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Gene: FOXA2 |
Gene summary for FOXA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FOXA2 | Gene ID | 3170 |
| Gene name | forkhead box A2 | |
| Gene Alias | HNF-3-beta | |
| Cytomap | 20p11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000429 | UniProtAcc | B0ZTD4 |
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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 |
| 3170 | FOXA2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.47e-03 | 1.03e-01 | 0.0155 |
| 3170 | FOXA2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.42e-05 | 1.98e-01 | -0.1808 |
| 3170 | FOXA2 | HTA11_78_2000001011 | Human | Colorectum | AD | 6.21e-16 | 4.30e-01 | -0.1088 |
| 3170 | FOXA2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.95e-18 | 4.07e-01 | -0.1954 |
| 3170 | FOXA2 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.50e-11 | 8.79e-01 | -0.2602 |
| 3170 | FOXA2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.50e-04 | 3.37e-01 | -0.2196 |
| 3170 | FOXA2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.57e-06 | 2.57e-01 | -0.1207 |
| 3170 | FOXA2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.63e-22 | 5.14e-01 | -0.1464 |
| 3170 | FOXA2 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.28e-10 | 2.59e-01 | -0.1001 |
| 3170 | FOXA2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.63e-07 | 2.56e-01 | -0.059 |
| 3170 | FOXA2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.14e-07 | 3.79e-01 | -0.1706 |
| 3170 | FOXA2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.03e-03 | 1.93e-01 | -0.2061 |
| 3170 | FOXA2 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.56e-06 | 2.90e-01 | -0.0842 |
| 3170 | FOXA2 | HTA11_7862_2000001011 | Human | Colorectum | AD | 5.15e-10 | 3.55e-01 | -0.0179 |
| 3170 | FOXA2 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.30e-20 | 4.39e-01 | 0.096 |
| 3170 | FOXA2 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.22e-05 | 4.41e-01 | 0.0446 |
| 3170 | FOXA2 | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.89e-10 | 4.21e-01 | 0.0528 |
| 3170 | FOXA2 | HTA11_6801_2000001011 | Human | Colorectum | SER | 2.21e-02 | 2.06e-01 | 0.0171 |
| 3170 | FOXA2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.05e-06 | 1.84e-01 | 0.0674 |
| 3170 | FOXA2 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.00e-08 | 4.88e-01 | 0.0112 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:004259312 | Liver | Cirrhotic | glucose homeostasis | 86/4634 | 258/18723 | 1.12e-03 | 7.73e-03 | 86 |
| GO:00713316 | Liver | Cirrhotic | cellular response to hexose stimulus | 55/4634 | 153/18723 | 1.27e-03 | 8.56e-03 | 55 |
| GO:003350012 | Liver | Cirrhotic | carbohydrate homeostasis | 86/4634 | 259/18723 | 1.28e-03 | 8.61e-03 | 86 |
| GO:00713266 | Liver | Cirrhotic | cellular response to monosaccharide stimulus | 55/4634 | 154/18723 | 1.51e-03 | 9.91e-03 | 55 |
| GO:00713226 | Liver | Cirrhotic | cellular response to carbohydrate stimulus | 57/4634 | 163/18723 | 2.18e-03 | 1.34e-02 | 57 |
| GO:005087812 | Liver | Cirrhotic | regulation of body fluid levels | 118/4634 | 379/18723 | 2.65e-03 | 1.55e-02 | 118 |
| GO:003367312 | Liver | Cirrhotic | negative regulation of kinase activity | 78/4634 | 237/18723 | 2.73e-03 | 1.59e-02 | 78 |
| GO:00459121 | Liver | Cirrhotic | negative regulation of carbohydrate metabolic process | 20/4634 | 48/18723 | 7.37e-03 | 3.52e-02 | 20 |
| GO:00106771 | Liver | Cirrhotic | negative regulation of cellular carbohydrate metabolic process | 18/4634 | 42/18723 | 7.64e-03 | 3.61e-02 | 18 |
| GO:000599621 | Liver | HCC | monosaccharide metabolic process | 167/7958 | 257/18723 | 2.31e-13 | 1.25e-11 | 167 |
| GO:001931821 | Liver | HCC | hexose metabolic process | 155/7958 | 237/18723 | 7.63e-13 | 3.90e-11 | 155 |
| GO:003166722 | Liver | HCC | response to nutrient levels | 276/7958 | 474/18723 | 2.30e-12 | 1.08e-10 | 276 |
| GO:001056322 | Liver | HCC | negative regulation of phosphorus metabolic process | 259/7958 | 442/18723 | 4.29e-12 | 1.92e-10 | 259 |
| GO:004593622 | Liver | HCC | negative regulation of phosphate metabolic process | 258/7958 | 441/18723 | 6.00e-12 | 2.60e-10 | 258 |
| GO:004232622 | Liver | HCC | negative regulation of phosphorylation | 227/7958 | 385/18723 | 3.98e-11 | 1.52e-09 | 227 |
| GO:000600621 | Liver | HCC | glucose metabolic process | 128/7958 | 196/18723 | 8.60e-11 | 3.06e-09 | 128 |
| GO:005134822 | Liver | HCC | negative regulation of transferase activity | 166/7958 | 268/18723 | 8.97e-11 | 3.18e-09 | 166 |
| GO:007149622 | Liver | HCC | cellular response to external stimulus | 191/7958 | 320/18723 | 3.40e-10 | 1.13e-08 | 191 |
| GO:003166812 | Liver | HCC | cellular response to extracellular stimulus | 149/7958 | 246/18723 | 7.35e-09 | 1.86e-07 | 149 |
| GO:003367322 | Liver | HCC | negative regulation of kinase activity | 144/7958 | 237/18723 | 9.76e-09 | 2.45e-07 | 144 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04213 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
| hsa042131 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
| hsa042132 | Colorectum | SER | Longevity regulating pathway - multiple species | 20/1580 | 62/8465 | 7.15e-03 | 3.77e-02 | 2.74e-02 | 20 |
| hsa042133 | Colorectum | SER | Longevity regulating pathway - multiple species | 20/1580 | 62/8465 | 7.15e-03 | 3.77e-02 | 2.74e-02 | 20 |
| hsa042134 | Colorectum | MSS | Longevity regulating pathway - multiple species | 27/1875 | 62/8465 | 1.33e-04 | 1.17e-03 | 7.18e-04 | 27 |
| hsa042135 | Colorectum | MSS | Longevity regulating pathway - multiple species | 27/1875 | 62/8465 | 1.33e-04 | 1.17e-03 | 7.18e-04 | 27 |
| hsa042138 | Liver | HCC | Longevity regulating pathway - multiple species | 41/4020 | 62/8465 | 2.30e-03 | 7.86e-03 | 4.37e-03 | 41 |
| hsa0421311 | Liver | HCC | Longevity regulating pathway - multiple species | 41/4020 | 62/8465 | 2.30e-03 | 7.86e-03 | 4.37e-03 | 41 |
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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 |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| FOXA2 | COL | Cervix | N_HPV | IGFL1,KATNA1,IL19, etc. | 4.19e-01 |  |
| FOXA2 | IMGOB | Colorectum | AD | ELAPOR1,RAB15,ST6GALNAC1, etc. | 1.90e-01 |  |
| FOXA2 | GOB | Colorectum | AD | ELAPOR1,RAB15,ST6GALNAC1, etc. | 2.15e-01 | |
| FOXA2 | GOB | Colorectum | ADJ | FOXA2(+) | 2.71e-01 |  |
| FOXA2 | IMGOB | Colorectum | ADJ | FOXA2(+) | 1.39e-01 | |
| FOXA2 | IMGOB | Colorectum | MSI-H | ELAPOR1,RAB15,ST6GALNAC1, etc. | 2.32e-01 |  |
| FOXA2 | IMGOB | Colorectum | MSS | ELAPOR1,RAB15,ST6GALNAC1, etc. | 5.88e-02 |  |
| FOXA2 | IMGOB | Colorectum | SER | ELAPOR1,RAB15,ST6GALNAC1, etc. | 5.77e-02 |  |
| FOXA2 | TUF | Colorectum | SER | ELAPOR1,RAB15,ST6GALNAC1, etc. | 4.51e-02 | |
| FOXA2 | DUCT1 | Pancreas | PanIN | LINC00261,SNORD3A,RCAN1, etc. | 2.90e-01 |  |
| ∗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 |
| FOXA2 | SNV | Missense_Mutation | novel | c.640C>T | p.Arg214Cys | p.R214C | Q9Y261 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A8OQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| FOXA2 | SNV | Missense_Mutation | novel | c.58N>A | p.Asp20Asn | p.D20N | Q9Y261 | protein_coding | deleterious(0) | probably_damaging(0.944) | TCGA-E2-A152-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | PD |
| FOXA2 | SNV | Missense_Mutation | novel | c.555G>C | p.Met185Ile | p.M185I | Q9Y261 | protein_coding | deleterious(0) | possibly_damaging(0.796) | TCGA-OL-A66O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| FOXA2 | deletion | Frame_Shift_Del | c.1278_1318delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | p.Ser427ArgfsTer43 | p.S427Rfs*43 | Q9Y261 | protein_coding | TCGA-AN-A0XU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
| FOXA2 | SNV | Missense_Mutation | novel | c.1285N>A | p.Ala429Thr | p.A429T | Q9Y261 | protein_coding | tolerated(0.14) | benign(0.393) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| FOXA2 | SNV | Missense_Mutation | c.1169C>T | p.Ser390Leu | p.S390L | Q9Y261 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| FOXA2 | SNV | Missense_Mutation | novel | c.336N>C | p.Leu112Phe | p.L112F | Q9Y261 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| FOXA2 | SNV | Missense_Mutation | novel | c.1152N>G | p.Ile384Met | p.I384M | Q9Y261 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-VS-A94X-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| FOXA2 | SNV | Missense_Mutation | novel | c.8N>T | p.Ser3Leu | p.S3L | Q9Y261 | protein_coding | deleterious_low_confidence(0.01) | benign(0.281) | TCGA-VS-A94Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| FOXA2 | SNV | Missense_Mutation | novel | c.1301N>T | p.Thr434Met | p.T434M | Q9Y261 | protein_coding | deleterious(0.04) | probably_damaging(0.947) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 |
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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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