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Gene: JARID2 |
Gene summary for JARID2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | JARID2 | Gene ID | 3720 |
| Gene name | jumonji and AT-rich interaction domain containing 2 | |
| Gene Alias | JMJ | |
| Cytomap | 6p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q92833 |
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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 |
| 3720 | JARID2 | N_HPV_2 | Human | Cervix | N_HPV | 5.19e-03 | 1.39e-01 | -0.0131 |
| 3720 | JARID2 | CCI_1 | Human | Cervix | CC | 8.70e-15 | 1.62e+00 | 0.528 |
| 3720 | JARID2 | CCI_2 | Human | Cervix | CC | 3.84e-18 | 2.48e+00 | 0.5249 |
| 3720 | JARID2 | CCI_3 | Human | Cervix | CC | 1.45e-18 | 1.18e+00 | 0.516 |
| 3720 | JARID2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.21e-19 | -5.20e-01 | 0.0155 |
| 3720 | JARID2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.15e-06 | -5.22e-01 | -0.1808 |
| 3720 | JARID2 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.80e-05 | -3.18e-01 | -0.1088 |
| 3720 | JARID2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.32e-06 | -5.78e-01 | -0.1207 |
| 3720 | JARID2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.26e-02 | -4.21e-01 | -0.1706 |
| 3720 | JARID2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.26e-02 | -6.46e-01 | -0.2061 |
| 3720 | JARID2 | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.10e-03 | -6.39e-01 | -0.1462 |
| 3720 | JARID2 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.54e-08 | -3.33e-01 | -0.0842 |
| 3720 | JARID2 | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.59e-02 | -4.72e-01 | 0.0528 |
| 3720 | JARID2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 7.46e-12 | -4.29e-01 | 0.294 |
| 3720 | JARID2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.40e-02 | 5.55e-01 | 0.281 |
| 3720 | JARID2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.31e-09 | -5.01e-01 | 0.3005 |
| 3720 | JARID2 | A001-C-207 | Human | Colorectum | FAP | 2.91e-02 | -2.62e-01 | 0.1278 |
| 3720 | JARID2 | A015-C-203 | Human | Colorectum | FAP | 1.11e-30 | -4.61e-01 | -0.1294 |
| 3720 | JARID2 | A015-C-204 | Human | Colorectum | FAP | 6.97e-07 | -4.21e-01 | -0.0228 |
| 3720 | JARID2 | A014-C-040 | Human | Colorectum | FAP | 1.02e-05 | -5.93e-01 | -0.1184 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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 |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:000188916 | Prostate | BPH | liver development | 45/3107 | 147/18723 | 1.76e-05 | 2.18e-04 | 45 |
| GO:00106112 | Prostate | BPH | regulation of cardiac muscle hypertrophy | 26/3107 | 69/18723 | 2.09e-05 | 2.55e-04 | 26 |
| GO:00148973 | Prostate | BPH | striated muscle hypertrophy | 34/3107 | 102/18723 | 2.63e-05 | 3.10e-04 | 34 |
| GO:00033004 | Prostate | BPH | cardiac muscle hypertrophy | 33/3107 | 99/18723 | 3.43e-05 | 3.82e-04 | 33 |
| GO:00488636 | Prostate | BPH | stem cell differentiation | 55/3107 | 206/18723 | 1.56e-04 | 1.36e-03 | 55 |
| GO:00349686 | Prostate | BPH | histone lysine methylation | 35/3107 | 115/18723 | 1.64e-04 | 1.42e-03 | 35 |
| GO:00435025 | Prostate | BPH | regulation of muscle adaptation | 31/3107 | 98/18723 | 1.75e-04 | 1.50e-03 | 31 |
| GO:00147066 | Prostate | BPH | striated muscle tissue development | 91/3107 | 384/18723 | 1.90e-04 | 1.57e-03 | 91 |
| GO:009025710 | Prostate | BPH | regulation of muscle system process | 64/3107 | 252/18723 | 2.26e-04 | 1.81e-03 | 64 |
| GO:00064796 | Prostate | BPH | protein methylation | 49/3107 | 181/18723 | 2.42e-04 | 1.93e-03 | 49 |
| GO:00082136 | Prostate | BPH | protein alkylation | 49/3107 | 181/18723 | 2.42e-04 | 1.93e-03 | 49 |
| GO:00165716 | Prostate | BPH | histone methylation | 40/3107 | 141/18723 | 3.09e-04 | 2.37e-03 | 40 |
| GO:00030127 | Prostate | BPH | muscle system process | 103/3107 | 452/18723 | 3.54e-04 | 2.62e-03 | 103 |
| GO:00310566 | Prostate | BPH | regulation of histone modification | 42/3107 | 152/18723 | 4.09e-04 | 2.97e-03 | 42 |
| GO:00165772 | Prostate | BPH | histone demethylation | 13/3107 | 31/18723 | 7.48e-04 | 4.95e-03 | 13 |
| GO:00330023 | Prostate | BPH | muscle cell proliferation | 61/3107 | 248/18723 | 7.61e-04 | 5.02e-03 | 61 |
| GO:00063382 | Prostate | BPH | chromatin remodeling | 62/3107 | 255/18723 | 9.47e-04 | 5.97e-03 | 62 |
| GO:00064822 | Prostate | BPH | protein demethylation | 13/3107 | 33/18723 | 1.50e-03 | 8.85e-03 | 13 |
| GO:00082142 | Prostate | BPH | protein dealkylation | 13/3107 | 33/18723 | 1.50e-03 | 8.85e-03 | 13 |
| GO:00485384 | Prostate | BPH | thymus development | 16/3107 | 45/18723 | 1.62e-03 | 9.39e-03 | 16 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ∗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 |
| JARID2 | SNV | Missense_Mutation | c.1100N>G | p.Pro367Arg | p.P367R | Q92833 | protein_coding | deleterious_low_confidence(0.02) | benign(0.168) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| JARID2 | SNV | Missense_Mutation | c.71C>T | p.Ser24Leu | p.S24L | Q92833 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-BH-A0AZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR | |
| JARID2 | SNV | Missense_Mutation | c.550N>A | p.Glu184Lys | p.E184K | Q92833 | protein_coding | tolerated(0.06) | benign(0.022) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| JARID2 | insertion | Nonsense_Mutation | novel | c.1023_1024insTTTGGTTTTAGTGGAAGCATTTGAAA | p.Val342PhefsTer8 | p.V342Ffs*8 | Q92833 | protein_coding | TCGA-A2-A0EX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| JARID2 | insertion | Frame_Shift_Ins | novel | c.961_962insAGGAGCACACGCTGCAGACACCTCACTTTCTGCAGAGCTGG | p.Ser321LysfsTer30 | p.S321Kfs*30 | Q92833 | protein_coding | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| JARID2 | insertion | Frame_Shift_Ins | novel | c.2634_2635insCAAA | p.Val879GlnfsTer21 | p.V879Qfs*21 | Q92833 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| JARID2 | insertion | In_Frame_Ins | novel | c.2635_2636insCATGTTCTGACCCATTCTTTGCCCCCA | p.Val879delinsAlaCysSerAspProPhePheAlaProIle | p.V879delinsACSDPFFAPI | Q92833 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| JARID2 | deletion | Frame_Shift_Del | novel | c.2472delN | p.Tyr826IlefsTer8 | p.Y826Ifs*8 | Q92833 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| JARID2 | insertion | Frame_Shift_Ins | novel | c.2810_2811insCC | p.Ile938ProfsTer48 | p.I938Pfs*48 | Q92833 | protein_coding | TCGA-E9-A1NA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| JARID2 | insertion | Nonsense_Mutation | novel | c.2812_2813insCCGTAGAAGGATGGTTCTGAGAATGAATTTCTGTGGC | p.Ile938ThrfsTer7 | p.I938Tfs*7 | Q92833 | protein_coding | TCGA-E9-A1NA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
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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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