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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 |
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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:00018927 | Breast | Precancer | embryonic placenta development | 14/1080 | 82/18723 | 2.30e-04 | 3.48e-03 | 14 |
GO:00486087 | Breast | Precancer | reproductive structure development | 43/1080 | 424/18723 | 2.36e-04 | 3.56e-03 | 43 |
GO:00614587 | Breast | Precancer | reproductive system development | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
GO:00018907 | Breast | Precancer | placenta development | 19/1080 | 144/18723 | 6.26e-04 | 7.78e-03 | 19 |
GO:00017017 | Breast | Precancer | in utero embryonic development | 35/1080 | 367/18723 | 2.47e-03 | 2.27e-02 | 35 |
GO:19900908 | Breast | Precancer | cellular response to nerve growth factor stimulus | 9/1080 | 53/18723 | 3.05e-03 | 2.62e-02 | 9 |
GO:19900896 | Breast | Precancer | response to nerve growth factor | 9/1080 | 56/18723 | 4.47e-03 | 3.47e-02 | 9 |
GO:004860812 | Breast | IDC | reproductive structure development | 60/1434 | 424/18723 | 2.71e-06 | 1.03e-04 | 60 |
GO:006145813 | Breast | IDC | reproductive system development | 60/1434 | 427/18723 | 3.41e-06 | 1.24e-04 | 60 |
GO:000189013 | Breast | IDC | placenta development | 25/1434 | 144/18723 | 9.19e-05 | 1.78e-03 | 25 |
GO:000189213 | Breast | IDC | embryonic placenta development | 16/1434 | 82/18723 | 4.28e-04 | 5.84e-03 | 16 |
GO:199008912 | Breast | IDC | response to nerve growth factor | 11/1434 | 56/18723 | 3.08e-03 | 2.61e-02 | 11 |
GO:000170113 | Breast | IDC | in utero embryonic development | 42/1434 | 367/18723 | 5.85e-03 | 4.24e-02 | 42 |
GO:004860821 | Breast | DCIS | reproductive structure development | 57/1390 | 424/18723 | 9.06e-06 | 2.45e-04 | 57 |
GO:006145822 | Breast | DCIS | reproductive system development | 57/1390 | 427/18723 | 1.12e-05 | 2.92e-04 | 57 |
GO:000189022 | Breast | DCIS | placenta development | 25/1390 | 144/18723 | 5.57e-05 | 1.13e-03 | 25 |
GO:000189221 | Breast | DCIS | embryonic placenta development | 16/1390 | 82/18723 | 3.02e-04 | 4.38e-03 | 16 |
GO:199008922 | Breast | DCIS | response to nerve growth factor | 11/1390 | 56/18723 | 2.42e-03 | 2.18e-02 | 11 |
GO:000170122 | Breast | DCIS | in utero embryonic development | 41/1390 | 367/18723 | 5.74e-03 | 4.13e-02 | 41 |
GO:00018908 | Cervix | CC | placenta development | 40/2311 | 144/18723 | 4.59e-07 | 1.77e-05 | 40 |
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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 |
∗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 |
BPTF | SNV | Missense_Mutation | rs764527892 | c.2867G>A | p.Arg956Gln | p.R956Q | Q12830 | protein_coding | tolerated(0.26) | benign(0.027) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BPTF | SNV | Missense_Mutation | c.7783N>T | p.Arg2595Cys | p.R2595C | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
BPTF | SNV | Missense_Mutation | novel | c.3574N>C | p.Lys1192Gln | p.K1192Q | Q12830 | protein_coding | tolerated_low_confidence(0.34) | benign(0.001) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BPTF | SNV | Missense_Mutation | rs556375365 | c.5498N>A | p.Arg1833Gln | p.R1833Q | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
BPTF | SNV | Missense_Mutation | novel | c.7614A>T | p.Lys2538Asn | p.K2538N | Q12830 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BPTF | SNV | Missense_Mutation | novel | c.7616A>T | p.Gln2539Leu | p.Q2539L | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BPTF | SNV | Missense_Mutation | c.2033N>C | p.Lys678Thr | p.K678T | Q12830 | protein_coding | deleterious(0.01) | possibly_damaging(0.466) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
BPTF | SNV | Missense_Mutation | novel | c.2696N>C | p.Glu899Ala | p.E899A | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
BPTF | SNV | Missense_Mutation | c.7667N>A | p.Ser2556Asn | p.S2556N | Q12830 | protein_coding | deleterious_low_confidence(0) | benign(0.036) | TCGA-CA-5254-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
BPTF | SNV | Missense_Mutation | novel | c.586N>G | p.Ser196Gly | p.S196G | Q12830 | protein_coding | deleterious(0) | probably_damaging(0.943) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
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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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