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Gene: NKX2-1 |
Gene summary for NKX2-1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NKX2-1 | Gene ID | 7080 |
| Gene name | NK2 homeobox 1 | |
| Gene Alias | BCH | |
| Cytomap | 14q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P43699 |
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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 |
| 7080 | NKX2-1 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 1.28e-08 | -3.70e-01 | 0.02 |
| 7080 | NKX2-1 | Adj_PTCwithHT_8 | Human | Thyroid | HT | 2.18e-03 | -3.70e-01 | 0.0267 |
| 7080 | NKX2-1 | PTCwithHT_6 | Human | Thyroid | HT | 2.77e-07 | -3.63e-01 | 0.02 |
| 7080 | NKX2-1 | PTCwithHT_8 | Human | Thyroid | HT | 7.48e-05 | -3.31e-01 | 0.0351 |
| 7080 | NKX2-1 | PTCwithoutHT_2 | Human | Thyroid | PTC | 1.14e-05 | -3.30e-01 | 0.0419 |
| 7080 | NKX2-1 | male-WTA | Human | Thyroid | PTC | 4.93e-69 | 8.37e-01 | 0.1037 |
| 7080 | NKX2-1 | female-WTA | Human | Thyroid | PTC | 5.32e-05 | 5.80e-01 | 0.0726 |
| 7080 | NKX2-1 | nodule-WTA | Human | Thyroid | goiters | 1.09e-02 | 2.64e-01 | 0.0534 |
| 7080 | NKX2-1 | PTC01 | Human | Thyroid | PTC | 4.20e-31 | 1.31e+00 | 0.1899 |
| 7080 | NKX2-1 | PTC03 | Human | Thyroid | PTC | 7.30e-10 | 1.06e+00 | 0.1784 |
| 7080 | NKX2-1 | PTC04 | Human | Thyroid | PTC | 5.01e-44 | 1.51e+00 | 0.1927 |
| 7080 | NKX2-1 | PTC05 | Human | Thyroid | PTC | 2.39e-36 | 2.21e+00 | 0.2065 |
| 7080 | NKX2-1 | PTC06 | Human | Thyroid | PTC | 1.96e-76 | 2.54e+00 | 0.2057 |
| 7080 | NKX2-1 | PTC07 | Human | Thyroid | PTC | 7.79e-96 | 1.99e+00 | 0.2044 |
| 7080 | NKX2-1 | ATC12 | Human | Thyroid | ATC | 2.71e-09 | -3.70e-01 | 0.34 |
| 7080 | NKX2-1 | ATC13 | Human | Thyroid | ATC | 2.77e-07 | -3.70e-01 | 0.34 |
| 7080 | NKX2-1 | ATC4 | Human | Thyroid | ATC | 1.53e-04 | -3.70e-01 | 0.34 |
| 7080 | NKX2-1 | ATC5 | Human | Thyroid | ATC | 1.28e-08 | -3.70e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:004873229 | Thyroid | goiters | gland development | 22/497 | 436/18723 | 3.19e-03 | 4.79e-02 | 22 |
| GO:0030878 | Thyroid | goiters | thyroid gland development | 4/497 | 24/18723 | 3.42e-03 | 4.97e-02 | 4 |
| GO:007155925 | Thyroid | ATC | response to transforming growth factor beta | 142/6293 | 256/18723 | 4.30e-13 | 1.94e-11 | 142 |
| GO:007156026 | Thyroid | ATC | cellular response to transforming growth factor beta stimulus | 137/6293 | 250/18723 | 3.69e-12 | 1.49e-10 | 137 |
| GO:000717924 | Thyroid | ATC | transforming growth factor beta receptor signaling pathway | 112/6293 | 198/18723 | 2.42e-11 | 8.44e-10 | 112 |
| GO:004873233 | Thyroid | ATC | gland development | 210/6293 | 436/18723 | 1.50e-10 | 4.59e-09 | 210 |
| GO:006156423 | Thyroid | ATC | axon development | 220/6293 | 467/18723 | 6.85e-10 | 1.80e-08 | 220 |
| GO:000740919 | Thyroid | ATC | axonogenesis | 197/6293 | 418/18723 | 5.09e-09 | 1.13e-07 | 197 |
| GO:000717823 | Thyroid | ATC | transmembrane receptor protein serine/threonine kinase signaling pathway | 170/6293 | 355/18723 | 1.40e-08 | 2.87e-07 | 170 |
| GO:000183722 | Thyroid | ATC | epithelial to mesenchymal transition | 87/6293 | 157/18723 | 1.50e-08 | 3.06e-07 | 87 |
| GO:001701522 | Thyroid | ATC | regulation of transforming growth factor beta receptor signaling pathway | 74/6293 | 128/18723 | 1.58e-08 | 3.20e-07 | 74 |
| GO:190384422 | Thyroid | ATC | regulation of cellular response to transforming growth factor beta stimulus | 75/6293 | 131/18723 | 2.26e-08 | 4.39e-07 | 75 |
| GO:006056222 | Thyroid | ATC | epithelial tube morphogenesis | 156/6293 | 325/18723 | 4.48e-08 | 8.14e-07 | 156 |
| GO:006145827 | Thyroid | ATC | reproductive system development | 193/6293 | 427/18723 | 3.32e-07 | 4.92e-06 | 193 |
| GO:004876221 | Thyroid | ATC | mesenchymal cell differentiation | 116/6293 | 236/18723 | 5.08e-07 | 7.30e-06 | 116 |
| GO:004851124 | Thyroid | ATC | rhythmic process | 141/6293 | 298/18723 | 5.58e-07 | 7.93e-06 | 141 |
| GO:003032321 | Thyroid | ATC | respiratory tube development | 93/6293 | 181/18723 | 5.67e-07 | 8.02e-06 | 93 |
| GO:004860825 | Thyroid | ATC | reproductive structure development | 190/6293 | 424/18723 | 8.40e-07 | 1.11e-05 | 190 |
| GO:003032421 | Thyroid | ATC | lung development | 90/6293 | 177/18723 | 1.53e-06 | 1.88e-05 | 90 |
| GO:006048521 | Thyroid | ATC | mesenchyme development | 136/6293 | 291/18723 | 2.04e-06 | 2.43e-05 | 136 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| NKX2-1 | AT2L | Lung | Healthy | PTGDS,KCTD12,FASN, etc. | 1.80e-01 |  |
| NKX2-1 | CLUB | Lung | IAC | SFTA3,MBIP,SFTPB, etc. | 2.40e-01 |  |
| NKX2-1 | END | Thyroid | Healthy | NPC2,TSHR,SPINT2, etc. | 2.29e-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 |
| NKX2-1 | SNV | Missense_Mutation | novel | c.997G>T | p.Ala333Ser | p.A333S | P43699 | protein_coding | tolerated_low_confidence(0.37) | benign(0.058) | TCGA-EW-A6SA-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| NKX2-1 | SNV | Missense_Mutation | c.259G>A | p.Ala87Thr | p.A87T | P43699 | protein_coding | tolerated(0.23) | benign(0.09) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NKX2-1 | SNV | Missense_Mutation | rs548436641 | c.1148N>T | p.Ser383Leu | p.S383L | P43699 | protein_coding | deleterious_low_confidence(0.05) | possibly_damaging(0.5) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| NKX2-1 | SNV | Missense_Mutation | c.572G>A | p.Arg191His | p.R191H | P43699 | protein_coding | deleterious(0) | probably_damaging(0.927) | TCGA-A6-2677-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Ancillary | leucovorin | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.650N>T | p.Ser217Leu | p.S217L | P43699 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.742N>T | p.Arg248Cys | p.R248C | P43699 | protein_coding | deleterious(0) | possibly_damaging(0.489) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.1130T>C | p.Leu377Pro | p.L377P | P43699 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.773) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.43N>A | p.Ala15Thr | p.A15T | P43699 | protein_coding | deleterious_low_confidence(0.01) | benign(0.031) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.28C>T | p.Arg10Trp | p.R10W | P43699 | protein_coding | deleterious_low_confidence(0) | benign(0.056) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NKX2-1 | SNV | Missense_Mutation | c.119N>T | p.Pro40Leu | p.P40L | P43699 | protein_coding | deleterious(0) | benign(0.017) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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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