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Gene: JADE1 |
Gene summary for JADE1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | JADE1 | Gene ID | 79960 |
| Gene name | jade family PHD finger 1 | |
| Gene Alias | PHF17 | |
| Cytomap | 4q28.2 | |
| Gene Type | protein-coding | GO ID | GO:0000082 | UniProtAcc | Q6IE81 |
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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 |
| 79960 | JADE1 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 6.67e-08 | -4.51e-01 | 0.02 |
| 79960 | JADE1 | Adj_PTCwithHT_8 | Human | Thyroid | HT | 3.86e-03 | -4.09e-01 | 0.0267 |
| 79960 | JADE1 | PTCwithHT_6 | Human | Thyroid | HT | 1.99e-03 | -4.52e-01 | 0.02 |
| 79960 | JADE1 | PTCwithHT_8 | Human | Thyroid | HT | 2.29e-06 | -4.46e-01 | 0.0351 |
| 79960 | JADE1 | PTCwithoutHT_2 | Human | Thyroid | PTC | 4.82e-05 | -4.03e-01 | 0.0419 |
| 79960 | JADE1 | male-WTA | Human | Thyroid | PTC | 3.85e-47 | 9.69e-02 | 0.1037 |
| 79960 | JADE1 | PTC01 | Human | Thyroid | PTC | 2.48e-10 | 5.94e-01 | 0.1899 |
| 79960 | JADE1 | PTC03 | Human | Thyroid | PTC | 1.13e-04 | -1.90e-01 | 0.1784 |
| 79960 | JADE1 | PTC04 | Human | Thyroid | PTC | 1.02e-04 | 4.05e-01 | 0.1927 |
| 79960 | JADE1 | PTC05 | Human | Thyroid | PTC | 6.90e-10 | 6.56e-01 | 0.2065 |
| 79960 | JADE1 | PTC06 | Human | Thyroid | PTC | 1.24e-17 | 6.11e-01 | 0.2057 |
| 79960 | JADE1 | PTC07 | Human | Thyroid | PTC | 2.53e-33 | 6.32e-01 | 0.2044 |
| 79960 | JADE1 | ATC08 | Human | Thyroid | ATC | 1.73e-03 | -4.07e-01 | 0.0541 |
| 79960 | JADE1 | ATC09 | Human | Thyroid | ATC | 3.23e-06 | -3.56e-01 | 0.2871 |
| 79960 | JADE1 | ATC11 | Human | Thyroid | ATC | 1.73e-04 | -1.81e-01 | 0.3386 |
| 79960 | JADE1 | ATC12 | Human | Thyroid | ATC | 1.24e-10 | -3.54e-01 | 0.34 |
| 79960 | JADE1 | ATC13 | Human | Thyroid | ATC | 1.69e-14 | -2.49e-01 | 0.34 |
| 79960 | JADE1 | ATC1 | Human | Thyroid | ATC | 5.64e-05 | -3.52e-01 | 0.2878 |
| 79960 | JADE1 | ATC2 | Human | Thyroid | ATC | 7.33e-07 | 2.99e-01 | 0.34 |
| 79960 | JADE1 | ATC3 | Human | Thyroid | ATC | 3.92e-06 | -1.53e-01 | 0.338 |
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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:001604926 | Thyroid | HT | cell growth | 58/1272 | 482/18723 | 1.56e-05 | 3.82e-04 | 58 |
| GO:000155825 | Thyroid | HT | regulation of cell growth | 47/1272 | 414/18723 | 3.77e-04 | 4.76e-03 | 47 |
| GO:00459269 | Thyroid | HT | negative regulation of growth | 31/1272 | 249/18723 | 8.02e-04 | 8.75e-03 | 31 |
| GO:001605520 | Thyroid | HT | Wnt signaling pathway | 48/1272 | 444/18723 | 9.68e-04 | 9.93e-03 | 48 |
| GO:019873820 | Thyroid | HT | cell-cell signaling by wnt | 48/1272 | 446/18723 | 1.07e-03 | 1.07e-02 | 48 |
| GO:006007019 | Thyroid | HT | canonical Wnt signaling pathway | 34/1272 | 303/18723 | 2.76e-03 | 2.27e-02 | 34 |
| GO:006082820 | Thyroid | HT | regulation of canonical Wnt signaling pathway | 29/1272 | 253/18723 | 4.01e-03 | 2.96e-02 | 29 |
| GO:003011120 | Thyroid | HT | regulation of Wnt signaling pathway | 35/1272 | 328/18723 | 5.41e-03 | 3.58e-02 | 35 |
| GO:20000458 | Thyroid | HT | regulation of G1/S transition of mitotic cell cycle | 18/1272 | 142/18723 | 7.71e-03 | 4.54e-02 | 18 |
| GO:000734618 | Thyroid | HT | regulation of mitotic cell cycle | 45/1272 | 457/18723 | 7.86e-03 | 4.61e-02 | 45 |
| GO:001657010 | Thyroid | PTC | histone modification | 235/5968 | 463/18723 | 1.17e-17 | 1.15e-15 | 235 |
| GO:00064737 | Thyroid | PTC | protein acetylation | 116/5968 | 201/18723 | 3.05e-14 | 1.92e-12 | 116 |
| GO:0016055110 | Thyroid | PTC | Wnt signaling pathway | 217/5968 | 444/18723 | 3.71e-14 | 2.30e-12 | 217 |
| GO:00435437 | Thyroid | PTC | protein acylation | 134/5968 | 243/18723 | 4.22e-14 | 2.58e-12 | 134 |
| GO:0198738110 | Thyroid | PTC | cell-cell signaling by wnt | 217/5968 | 446/18723 | 6.68e-14 | 3.73e-12 | 217 |
| GO:00182059 | Thyroid | PTC | peptidyl-lysine modification | 188/5968 | 376/18723 | 1.34e-13 | 7.09e-12 | 188 |
| GO:00183947 | Thyroid | PTC | peptidyl-lysine acetylation | 99/5968 | 169/18723 | 6.54e-13 | 3.08e-11 | 99 |
| GO:0016049112 | Thyroid | PTC | cell growth | 225/5968 | 482/18723 | 4.75e-12 | 2.07e-10 | 225 |
| GO:0030111110 | Thyroid | PTC | regulation of Wnt signaling pathway | 163/5968 | 328/18723 | 1.05e-11 | 4.29e-10 | 163 |
| GO:00064757 | Thyroid | PTC | internal protein amino acid acetylation | 92/5968 | 160/18723 | 1.80e-11 | 7.06e-10 | 92 |
| Page: 1 2 3 4 5 |
| 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 |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗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 |
| JADE1 | SNV | Missense_Mutation | c.1727N>G | p.Ser576Cys | p.S576C | Q6IE81 | protein_coding | deleterious(0.01) | benign(0) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD | |
| JADE1 | SNV | Missense_Mutation | novel | c.128A>C | p.Lys43Thr | p.K43T | Q6IE81 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| JADE1 | SNV | Missense_Mutation | novel | c.1988G>C | p.Arg663Pro | p.R663P | Q6IE81 | protein_coding | tolerated(0.22) | benign(0.006) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| JADE1 | SNV | Missense_Mutation | novel | c.86C>G | p.Ser29Cys | p.S29C | Q6IE81 | protein_coding | tolerated(0.06) | probably_damaging(0.979) | TCGA-AR-A2LE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | PD |
| JADE1 | SNV | Missense_Mutation | c.307G>A | p.Glu103Lys | p.E103K | Q6IE81 | protein_coding | deleterious(0.01) | possibly_damaging(0.688) | TCGA-C8-A12P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| JADE1 | insertion | Nonsense_Mutation | novel | c.100_101insACCCATGTTGATGGGGTACATGGAGAGGAGGAACCCACAGAGT | p.Ser34AsnfsTer4 | p.S34Nfs*4 | Q6IE81 | protein_coding | TCGA-A8-A06O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | SD | ||
| JADE1 | insertion | Frame_Shift_Ins | novel | c.1418_1419insGAATAGACCATTAT | p.Glu474AsnfsTer5 | p.E474Nfs*5 | Q6IE81 | protein_coding | TCGA-A8-A096-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| JADE1 | insertion | Nonsense_Mutation | novel | c.1235_1236insCATCTCTATAAAAAAAATTCCAAGCCTTACCTCTTTTAAAACATGACA | p.Arg412_Val413insIleSerIleLysLysIleProSerLeuThrSerPheLysThrTerGln | p.R412_V413insISIKKIPSLTSFKT*Q | Q6IE81 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
| JADE1 | insertion | Frame_Shift_Ins | novel | c.281_282insGTGG | p.Gln95TrpfsTer10 | p.Q95Wfs*10 | Q6IE81 | protein_coding | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| JADE1 | insertion | Nonsense_Mutation | novel | c.283_284insCTTGATACAGCATCCCTGCACAGAATGAGCACATT | p.Gln95ProfsTer2 | p.Q95Pfs*2 | Q6IE81 | protein_coding | TCGA-BH-A0BR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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