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Gene: FOXA1 |
Gene summary for FOXA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FOXA1 | Gene ID | 3169 |
| Gene name | forkhead box A1 | |
| Gene Alias | HNF3A | |
| Cytomap | 14q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P55317 |
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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 |
| 3169 | FOXA1 | GSM4909281 | Human | Breast | IDC | 1.77e-06 | -2.00e-01 | 0.21 |
| 3169 | FOXA1 | GSM4909282 | Human | Breast | IDC | 3.78e-06 | -1.95e-01 | -0.0288 |
| 3169 | FOXA1 | GSM4909285 | Human | Breast | IDC | 4.58e-02 | -1.76e-01 | 0.21 |
| 3169 | FOXA1 | GSM4909287 | Human | Breast | IDC | 1.20e-05 | -1.95e-01 | 0.2057 |
| 3169 | FOXA1 | GSM4909290 | Human | Breast | IDC | 2.02e-13 | 5.63e-01 | 0.2096 |
| 3169 | FOXA1 | GSM4909293 | Human | Breast | IDC | 4.37e-19 | 4.70e-01 | 0.1581 |
| 3169 | FOXA1 | GSM4909295 | Human | Breast | IDC | 1.38e-02 | -2.00e-01 | 0.0898 |
| 3169 | FOXA1 | GSM4909298 | Human | Breast | IDC | 2.09e-23 | 5.45e-01 | 0.1551 |
| 3169 | FOXA1 | GSM4909301 | Human | Breast | IDC | 4.93e-12 | 5.08e-01 | 0.1577 |
| 3169 | FOXA1 | GSM4909304 | Human | Breast | IDC | 1.54e-23 | 5.17e-01 | 0.1636 |
| 3169 | FOXA1 | GSM4909306 | Human | Breast | IDC | 7.79e-10 | 3.56e-01 | 0.1564 |
| 3169 | FOXA1 | GSM4909307 | Human | Breast | IDC | 1.69e-08 | 4.38e-01 | 0.1569 |
| 3169 | FOXA1 | GSM4909308 | Human | Breast | IDC | 1.09e-24 | 6.17e-01 | 0.158 |
| 3169 | FOXA1 | GSM4909311 | Human | Breast | IDC | 3.98e-02 | -1.18e-01 | 0.1534 |
| 3169 | FOXA1 | GSM4909319 | Human | Breast | IDC | 4.12e-06 | -1.59e-01 | 0.1563 |
| 3169 | FOXA1 | brca2 | Human | Breast | Precancer | 9.46e-05 | 2.12e-01 | -0.024 |
| 3169 | FOXA1 | M1 | Human | Breast | IDC | 7.93e-09 | 4.49e-01 | 0.1577 |
| 3169 | FOXA1 | M5 | Human | Breast | IDC | 4.65e-05 | 6.70e-01 | 0.1598 |
| 3169 | FOXA1 | NCCBC14 | Human | Breast | DCIS | 7.58e-05 | 3.88e-01 | 0.2021 |
| 3169 | FOXA1 | NCCBC5 | Human | Breast | DCIS | 2.29e-02 | 1.22e-01 | 0.2046 |
| Page: 1 2 3 4 5 |
| 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 | ||
| 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 | ||
| 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 |
| ∗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:00018377 | Oral cavity | OSCC | epithelial to mesenchymal transition | 82/7305 | 157/18723 | 5.09e-04 | 2.98e-03 | 82 |
| GO:00303248 | Oral cavity | OSCC | lung development | 91/7305 | 177/18723 | 5.18e-04 | 3.01e-03 | 91 |
| GO:00305206 | Oral cavity | OSCC | intracellular estrogen receptor signaling pathway | 33/7305 | 54/18723 | 8.25e-04 | 4.38e-03 | 33 |
| GO:00016558 | Oral cavity | OSCC | urogenital system development | 160/7305 | 338/18723 | 1.03e-03 | 5.31e-03 | 160 |
| GO:000632510 | Oral cavity | OSCC | chromatin organization | 190/7305 | 409/18723 | 1.17e-03 | 5.97e-03 | 190 |
| GO:004259316 | Oral cavity | OSCC | glucose homeostasis | 125/7305 | 258/18723 | 1.21e-03 | 6.08e-03 | 125 |
| GO:00107173 | Oral cavity | OSCC | regulation of epithelial to mesenchymal transition | 54/7305 | 99/18723 | 1.21e-03 | 6.10e-03 | 54 |
| GO:002240917 | Oral cavity | OSCC | positive regulation of cell-cell adhesion | 136/7305 | 284/18723 | 1.35e-03 | 6.62e-03 | 136 |
| GO:003350016 | Oral cavity | OSCC | carbohydrate homeostasis | 125/7305 | 259/18723 | 1.44e-03 | 6.97e-03 | 125 |
| GO:00605416 | Oral cavity | OSCC | respiratory system development | 100/7305 | 203/18723 | 1.83e-03 | 8.60e-03 | 100 |
| GO:002261214 | Oral cavity | OSCC | gland morphogenesis | 62/7305 | 118/18723 | 1.91e-03 | 8.94e-03 | 62 |
| GO:00219158 | Oral cavity | OSCC | neural tube development | 77/7305 | 152/18723 | 2.26e-03 | 1.00e-02 | 77 |
| GO:00308505 | Oral cavity | OSCC | prostate gland development | 27/7305 | 45/18723 | 3.49e-03 | 1.47e-02 | 27 |
| GO:00331462 | Oral cavity | OSCC | regulation of intracellular estrogen receptor signaling pathway | 22/7305 | 35/18723 | 3.65e-03 | 1.51e-02 | 22 |
| GO:00604256 | Oral cavity | OSCC | lung morphogenesis | 29/7305 | 50/18723 | 5.01e-03 | 1.96e-02 | 29 |
| GO:00605629 | Oral cavity | OSCC | epithelial tube morphogenesis | 149/7305 | 325/18723 | 6.73e-03 | 2.50e-02 | 149 |
| GO:00487627 | Oral cavity | OSCC | mesenchymal cell differentiation | 109/7305 | 236/18723 | 1.43e-02 | 4.69e-02 | 109 |
| GO:00488637 | Oral cavity | OSCC | stem cell differentiation | 96/7305 | 206/18723 | 1.55e-02 | 4.99e-02 | 96 |
| GO:000734614 | Oral cavity | LP | regulation of mitotic cell cycle | 163/4623 | 457/18723 | 7.64e-08 | 2.56e-06 | 163 |
| GO:0048545110 | Oral cavity | LP | response to steroid hormone | 122/4623 | 339/18723 | 1.91e-06 | 4.39e-05 | 122 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| 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 |
| 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 |
| FOXA1 | MLUM | Breast | ADJ | DHCR24,GATA3,SLC39A6, etc. | 3.09e-01 |  |
| FOXA1 | MLUM | Breast | IDC | DHCR24,GATA3,SLC39A6, etc. | 5.10e-01 |  |
| FOXA1 | MLUM | Breast | Precancer | DHCR24,GATA3,SLC39A6, etc. | 2.54e-01 |  |
| FOXA1 | PLA | Breast | ADJ | SLC39A6,TFF3,AGR3, etc. | 1.41e-01 | |
| FOXA1 | NK | Breast | DCIS | SLC39A6,TFF3,AGR3, etc. | 1.29e-01 |  |
| FOXA1 | PLA | Breast | DCIS | SLC39A6,TFF3,AGR3, etc. | 1.30e-01 | |
| FOXA1 | BMEM | Breast | DCIS | SLC39A6,TFF3,AGR3, etc. | 1.19e-01 | |
| FOXA1 | BMEM | Breast | Healthy | SLC39A6,TFF3,AGR3, etc. | 9.47e-02 |  |
| FOXA1 | NK | Breast | Healthy | SLC39A6,TFF3,AGR3, etc. | 1.03e-01 | |
| FOXA1 | NK | Breast | IDC | SLC39A6,TFF3,AGR3, etc. | 9.31e-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 |
| FOXA1 | SNV | Missense_Mutation | novel | c.637C>T | p.Arg213Cys | p.R213C | P55317 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| FOXA1 | SNV | Missense_Mutation | novel | c.22G>A | p.Glu8Lys | p.E8K | P55317 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| FOXA1 | SNV | Missense_Mutation | c.1350N>G | p.Ile450Met | p.I450M | P55317 | protein_coding | tolerated(0.35) | benign(0.07) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | |
| FOXA1 | SNV | Missense_Mutation | c.739N>T | p.His247Tyr | p.H247Y | P55317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | |
| FOXA1 | SNV | Missense_Mutation | c.749N>T | p.Ser250Phe | p.S250F | P55317 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A082-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| FOXA1 | SNV | Missense_Mutation | c.676N>A | p.Asp226Asn | p.D226N | P55317 | protein_coding | deleterious(0) | possibly_damaging(0.864) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| FOXA1 | SNV | Missense_Mutation | novel | c.764N>T | p.Glu255Val | p.E255V | P55317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AC-A2FM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| FOXA1 | SNV | Missense_Mutation | c.526A>G | p.Ile176Val | p.I176V | P55317 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AC-A3EH-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| FOXA1 | SNV | Missense_Mutation | novel | c.677A>G | p.Asp226Gly | p.D226G | P55317 | protein_coding | deleterious(0) | possibly_damaging(0.762) | TCGA-AC-A4ZE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| FOXA1 | SNV | Missense_Mutation | novel | c.1213N>T | p.Leu405Phe | p.L405F | P55317 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A0FF-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 |
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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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