e-01 | -0.1526 |
| 672 | BRCA1 | HTA11_696_2000001011 | Human | Colorectum | AD | 8.52e-07 | 4.31e-01 | -0.1464 |
| 672 | BRCA1 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.67e-07 | 4.20e-01 | -0.1001 |
| 672 | BRCA1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.64e-06 | 4.58e-01 | -0.059 |
| 672 | BRCA1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.36e-07 | 3.89e-01 | 0.0674 |
| 672 | BRCA1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.31e-13 | 5.48e-01 | 0.294 |
| 672 | BRCA1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.63e-08 | 4.51e-01 | 0.281 |
| 672 | BRCA1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.77e-11 | 5.33e-01 | 0.3859 |
| 672 | BRCA1 | LZE2T | Human | Esophagus | ESCC | 3.94e-07 | 6.42e-01 | 0.082 |
| 672 | BRCA1 | LZE7T | Human | Esophagus | ESCC | 1.02e-03 | 2.39e-01 | 0.0667 |
| 672 | BRCA1 | LZE21T | Human | Esophagus | ESCC | 6.52e-03 | 2.43e-01 | 0.0655 |
| 672 | BRCA1 | P1T-E | Human | Esophagus | ESCC | 1.64e-05 | 3.37e-01 | 0.0875 |
| 672 | BRCA1 | P2T-E | Human | Esophagus | ESCC | 2.33e-12 | 4.11e-01 | 0.1177 |
| 672 | BRCA1 | P4T-E | Human | Esophagus | ESCC | 1.78e-10 | 2.75e-01 | 0.1323 |
| 672 | BRCA1 | P5T-E | Human | Esophagus | ESCC | 2.65e-08 | 2.36e-01 | 0.1327 |
| 672 | BRCA1 | P8T-E | Human | Esophagus | ESCC | 1.49e-03 | 1.40e-01 | 0.0889 |
| 672 | BRCA1 | P9T-E | Human | Esophagus | ESCC | 8.38e-03 | 1.18e-01 | 0.1131 |
| 672 | BRCA1 | P10T-E | Human | Esophagus | ESCC | 3.00e-03 | 6.98e-02 | 0.116 |
| Page: 1 2 3 4 |
| 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:0097193 | Colorectum | AD | intrinsic apoptotic signaling pathway | 108/3918 | 288/18723 | 6.25e-11 | 6.41e-09 | 108 |
| GO:2001233 | Colorectum | AD | regulation of apoptotic signaling pathway | 119/3918 | 356/18723 | 2.14e-08 | 1.21e-06 | 119 |
| GO:1903320 | Colorectum | AD | regulation of protein modification by small protein conjugation or removal | 86/3918 | 242/18723 | 9.43e-08 | 4.65e-06 | 86 |
| GO:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0051052 | Colorectum | AD | regulation of DNA metabolic process | 116/3918 | 359/18723 | 2.47e-07 | 1.00e-05 | 116 |
| GO:0051054 | Colorectum | AD | positive regulation of DNA metabolic process | 73/3918 | 201/18723 | 3.27e-07 | 1.29e-05 | 73 |
| GO:0071383 | Colorectum | AD | cellular response to steroid hormone stimulus | 73/3918 | 204/18723 | 6.31e-07 | 2.24e-05 | 73 |
| GO:0030522 | Colorectum | AD | intracellular receptor signaling pathway | 87/3918 | 265/18723 | 3.69e-06 | 1.03e-04 | 87 |
| GO:0031396 | Colorectum | AD | regulation of protein ubiquitination | 72/3918 | 210/18723 | 4.50e-06 | 1.21e-04 | 72 |
| GO:0043401 | Colorectum | AD | steroid hormone mediated signaling pathway | 51/3918 | 136/18723 | 6.52e-06 | 1.63e-04 | 51 |
| GO:0000209 | Colorectum | AD | protein polyubiquitination | 78/3918 | 236/18723 | 8.71e-06 | 2.06e-04 | 78 |
| GO:0051494 | Colorectum | AD | negative regulation of cytoskeleton organization | 58/3918 | 163/18723 | 1.04e-05 | 2.40e-04 | 58 |
| GO:0048545 | Colorectum | AD | response to steroid hormone | 104/3918 | 339/18723 | 1.33e-05 | 2.90e-04 | 104 |
| GO:2001234 | Colorectum | AD | negative regulation of apoptotic signaling pathway | 74/3918 | 224/18723 | 1.49e-05 | 3.18e-04 | 74 |
| GO:0009755 | Colorectum | AD | hormone-mediated signaling pathway | 64/3918 | 190/18723 | 2.78e-05 | 5.24e-04 | 64 |
| GO:2001020 | Colorectum | AD | regulation of response to DNA damage stimulus | 71/3918 | 219/18723 | 4.38e-05 | 7.65e-04 | 71 |
| GO:0030518 | Colorectum | AD | intracellular steroid hormone receptor signaling pathway | 43/3918 | 116/18723 | 4.61e-05 | 7.97e-04 | 43 |
| GO:0006631 | Colorectum | AD | fatty acid metabolic process | 114/3918 | 390/18723 | 5.58e-05 | 9.44e-04 | 114 |
| GO:0097191 | Colorectum | AD | extrinsic apoptotic signaling pathway | 68/3918 | 219/18723 | 2.64e-04 | 3.27e-03 | 68 |
| GO:0072593 | Colorectum | AD | reactive oxygen species metabolic process | 73/3918 | 239/18723 | 2.79e-04 | 3.42e-03 | 73 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04120 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa041201 | Colorectum | AD | Ubiquitin mediated proteolysis | 58/2092 | 142/8465 | 1.46e-05 | 1.53e-04 | 9.76e-05 | 58 |
| hsa041202 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa041203 | Colorectum | SER | Ubiquitin mediated proteolysis | 39/1580 | 142/8465 | 6.18e-03 | 3.66e-02 | 2.66e-02 | 39 |
| hsa041204 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa01524 | Colorectum | MSS | Platinum drug resistance | 25/1875 | 73/8465 | 1.17e-02 | 3.99e-02 | 2.44e-02 | 25 |
| hsa041205 | Colorectum | MSS | Ubiquitin mediated proteolysis | 55/1875 | 142/8465 | 5.02e-06 | 6.00e-05 | 3.68e-05 | 55 |
| hsa015241 | Colorectum | MSS | Platinum drug resistance | 25/1875 | 73/8465 | 1.17e-02 | 3.99e-02 | 2.44e-02 | 25 |
| hsa0412027 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa015247 | Esophagus | ESCC | Platinum drug resistance | 56/4205 | 73/8465 | 1.85e-06 | 1.13e-05 | 5.78e-06 | 56 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0412036 | Esophagus | ESCC | Ubiquitin mediated proteolysis | 122/4205 | 142/8465 | 6.53e-20 | 7.29e-18 | 3.74e-18 | 122 |
| hsa0152414 | Esophagus | ESCC | Platinum drug resistance | 56/4205 | 73/8465 | 1.85e-06 | 1.13e-05 | 5.78e-06 | 56 |
| hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0412041 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa015242 | Liver | HCC | Platinum drug resistance | 52/4020 | 73/8465 | 3.14e-05 | 1.88e-04 | 1.04e-04 | 52 |
| hsa0412051 | Liver | HCC | Ubiquitin mediated proteolysis | 110/4020 | 142/8465 | 1.67e-13 | 3.74e-12 | 2.08e-12 | 110 |
| hsa015243 | Liver | HCC | Platinum drug resistance | 52/4020 | 73/8465 | 3.14e-05 | 1.88e-04 | 1.04e-04 | 52 |
| hsa0412020 | Oral cavity | OSCC | Ubiquitin mediated proteolysis | 105/3704 | 142/8465 | 1.83e-13 | 4.37e-12 | 2.23e-12 | 105 |
| hsa015246 | Oral cavity | OSCC | Platinum drug resistance | 51/3704 | 73/8465 | 5.41e-06 | 2.75e-05 | 1.40e-05 | 51 |
| Page: 1 2 |
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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 |
| BRCA1 | TAC | Colorectum | ADJ | KNTC1,FANCA,RAD51AP1, etc. | 1.82e-01 |  |
| BRCA1 | ASC | Colorectum | SER | BRIP1,FANCA,DTL, etc. | 1.14e-01 |  |
| BRCA1 | CD8TEX | Endometrium | Healthy | ATAD5,FAM208A,CASP8AP2, etc. | 1.40e-01 |  |
| BRCA1 | PRO | Esophagus | ESCC | DTL,HELLS,BRCA2, etc. | 1.45e-01 |  |
| BRCA1 | PRO | Esophagus | HGIN | DTL,HELLS,BRCA2, etc. | 3.68e-01 |  |
| BRCA1 | BMEM | Liver | Healthy | KMO,COA7,HMGB1, etc. | 6.26e-02 |  |
| BRCA1 | BAS | Oral cavity | Healthy | MCM3,DUT,MCM5, etc. | 2.11e-01 |  |
| BRCA1 | STM | Pancreas | PanIN | HNRNPUL1,SLX4IP,BRIP1, etc. | 2.91e-01 |  |
| BRCA1 | NKT | Pancreas | ADJ | NBR2,ATAD5,BRIP1, etc. | 3.66e-01 |  |
| BRCA1 | MDSC | Prostate | ADJ | LIG1,MCM4,MCM7, etc. | 8.17e-02 |  |
| ∗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 2 |
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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 |
| BRCA1 | SNV | Missense_Mutation | c.3298N>A | p.Gly1100Arg | p.G1100R | P38398 | protein_coding | tolerated(0.19) | benign(0.053) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| BRCA1 | deletion | Frame_Shift_Del | rs80357522 | c.1961delN | p.Lys654SerfsTer47 | p.K654Sfs*47 | P38398 | protein_coding | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| BRCA1 | insertion | Frame_Shift_Ins | novel | c.2214_2215dupTA | p.Lys739IlefsTer15 | p.K739Ifs*15 | P38398 | protein_coding | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| BRCA1 | deletion | Frame_Shift_Del | rs80357522 | c.1961delN | p.Lys654SerfsTer47 | p.K654Sfs*47 | P38398 | protein_coding | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| BRCA1 | SNV | Missense_Mutation | novel | c.2063N>T | p.Thr688Ile | p.T688I | P38398 | protein_coding | tolerated(1) | benign(0.007) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| BRCA1 | SNV | Missense_Mutation | novel | c.240N>G | p.Ser80Arg | p.S80R | P38398 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| BRCA1 | SNV | Missense_Mutation | novel | c.3728N>A | p.Arg1243Lys | p.R1243K | P38398 | protein_coding | tolerated(0.36) | benign(0.026) | TCGA-A5-A0R9-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| BRCA1 | SNV | Missense_Mutation | rs80357049 | c.3082N>T | p.Arg1028Cys | p.R1028C | P38398 | protein_coding | tolerated(0.13) | possibly_damaging(0.54) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| BRCA1 | SNV | Missense_Mutation | novel | c.385N>T | p.Gly129Cys | p.G129C | P38398 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| BRCA1 | SNV | Missense_Mutation | novel | c.3303N>G | p.Ser1101Arg | p.S1101R | P38398 | protein_coding | tolerated(0.11) | benign(0.26) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
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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 |
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | DOXORUBICIN HYDROCHLORIDE | DOXORUBICIN HYDROCHLORIDE | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | ACRIFLAVINE CHLORIDE | ACRIFLAVINE | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | 7-O-ACETYLAFROMOSIN | CHEMBL446567 | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | PIFEXOLE | PIFEXOLE | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | DOXORUBICIN | DOXORUBICIN | 12698198 | |
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | DNDI1417078 | CHEMBL1320798 | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | Cyclophosphamide | CYCLOPHOSPHAMIDE | 25589624 | |
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | HORMONES | 9133444 | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | MITOMYCIN C | 15782115 | ||
| 672 | BRCA1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE | ABT-767 |
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