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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. |
∗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:000167822 | Liver | HCC | cellular glucose homeostasis | 95/7958 | 172/18723 | 4.95e-04 | 3.24e-03 | 95 |
GO:00075992 | Liver | HCC | hemostasis | 119/7958 | 222/18723 | 5.25e-04 | 3.41e-03 | 119 |
GO:000632511 | Liver | HCC | chromatin organization | 206/7958 | 409/18723 | 7.23e-04 | 4.41e-03 | 206 |
GO:007133112 | Liver | HCC | cellular response to hexose stimulus | 85/7958 | 153/18723 | 7.47e-04 | 4.52e-03 | 85 |
GO:007133312 | Liver | HCC | cellular response to glucose stimulus | 84/7958 | 151/18723 | 7.57e-04 | 4.56e-03 | 84 |
GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
GO:00508172 | Liver | HCC | coagulation | 118/7958 | 222/18723 | 8.41e-04 | 5.03e-03 | 118 |
GO:007132612 | Liver | HCC | cellular response to monosaccharide stimulus | 85/7958 | 154/18723 | 9.78e-04 | 5.68e-03 | 85 |
GO:005087822 | Liver | HCC | regulation of body fluid levels | 191/7958 | 379/18723 | 1.06e-03 | 6.11e-03 | 191 |
GO:007132212 | Liver | HCC | cellular response to carbohydrate stimulus | 89/7958 | 163/18723 | 1.19e-03 | 6.62e-03 | 89 |
GO:00106772 | Liver | HCC | negative regulation of cellular carbohydrate metabolic process | 28/7958 | 42/18723 | 1.35e-03 | 7.26e-03 | 28 |
GO:00459122 | Liver | HCC | negative regulation of carbohydrate metabolic process | 31/7958 | 48/18723 | 1.66e-03 | 8.71e-03 | 31 |
GO:004578512 | Liver | HCC | positive regulation of cell adhesion | 215/7958 | 437/18723 | 2.53e-03 | 1.22e-02 | 215 |
GO:00357733 | Liver | HCC | insulin secretion involved in cellular response to glucose stimulus | 42/7958 | 73/18723 | 6.78e-03 | 2.73e-02 | 42 |
GO:003559212 | Liver | HCC | establishment of protein localization to extracellular region | 176/7958 | 360/18723 | 7.96e-03 | 3.15e-02 | 176 |
GO:000930612 | Liver | HCC | protein secretion | 175/7958 | 359/18723 | 9.32e-03 | 3.57e-02 | 175 |
GO:1903299 | Liver | HCC | regulation of hexokinase activity | 9/7958 | 11/18723 | 9.51e-03 | 3.60e-02 | 9 |
GO:00611784 | Liver | HCC | regulation of insulin secretion involved in cellular response to glucose stimulus | 37/7958 | 64/18723 | 9.63e-03 | 3.63e-02 | 37 |
GO:0031670 | Liver | HCC | cellular response to nutrient | 27/7958 | 45/18723 | 1.35e-02 | 4.80e-02 | 27 |
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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 |
∗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 |
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 |
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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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