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Gene: BARD1 |
Gene summary for BARD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BARD1 | Gene ID | 580 |
| Gene name | BRCA1 associated RING domain 1 | |
| Gene Alias | BARD1 | |
| Cytomap | 2q35 | |
| Gene Type | protein-coding | GO ID | GO:0000209 | UniProtAcc | A0AVN2 |
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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 |
| 580 | BARD1 | CA_HPV_2 | Human | Cervix | CC | 7.31e-03 | 2.32e-01 | 0.0391 |
| 580 | BARD1 | CCI_2 | Human | Cervix | CC | 1.22e-05 | 7.57e-01 | 0.5249 |
| 580 | BARD1 | CCI_3 | Human | Cervix | CC | 1.24e-05 | 5.96e-01 | 0.516 |
| 580 | BARD1 | LZE4T | Human | Esophagus | ESCC | 5.62e-05 | 2.00e-01 | 0.0811 |
| 580 | BARD1 | LZE8T | Human | Esophagus | ESCC | 1.57e-04 | 1.90e-01 | 0.067 |
| 580 | BARD1 | LZE20T | Human | Esophagus | ESCC | 1.03e-04 | 1.43e-01 | 0.0662 |
| 580 | BARD1 | LZE24T | Human | Esophagus | ESCC | 2.23e-06 | 2.00e-01 | 0.0596 |
| 580 | BARD1 | LZE21T | Human | Esophagus | ESCC | 1.45e-02 | 1.74e-01 | 0.0655 |
| 580 | BARD1 | LZE6T | Human | Esophagus | ESCC | 7.37e-03 | 2.03e-01 | 0.0845 |
| 580 | BARD1 | P1T-E | Human | Esophagus | ESCC | 1.02e-11 | 4.93e-01 | 0.0875 |
| 580 | BARD1 | P2T-E | Human | Esophagus | ESCC | 4.57e-21 | 4.98e-01 | 0.1177 |
| 580 | BARD1 | P4T-E | Human | Esophagus | ESCC | 7.28e-08 | 2.16e-01 | 0.1323 |
| 580 | BARD1 | P5T-E | Human | Esophagus | ESCC | 4.26e-14 | 3.52e-01 | 0.1327 |
| 580 | BARD1 | P8T-E | Human | Esophagus | ESCC | 8.30e-19 | 3.61e-01 | 0.0889 |
| 580 | BARD1 | P9T-E | Human | Esophagus | ESCC | 5.51e-07 | 2.02e-01 | 0.1131 |
| 580 | BARD1 | P10T-E | Human | Esophagus | ESCC | 7.75e-16 | 3.37e-01 | 0.116 |
| 580 | BARD1 | P11T-E | Human | Esophagus | ESCC | 1.53e-04 | 1.90e-01 | 0.1426 |
| 580 | BARD1 | P12T-E | Human | Esophagus | ESCC | 3.57e-21 | 3.40e-01 | 0.1122 |
| 580 | BARD1 | P15T-E | Human | Esophagus | ESCC | 4.65e-20 | 4.44e-01 | 0.1149 |
| 580 | BARD1 | P16T-E | Human | Esophagus | ESCC | 9.33e-09 | 2.12e-01 | 0.1153 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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:004217610 | Cervix | CC | regulation of protein catabolic process | 104/2311 | 391/18723 | 9.39e-15 | 9.36e-12 | 104 |
| GO:004573210 | Cervix | CC | positive regulation of protein catabolic process | 65/2311 | 231/18723 | 7.44e-11 | 1.39e-08 | 65 |
| GO:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
| GO:00512359 | Cervix | CC | maintenance of location | 78/2311 | 327/18723 | 5.18e-09 | 4.92e-07 | 78 |
| GO:00069139 | Cervix | CC | nucleocytoplasmic transport | 71/2311 | 301/18723 | 4.04e-08 | 2.54e-06 | 71 |
| GO:00511699 | Cervix | CC | nuclear transport | 71/2311 | 301/18723 | 4.04e-08 | 2.54e-06 | 71 |
| GO:005165110 | Cervix | CC | maintenance of location in cell | 55/2311 | 214/18723 | 6.63e-08 | 3.85e-06 | 55 |
| GO:00345048 | Cervix | CC | protein localization to nucleus | 68/2311 | 290/18723 | 9.91e-08 | 5.25e-06 | 68 |
| GO:00002097 | Cervix | CC | protein polyubiquitination | 58/2311 | 236/18723 | 1.57e-07 | 7.41e-06 | 58 |
| GO:19033119 | Cervix | CC | regulation of mRNA metabolic process | 64/2311 | 288/18723 | 1.71e-06 | 5.64e-05 | 64 |
| GO:00468229 | Cervix | CC | regulation of nucleocytoplasmic transport | 31/2311 | 106/18723 | 2.68e-06 | 7.87e-05 | 31 |
| GO:00323868 | Cervix | CC | regulation of intracellular transport | 71/2311 | 337/18723 | 3.70e-06 | 9.74e-05 | 71 |
| GO:00331579 | Cervix | CC | regulation of intracellular protein transport | 52/2311 | 229/18723 | 8.16e-06 | 1.88e-04 | 52 |
| GO:00511689 | Cervix | CC | nuclear export | 38/2311 | 154/18723 | 1.86e-05 | 3.46e-04 | 38 |
| GO:00325077 | Cervix | CC | maintenance of protein location in cell | 21/2311 | 65/18723 | 2.03e-05 | 3.71e-04 | 21 |
| GO:00018949 | Cervix | CC | tissue homeostasis | 57/2311 | 268/18723 | 2.43e-05 | 4.21e-04 | 57 |
| GO:004518510 | Cervix | CC | maintenance of protein location | 26/2311 | 94/18723 | 4.85e-05 | 7.34e-04 | 26 |
| GO:00602498 | Cervix | CC | anatomical structure homeostasis | 63/2311 | 314/18723 | 6.03e-05 | 8.68e-04 | 63 |
| GO:00506849 | Cervix | CC | regulation of mRNA processing | 33/2311 | 137/18723 | 1.06e-04 | 1.35e-03 | 33 |
| GO:00468259 | Cervix | CC | regulation of protein export from nucleus | 12/2311 | 30/18723 | 1.23e-04 | 1.53e-03 | 12 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
| BARD1 | SNV | Missense_Mutation | novel | c.832G>T | p.Val278Phe | p.V278F | Q99728 | protein_coding | tolerated(0.18) | benign(0.005) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| BARD1 | SNV | Missense_Mutation | c.664N>T | p.Ala222Ser | p.A222S | Q99728 | protein_coding | tolerated(0.64) | benign(0.036) | TCGA-EK-A3GM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BARD1 | SNV | Missense_Mutation | c.547N>C | p.Val183Leu | p.V183L | Q99728 | protein_coding | tolerated(0.21) | benign(0.077) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| BARD1 | SNV | Missense_Mutation | c.1323A>G | p.Ile441Met | p.I441M | Q99728 | protein_coding | deleterious(0) | possibly_damaging(0.69) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| BARD1 | SNV | Missense_Mutation | novel | c.914N>C | p.Lys305Thr | p.K305T | Q99728 | protein_coding | tolerated(0.18) | benign(0) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| BARD1 | SNV | Missense_Mutation | novel | c.422N>C | p.Asn141Thr | p.N141T | Q99728 | protein_coding | tolerated(0.1) | benign(0.081) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| BARD1 | SNV | Missense_Mutation | rs758749603 | c.420G>T | p.Lys140Asn | p.K140N | Q99728 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| BARD1 | SNV | Missense_Mutation | novel | c.695N>G | p.Lys232Arg | p.K232R | Q99728 | protein_coding | tolerated(0.09) | benign(0.395) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| BARD1 | SNV | Missense_Mutation | novel | c.34N>T | p.Pro12Ser | p.P12S | Q99728 | protein_coding | deleterious_low_confidence(0.03) | benign(0.306) | TCGA-A5-A2K3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
| BARD1 | SNV | Missense_Mutation | novel | c.938N>A | p.Ser313Tyr | p.S313Y | Q99728 | protein_coding | deleterious(0.01) | possibly_damaging(0.77) | 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 |
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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 |
| 580 | BARD1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR | APITOLISIB | APITOLISIB | 28389374 | |
| 580 | BARD1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR | carboplatin | CARBOPLATIN | 30071039 | |
| 580 | BARD1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR | trastuzumab | TRASTUZUMAB | 30071039 | |
| 580 | BARD1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR | docetaxel | DOCETAXEL | 30071039 | |
| 580 | BARD1 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR | OLAPARIB | OLAPARIB | 28389374,27197561 |
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