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Gene: BRAF |
Gene summary for BRAF |
Gene summary. |
Gene information | Species | Human | Gene symbol | BRAF | Gene ID | 673 |
Gene name | B-Raf proto-oncogene, serine/threonine kinase | |
Gene Alias | B-RAF1 | |
Cytomap | 7q34 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P15056 |
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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 |
673 | BRAF | CCI_3 | Human | Cervix | CC | 3.83e-03 | 5.86e-01 | 0.516 |
673 | BRAF | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.44e-10 | -3.82e-01 | 0.0155 |
673 | BRAF | HTA11_347_2000001011 | Human | Colorectum | AD | 1.74e-02 | 4.16e-01 | -0.1954 |
673 | BRAF | HTA11_866_3004761011 | Human | Colorectum | AD | 3.43e-04 | -3.75e-01 | 0.096 |
673 | BRAF | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.40e-04 | -3.57e-01 | 0.3005 |
673 | BRAF | A001-C-207 | Human | Colorectum | FAP | 2.43e-05 | -3.29e-01 | 0.1278 |
673 | BRAF | A015-C-203 | Human | Colorectum | FAP | 5.20e-39 | -7.01e-01 | -0.1294 |
673 | BRAF | A015-C-204 | Human | Colorectum | FAP | 2.11e-11 | -4.81e-01 | -0.0228 |
673 | BRAF | A014-C-040 | Human | Colorectum | FAP | 8.13e-06 | -3.58e-01 | -0.1184 |
673 | BRAF | A002-C-201 | Human | Colorectum | FAP | 4.49e-18 | -4.36e-01 | 0.0324 |
673 | BRAF | A001-C-119 | Human | Colorectum | FAP | 1.39e-11 | -5.17e-01 | -0.1557 |
673 | BRAF | A001-C-108 | Human | Colorectum | FAP | 4.76e-20 | -4.38e-01 | -0.0272 |
673 | BRAF | A002-C-205 | Human | Colorectum | FAP | 5.27e-27 | -4.54e-01 | -0.1236 |
673 | BRAF | A001-C-104 | Human | Colorectum | FAP | 7.13e-07 | -2.98e-01 | 0.0184 |
673 | BRAF | A015-C-005 | Human | Colorectum | FAP | 2.75e-05 | -3.01e-01 | -0.0336 |
673 | BRAF | A015-C-006 | Human | Colorectum | FAP | 1.71e-25 | -7.36e-01 | -0.0994 |
673 | BRAF | A015-C-106 | Human | Colorectum | FAP | 6.28e-13 | -3.85e-01 | -0.0511 |
673 | BRAF | A002-C-114 | Human | Colorectum | FAP | 3.23e-30 | -6.78e-01 | -0.1561 |
673 | BRAF | A015-C-104 | Human | Colorectum | FAP | 3.69e-43 | -7.49e-01 | -0.1899 |
673 | BRAF | A001-C-014 | Human | Colorectum | FAP | 7.78e-17 | -3.72e-01 | 0.0135 |
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Transcriptomic changes along malignancy continuum. |
∗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:009015031 | Thyroid | ATC | establishment of protein localization to membrane | 150/6293 | 260/18723 | 1.05e-15 | 7.96e-14 | 150 |
GO:0038127111 | Thyroid | ATC | ERBB signaling pathway | 71/6293 | 121/18723 | 1.31e-08 | 2.69e-07 | 71 |
GO:001810519 | Thyroid | ATC | peptidyl-serine phosphorylation | 153/6293 | 315/18723 | 2.28e-08 | 4.42e-07 | 153 |
GO:001820917 | Thyroid | ATC | peptidyl-serine modification | 161/6293 | 338/18723 | 5.23e-08 | 9.44e-07 | 161 |
GO:0007173111 | Thyroid | ATC | epidermal growth factor receptor signaling pathway | 63/6293 | 108/18723 | 1.15e-07 | 1.92e-06 | 63 |
GO:0010038210 | Thyroid | ATC | response to metal ion | 165/6293 | 373/18723 | 1.07e-05 | 1.05e-04 | 165 |
GO:005159225 | Thyroid | ATC | response to calcium ion | 69/6293 | 149/18723 | 8.43e-04 | 4.62e-03 | 69 |
GO:007124124 | Thyroid | ATC | cellular response to inorganic substance | 98/6293 | 226/18723 | 1.35e-03 | 7.02e-03 | 98 |
GO:003313512 | Thyroid | ATC | regulation of peptidyl-serine phosphorylation | 65/6293 | 144/18723 | 2.57e-03 | 1.18e-02 | 65 |
GO:007124823 | Thyroid | ATC | cellular response to metal ion | 82/6293 | 197/18723 | 1.11e-02 | 3.99e-02 | 82 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0520820 | Cervix | CC | Chemical carcinogenesis - reactive oxygen species | 92/1267 | 223/8465 | 4.71e-22 | 5.09e-20 | 3.01e-20 | 92 |
hsa0501018 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
hsa0502218 | Cervix | CC | Pathways of neurodegeneration - multiple diseases | 128/1267 | 476/8465 | 2.87e-12 | 9.29e-11 | 5.50e-11 | 128 |
hsa0520516 | Cervix | CC | Proteoglycans in cancer | 60/1267 | 205/8465 | 9.13e-08 | 1.18e-06 | 7.00e-07 | 60 |
hsa0451010 | Cervix | CC | Focal adhesion | 59/1267 | 203/8465 | 1.53e-07 | 1.84e-06 | 1.09e-06 | 59 |
hsa0481016 | Cervix | CC | Regulation of actin cytoskeleton | 64/1267 | 229/8465 | 2.24e-07 | 2.59e-06 | 1.53e-06 | 64 |
hsa0401512 | Cervix | CC | Rap1 signaling pathway | 56/1267 | 210/8465 | 6.23e-06 | 5.61e-05 | 3.32e-05 | 56 |
hsa0401210 | Cervix | CC | ErbB signaling pathway | 28/1267 | 85/8465 | 2.40e-05 | 1.82e-04 | 1.08e-04 | 28 |
hsa0521010 | Cervix | CC | Colorectal cancer | 27/1267 | 86/8465 | 8.60e-05 | 5.57e-04 | 3.30e-04 | 27 |
hsa052197 | Cervix | CC | Bladder cancer | 16/1267 | 41/8465 | 1.45e-04 | 9.05e-04 | 5.35e-04 | 16 |
hsa052148 | Cervix | CC | Glioma | 24/1267 | 75/8465 | 1.51e-04 | 9.20e-04 | 5.44e-04 | 24 |
hsa052128 | Cervix | CC | Pancreatic cancer | 24/1267 | 76/8465 | 1.89e-04 | 1.11e-03 | 6.55e-04 | 24 |
hsa015223 | Cervix | CC | Endocrine resistance | 28/1267 | 98/8465 | 3.82e-04 | 1.87e-03 | 1.11e-03 | 28 |
hsa052157 | Cervix | CC | Prostate cancer | 27/1267 | 97/8465 | 7.54e-04 | 3.39e-03 | 2.01e-03 | 27 |
hsa0521310 | Cervix | CC | Endometrial cancer | 18/1267 | 58/8465 | 1.46e-03 | 6.30e-03 | 3.73e-03 | 18 |
hsa052234 | Cervix | CC | Non-small cell lung cancer | 21/1267 | 72/8465 | 1.48e-03 | 6.32e-03 | 3.74e-03 | 21 |
hsa0522510 | Cervix | CC | Hepatocellular carcinoma | 40/1267 | 168/8465 | 1.52e-03 | 6.39e-03 | 3.78e-03 | 40 |
hsa052119 | Cervix | CC | Renal cell carcinoma | 20/1267 | 69/8465 | 2.07e-03 | 8.17e-03 | 4.83e-03 | 20 |
hsa0522014 | Cervix | CC | Chronic myeloid leukemia | 21/1267 | 76/8465 | 3.08e-03 | 1.19e-02 | 7.03e-03 | 21 |
hsa0492812 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
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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 |
BRAF | SNV | Missense_Mutation | novel | c.335N>G | p.Ser112Cys | p.S112C | P15056 | protein_coding | deleterious(0.04) | possibly_damaging(0.846) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
BRAF | SNV | Missense_Mutation | c.1345N>A | p.Asp449Asn | p.D449N | P15056 | protein_coding | tolerated(0.67) | possibly_damaging(0.876) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
BRAF | SNV | Missense_Mutation | c.2093A>G | p.Lys698Arg | p.K698R | P15056 | protein_coding | deleterious(0.01) | benign(0.011) | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
BRAF | SNV | Missense_Mutation | novel | c.1297N>A | p.Glu433Lys | p.E433K | P15056 | protein_coding | tolerated(0.22) | benign(0.04) | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
BRAF | SNV | Missense_Mutation | c.1610T>C | p.Leu537Ser | p.L537S | P15056 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E2-A150-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
BRAF | SNV | Missense_Mutation | c.1040N>T | p.Arg347Leu | p.R347L | P15056 | protein_coding | tolerated(0.18) | benign(0.224) | TCGA-E2-A1B5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
BRAF | SNV | Missense_Mutation | novel | c.1706N>A | p.Ala569Asp | p.A569D | P15056 | protein_coding | deleterious(0) | benign(0.265) | TCGA-S3-AA10-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | CR |
BRAF | insertion | Nonsense_Mutation | novel | c.267_268insAATAAGTAACTTGTTCTTGTCCGTCATACTCCCAGTTTAACAATT | p.Leu89_Asp90insAsnLysTerLeuValLeuValArgHisThrProSerLeuThrIle | p.L89_D90insNK*LVLVRHTPSLTI | P15056 | protein_coding | TCGA-A8-A09N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
BRAF | insertion | Frame_Shift_Ins | novel | c.2146_2147insCACCTCGCCGGCCTGGTTTTTATTT | p.Leu716ProfsTer37 | p.L716Pfs*37 | P15056 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
BRAF | SNV | Missense_Mutation | c.1202N>T | p.Thr401Ile | p.T401I | P15056 | protein_coding | tolerated(0.08) | benign(0.026) | TCGA-EA-A1QT-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | TRAMETINIB DIMETHYL SULFOXIDE | 25435907,28480077,28078132 | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | DUAL IGF-1R/INSR INHIBITOR BMS-754807 | 25527633 | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | AMG 232 | 25567130 | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | PLX3397 | PEXIDARTINIB | 25939769 | |
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | PLX7904 | 26466569,27523909 | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | PLX8394 | PLX8394 | 27834212,24422853 | |
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | Vemurafenib | VEMURAFENIB | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | Pimasertib | PIMASERTIB | 23629727 | |
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | vemurafenib | VEMURAFENIB | ||
673 | BRAF | KINASE, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE, DRUG RESISTANCE, ENZYME, DRUGGABLE GENOME | GSK2126458 | OMIPALISIB | 22389471 |
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