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Gene: BMP6 |
Gene summary for BMP6 |
Gene summary. |
Gene information | Species | Human | Gene symbol | BMP6 | Gene ID | 654 |
Gene name | bone morphogenetic protein 6 | |
Gene Alias | VGR | |
Cytomap | 6p24.3 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | B4DUF7 |
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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 |
654 | BMP6 | GSM5353218_PA_PB1B_Pool_1_2_S74_L003 | Human | Prostate | Tumor | 3.54e-05 | 6.25e-01 | 0.1479 |
654 | BMP6 | GSM5353220_PA_PB1B_Pool_3_S51_L002 | Human | Prostate | Tumor | 2.22e-03 | 5.50e-01 | 0.1531 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Prostate | BPH: Benign Prostatic Hyperplasia |
∗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:000206418 | Prostate | Tumor | epithelial cell development | 88/3246 | 220/18723 | 1.30e-15 | 2.38e-13 | 88 |
GO:004854519 | Prostate | Tumor | response to steroid hormone | 118/3246 | 339/18723 | 4.46e-15 | 6.94e-13 | 118 |
GO:006145816 | Prostate | Tumor | reproductive system development | 133/3246 | 427/18723 | 1.24e-12 | 1.15e-10 | 133 |
GO:190495118 | Prostate | Tumor | positive regulation of establishment of protein localization | 106/3246 | 319/18723 | 3.13e-12 | 2.70e-10 | 106 |
GO:004860815 | Prostate | Tumor | reproductive structure development | 131/3246 | 424/18723 | 3.48e-12 | 2.89e-10 | 131 |
GO:007149619 | Prostate | Tumor | cellular response to external stimulus | 103/3246 | 320/18723 | 5.29e-11 | 3.41e-09 | 103 |
GO:005122218 | Prostate | Tumor | positive regulation of protein transport | 97/3246 | 303/18723 | 2.67e-10 | 1.48e-08 | 97 |
GO:000164915 | Prostate | Tumor | osteoblast differentiation | 77/3246 | 229/18723 | 1.55e-09 | 7.26e-08 | 77 |
GO:005067316 | Prostate | Tumor | epithelial cell proliferation | 125/3246 | 437/18723 | 2.56e-09 | 1.08e-07 | 125 |
GO:005067815 | Prostate | Tumor | regulation of epithelial cell proliferation | 110/3246 | 381/18723 | 1.32e-08 | 4.82e-07 | 110 |
GO:001003819 | Prostate | Tumor | response to metal ion | 107/3246 | 373/18723 | 3.02e-08 | 9.77e-07 | 107 |
GO:000315815 | Prostate | Tumor | endothelium development | 50/3246 | 136/18723 | 4.60e-08 | 1.42e-06 | 50 |
GO:004544614 | Prostate | Tumor | endothelial cell differentiation | 45/3246 | 118/18723 | 6.08e-08 | 1.80e-06 | 45 |
GO:003196017 | Prostate | Tumor | response to corticosteroid | 57/3246 | 167/18723 | 1.11e-07 | 2.94e-06 | 57 |
GO:005138417 | Prostate | Tumor | response to glucocorticoid | 52/3246 | 148/18723 | 1.38e-07 | 3.50e-06 | 52 |
GO:003085614 | Prostate | Tumor | regulation of epithelial cell differentiation | 52/3246 | 154/18723 | 5.76e-07 | 1.22e-05 | 52 |
GO:000150314 | Prostate | Tumor | ossification | 109/3246 | 408/18723 | 1.13e-06 | 2.14e-05 | 109 |
GO:007121415 | Prostate | Tumor | cellular response to abiotic stimulus | 92/3246 | 331/18723 | 1.25e-06 | 2.32e-05 | 92 |
GO:010400415 | Prostate | Tumor | cellular response to environmental stimulus | 92/3246 | 331/18723 | 1.25e-06 | 2.32e-05 | 92 |
GO:007124114 | Prostate | Tumor | cellular response to inorganic substance | 66/3246 | 226/18723 | 6.63e-06 | 1.00e-04 | 66 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0439024 | Prostate | Tumor | Hippo signaling pathway | 54/1791 | 157/8465 | 7.52e-05 | 5.30e-04 | 3.28e-04 | 54 |
hsa0435021 | Prostate | Tumor | TGF-beta signaling pathway | 39/1791 | 108/8465 | 2.33e-04 | 1.35e-03 | 8.39e-04 | 39 |
hsa0439034 | Prostate | Tumor | Hippo signaling pathway | 54/1791 | 157/8465 | 7.52e-05 | 5.30e-04 | 3.28e-04 | 54 |
hsa0435031 | Prostate | Tumor | TGF-beta signaling pathway | 39/1791 | 108/8465 | 2.33e-04 | 1.35e-03 | 8.39e-04 | 39 |
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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 |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | CRC | AD |
BMP6 | BMPR1A_ACVR2A | BMP6_BMPR1A_ACVR2A | BMP | CRC | ADJ |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | CRC | ADJ |
BMP6 | BMPR1A_ACVR2A | BMP6_BMPR1A_ACVR2A | BMP | CRC | FAP |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | CRC | FAP |
BMP6 | ACVR1_ACVR2A | BMP6_ACVR1_ACVR2A | BMP | CRC | MSI-H |
BMP6 | ACVR1_ACVR2B | BMP6_ACVR1_ACVR2B | BMP | CRC | MSI-H |
BMP6 | ACVR1_BMPR2 | BMP6_ACVR1_BMPR2 | BMP | CRC | MSI-H |
BMP6 | BMPR1A_ACVR2A | BMP6_BMPR1A_ACVR2A | BMP | CRC | MSI-H |
BMP6 | BMPR1A_ACVR2B | BMP6_BMPR1A_ACVR2B | BMP | CRC | MSI-H |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | CRC | MSI-H |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | CRC | SER |
BMP6 | ACVR1_BMPR2 | BMP6_ACVR1_BMPR2 | BMP | HNSCC | Precancer |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | HNSCC | Precancer |
BMP6 | ACVR1_ACVR2A | BMP6_ACVR1_ACVR2A | BMP | Liver | Healthy |
BMP6 | ACVR1_ACVR2B | BMP6_ACVR1_ACVR2B | BMP | Liver | Healthy |
BMP6 | ACVR1_BMPR2 | BMP6_ACVR1_BMPR2 | BMP | Liver | Healthy |
BMP6 | BMPR1A_ACVR2A | BMP6_BMPR1A_ACVR2A | BMP | Liver | Healthy |
BMP6 | BMPR1A_ACVR2B | BMP6_BMPR1A_ACVR2B | BMP | Liver | Healthy |
BMP6 | BMPR1A_BMPR2 | BMP6_BMPR1A_BMPR2 | BMP | Liver | Healthy |
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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 |
BMP6 | SNV | Missense_Mutation | c.1160G>C | p.Arg387Pro | p.R387P | P22004 | protein_coding | tolerated(0.06) | probably_damaging(0.935) | TCGA-64-1679-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
BMP6 | SNV | Missense_Mutation | novel | c.1133N>C | p.Ser378Thr | p.S378T | P22004 | protein_coding | tolerated(0.23) | benign(0.011) | TCGA-73-A9RS-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PD |
BMP6 | SNV | Missense_Mutation | c.671N>G | p.Tyr224Cys | p.Y224C | P22004 | protein_coding | tolerated(0.15) | probably_damaging(0.932) | TCGA-78-7158-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
BMP6 | SNV | Missense_Mutation | novel | c.1187N>T | p.Arg396Leu | p.R396L | P22004 | protein_coding | tolerated(0.43) | possibly_damaging(0.9) | TCGA-97-8172-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
BMP6 | SNV | Missense_Mutation | novel | c.1027N>T | p.Ala343Ser | p.A343S | P22004 | protein_coding | tolerated(0.75) | benign(0.017) | TCGA-37-4130-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
BMP6 | SNV | Missense_Mutation | novel | c.1199N>A | p.Ala400Asp | p.A400D | P22004 | protein_coding | tolerated(0.21) | benign(0.211) | TCGA-56-8626-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
BMP6 | SNV | Missense_Mutation | rs377711135 | c.1351N>A | p.Ala451Thr | p.A451T | P22004 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-63-A5MM-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
BMP6 | SNV | Missense_Mutation | novel | c.1196N>T | p.Ser399Ile | p.S399I | P22004 | protein_coding | tolerated(0.38) | benign(0.342) | TCGA-BA-A4II-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
BMP6 | SNV | Missense_Mutation | novel | c.427N>A | p.Leu143Met | p.L143M | P22004 | protein_coding | tolerated(1) | benign(0.07) | TCGA-CR-7367-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | paclitaxel | SD |
BMP6 | SNV | Missense_Mutation | rs147293908 | c.946C>G | p.Leu316Val | p.L316V | P22004 | protein_coding | tolerated(0.52) | possibly_damaging(0.506) | TCGA-CV-7427-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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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