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Gene: BPTF |
Gene summary for BPTF |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BPTF | Gene ID | 2186 |
| Gene name | bromodomain PHD finger transcription factor | |
| Gene Alias | FAC1 | |
| Cytomap | 17q24.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q12830 |
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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 |
| 2186 | BPTF | GSM4909285 | Human | Breast | IDC | 8.99e-10 | 1.40e-01 | 0.21 |
| 2186 | BPTF | GSM4909286 | Human | Breast | IDC | 4.59e-11 | 1.91e-01 | 0.1081 |
| 2186 | BPTF | GSM4909293 | Human | Breast | IDC | 6.42e-19 | 3.55e-01 | 0.1581 |
| 2186 | BPTF | GSM4909298 | Human | Breast | IDC | 1.52e-22 | 4.04e-01 | 0.1551 |
| 2186 | BPTF | GSM4909308 | Human | Breast | IDC | 2.58e-05 | 2.51e-01 | 0.158 |
| 2186 | BPTF | GSM4909311 | Human | Breast | IDC | 3.45e-07 | -1.87e-01 | 0.1534 |
| 2186 | BPTF | GSM4909317 | Human | Breast | IDC | 3.42e-08 | 4.10e-01 | 0.1355 |
| 2186 | BPTF | GSM4909319 | Human | Breast | IDC | 5.19e-09 | -1.95e-01 | 0.1563 |
| 2186 | BPTF | brca10 | Human | Breast | Precancer | 1.15e-04 | -2.64e-01 | -0.0029 |
| 2186 | BPTF | M1 | Human | Breast | IDC | 9.42e-29 | 8.76e-01 | 0.1577 |
| 2186 | BPTF | NCCBC14 | Human | Breast | DCIS | 2.78e-05 | 2.66e-01 | 0.2021 |
| 2186 | BPTF | NCCBC2 | Human | Breast | DCIS | 9.95e-12 | 8.70e-01 | 0.1554 |
| 2186 | BPTF | NCCBC3 | Human | Breast | DCIS | 3.49e-02 | 2.49e-01 | 0.1198 |
| 2186 | BPTF | NCCBC5 | Human | Breast | DCIS | 2.98e-03 | -1.05e-01 | 0.2046 |
| 2186 | BPTF | P1 | Human | Breast | IDC | 6.13e-17 | 5.89e-01 | 0.1527 |
| 2186 | BPTF | DCIS2 | Human | Breast | DCIS | 4.79e-65 | 5.62e-01 | 0.0085 |
| 2186 | BPTF | CA_HPV_1 | Human | Cervix | CC | 6.40e-11 | -2.27e-01 | 0.0264 |
| 2186 | BPTF | N_HPV_1 | Human | Cervix | N_HPV | 1.54e-04 | -1.25e-01 | 0.0079 |
| 2186 | BPTF | CCI_2 | Human | Cervix | CC | 1.59e-08 | 6.40e-01 | 0.5249 |
| 2186 | BPTF | CCI_3 | Human | Cervix | CC | 8.51e-04 | 6.56e-01 | 0.516 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0001890112 | Thyroid | PTC | placenta development | 66/5968 | 144/18723 | 3.06e-04 | 2.14e-03 | 66 |
| GO:000749213 | Thyroid | PTC | endoderm development | 39/5968 | 77/18723 | 4.64e-04 | 3.06e-03 | 39 |
| GO:00063385 | Thyroid | PTC | chromatin remodeling | 106/5968 | 255/18723 | 6.56e-04 | 4.13e-03 | 106 |
| GO:000170126 | Thyroid | ATC | in utero embryonic development | 183/6293 | 367/18723 | 6.62e-11 | 2.11e-09 | 183 |
| GO:0006325110 | Thyroid | ATC | chromatin organization | 189/6293 | 409/18723 | 6.40e-08 | 1.13e-06 | 189 |
| GO:006145827 | Thyroid | ATC | reproductive system development | 193/6293 | 427/18723 | 3.32e-07 | 4.92e-06 | 193 |
| GO:004860825 | Thyroid | ATC | reproductive structure development | 190/6293 | 424/18723 | 8.40e-07 | 1.11e-05 | 190 |
| GO:199009023 | Thyroid | ATC | cellular response to nerve growth factor stimulus | 32/6293 | 53/18723 | 5.83e-05 | 4.48e-04 | 32 |
| GO:199008924 | Thyroid | ATC | response to nerve growth factor | 33/6293 | 56/18723 | 8.86e-05 | 6.58e-04 | 33 |
| GO:000749222 | Thyroid | ATC | endoderm development | 42/6293 | 77/18723 | 1.24e-04 | 8.82e-04 | 42 |
| GO:000189026 | Thyroid | ATC | placenta development | 70/6293 | 144/18723 | 1.33e-04 | 9.33e-04 | 70 |
| GO:0001892111 | Thyroid | ATC | embryonic placenta development | 42/6293 | 82/18723 | 7.34e-04 | 4.11e-03 | 42 |
| GO:000633813 | Thyroid | ATC | chromatin remodeling | 109/6293 | 255/18723 | 1.38e-03 | 7.15e-03 | 109 |
| GO:00718242 | Thyroid | ATC | protein-DNA complex subunit organization | 103/6293 | 241/18723 | 1.84e-03 | 9.03e-03 | 103 |
| GO:00485688 | Thyroid | ATC | embryonic organ development | 172/6293 | 427/18723 | 2.08e-03 | 9.84e-03 | 172 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| 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 |
| BPTF | CD8TEFF | Breast | IDC | PLCG2,DDX17,SYNE2, etc. | 7.55e-02 |  |
| BPTF | ASC | Colorectum | SER | ARL17B,HNF1A-AS1,MT-ATP8, etc. | 1.20e-01 |  |
| BPTF | CD8TEXINT | Stomach | CAG | GRAMD2B,MCTP2,PACS1, etc. | 1.82e-02 |  |
| BPTF | CD4TN | Stomach | CAG | GRAMD2B,MCTP2,PACS1, etc. | 1.17e-02 | |
| BPTF | CD4TN | Stomach | CSG | GRAMD2B,MCTP2,PACS1, etc. | 8.54e-02 |  |
| BPTF | MAIT | Stomach | SIM | GRAMD2B,MCTP2,PACS1, etc. | 4.20e-02 |  |
| BPTF | LYMEND | Stomach | ADJ | PHF14,PLA2G2A,MT-ND2, etc. | 1.50e-02 |  |
| BPTF | MVA | Stomach | CAG | PHF14,PLA2G2A,MT-ND2, etc. | 6.16e-02 | |
| BPTF | CAF | Stomach | CSG | PHF14,PLA2G2A,MT-ND2, etc. | 1.16e-01 | |
| BPTF | MVA | Stomach | Healthy | PHF14,PLA2G2A,MT-ND2, etc. | 3.92e-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 |
| BPTF | SNV | Missense_Mutation | novel | c.4221N>G | p.Ile1407Met | p.I1407M | Q12830 | protein_coding | tolerated_low_confidence(0.28) | benign(0.295) | TCGA-A7-A4SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| BPTF | SNV | Missense_Mutation | novel | c.587N>A | p.Ser196Asn | p.S196N | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.943) | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD |
| BPTF | SNV | Missense_Mutation | c.6194N>C | p.Arg2065Thr | p.R2065T | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.919) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| BPTF | SNV | Missense_Mutation | c.5514N>G | p.Ile1838Met | p.I1838M | Q12830 | protein_coding | deleterious(0.01) | possibly_damaging(0.847) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| BPTF | SNV | Missense_Mutation | c.6368N>T | p.Ser2123Leu | p.S2123L | Q12830 | protein_coding | deleterious(0.02) | benign(0.164) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR | |
| BPTF | SNV | Missense_Mutation | c.5401C>A | p.Pro1801Thr | p.P1801T | Q12830 | protein_coding | deleterious(0.01) | possibly_damaging(0.908) | TCGA-C8-A132-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| BPTF | SNV | Missense_Mutation | c.2908N>C | p.Asp970His | p.D970H | Q12830 | protein_coding | tolerated(0.07) | possibly_damaging(0.548) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BPTF | SNV | Missense_Mutation | c.4442N>G | p.Ser1481Cys | p.S1481C | Q12830 | protein_coding | tolerated_low_confidence(0.14) | possibly_damaging(0.634) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| BPTF | SNV | Missense_Mutation | c.2053N>C | p.Glu685Gln | p.E685Q | Q12830 | protein_coding | deleterious(0.02) | benign(0.076) | TCGA-D8-A1JC-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| BPTF | SNV | Missense_Mutation | c.751G>A | p.Glu251Lys | p.E251K | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D8-A27G-01 | Breast | breast invasive 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 19 20 21 22 23 24 25 |
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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 |
| 2186 | BPTF | TRANSCRIPTION FACTOR | inhibitor | 252827533 |
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