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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 |
| Page: 1 |
| 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). |
| 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:005507615 | Prostate | Tumor | transition metal ion homeostasis | 45/3246 | 138/18723 | 9.11e-06 | 1.33e-04 | 45 |
| GO:000165513 | Prostate | Tumor | urogenital system development | 90/3246 | 338/18723 | 1.08e-05 | 1.56e-04 | 90 |
| GO:000716215 | Prostate | Tumor | negative regulation of cell adhesion | 82/3246 | 303/18723 | 1.38e-05 | 1.89e-04 | 82 |
| GO:004521617 | Prostate | Tumor | cell-cell junction organization | 59/3246 | 200/18723 | 1.43e-05 | 1.94e-04 | 59 |
| GO:005507213 | Prostate | Tumor | iron ion homeostasis | 31/3246 | 85/18723 | 1.89e-05 | 2.47e-04 | 31 |
| GO:002240717 | Prostate | Tumor | regulation of cell-cell adhesion | 112/3246 | 448/18723 | 2.20e-05 | 2.80e-04 | 112 |
| GO:007124815 | Prostate | Tumor | cellular response to metal ion | 56/3246 | 197/18723 | 7.26e-05 | 7.65e-04 | 56 |
| GO:004691614 | Prostate | Tumor | cellular transition metal ion homeostasis | 37/3246 | 115/18723 | 7.56e-05 | 7.88e-04 | 37 |
| GO:004566711 | Prostate | Tumor | regulation of osteoblast differentiation | 41/3246 | 132/18723 | 7.83e-05 | 8.14e-04 | 41 |
| GO:000717815 | Prostate | Tumor | transmembrane receptor protein serine/threonine kinase signaling pathway | 90/3246 | 355/18723 | 7.93e-05 | 8.19e-04 | 90 |
| GO:000961214 | Prostate | Tumor | response to mechanical stimulus | 60/3246 | 216/18723 | 8.45e-05 | 8.46e-04 | 60 |
| GO:005067914 | Prostate | Tumor | positive regulation of epithelial cell proliferation | 58/3246 | 207/18723 | 8.47e-05 | 8.47e-04 | 58 |
| GO:004666111 | Prostate | Tumor | male sex differentiation | 48/3246 | 165/18723 | 1.25e-04 | 1.16e-03 | 48 |
| GO:007126013 | Prostate | Tumor | cellular response to mechanical stimulus | 28/3246 | 81/18723 | 1.39e-04 | 1.27e-03 | 28 |
| GO:000754811 | Prostate | Tumor | sex differentiation | 71/3246 | 276/18723 | 2.70e-04 | 2.24e-03 | 71 |
| GO:006201214 | Prostate | Tumor | regulation of small molecule metabolic process | 83/3246 | 334/18723 | 2.96e-04 | 2.39e-03 | 83 |
| GO:000182213 | Prostate | Tumor | kidney development | 74/3246 | 293/18723 | 3.68e-04 | 2.87e-03 | 74 |
| GO:001003911 | Prostate | Tumor | response to iron ion | 14/3246 | 32/18723 | 4.43e-04 | 3.37e-03 | 14 |
| GO:007169214 | Prostate | Tumor | protein localization to extracellular region | 89/3246 | 368/18723 | 4.80e-04 | 3.57e-03 | 89 |
| GO:000930615 | Prostate | Tumor | protein secretion | 87/3246 | 359/18723 | 5.15e-04 | 3.78e-03 | 87 |
| Page: 1 2 3 4 |
| 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 |
| Page: 1 |
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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 |
| Page: 1 2 |
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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. |
| Page: 1 |
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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 | rs566660170 | c.692G>A | p.Arg231His | p.R231H | P22004 | protein_coding | tolerated(0.42) | benign(0.009) | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR |
| BMP6 | SNV | Missense_Mutation | novel | c.1509N>T | p.Arg503Ser | p.R503S | P22004 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| BMP6 | SNV | Missense_Mutation | c.832N>G | p.Gln278Glu | p.Q278E | P22004 | protein_coding | tolerated(0.55) | probably_damaging(0.991) | TCGA-E2-A15S-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| BMP6 | insertion | Nonsense_Mutation | novel | c.1421_1422insATAGGACATACATTTATTTGGGCATTTAAACAAATTTTAATTGAGA | p.Lys475Ter | p.K475* | P22004 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| BMP6 | insertion | Nonsense_Mutation | novel | c.1472_1473insGCAGCCATTACCAAACACCCAGAGCTTGATTGAAGGCTGAGC | p.Phe491delinsLeuGlnProLeuProAsnThrGlnSerLeuIleGluGlyTerAla | p.F491delinsLQPLPNTQSLIEG*A | P22004 | protein_coding | TCGA-A8-A0A2-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| BMP6 | SNV | Missense_Mutation | rs771664465 | c.934N>A | p.Ala312Thr | p.A312T | P22004 | protein_coding | deleterious(0.05) | possibly_damaging(0.53) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| BMP6 | SNV | Missense_Mutation | rs781335360 | c.991N>A | p.Val331Met | p.V331M | P22004 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-VS-A9V4-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| BMP6 | SNV | Missense_Mutation | rs577694907 | c.1139G>A | p.Arg380His | p.R380H | P22004 | protein_coding | deleterious(0.05) | benign(0.072) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| BMP6 | SNV | Missense_Mutation | c.1394N>C | p.Val465Ala | p.V465A | P22004 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| BMP6 | SNV | Missense_Mutation | c.1227A>C | p.Lys409Asn | p.K409N | P22004 | protein_coding | deleterious(0.02) | probably_damaging(0.975) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 |
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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 |
| Page: 1 |
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