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Gene: KDM4B |
Gene summary for KDM4B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | KDM4B | Gene ID | 23030 |
| Gene name | lysine demethylase 4B | |
| Gene Alias | JMJD2B | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006325 | UniProtAcc | A0A0C4DFL8 |
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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 |
| 23030 | KDM4B | GSM4909293 | Human | Breast | IDC | 1.59e-17 | 3.97e-01 | 0.1581 |
| 23030 | KDM4B | GSM4909298 | Human | Breast | IDC | 3.79e-09 | 3.25e-01 | 0.1551 |
| 23030 | KDM4B | GSM4909301 | Human | Breast | IDC | 3.50e-05 | 3.63e-01 | 0.1577 |
| 23030 | KDM4B | GSM4909302 | Human | Breast | IDC | 1.21e-12 | 5.16e-01 | 0.1545 |
| 23030 | KDM4B | GSM4909306 | Human | Breast | IDC | 1.14e-04 | 3.22e-01 | 0.1564 |
| 23030 | KDM4B | GSM4909311 | Human | Breast | IDC | 2.40e-06 | 1.18e-01 | 0.1534 |
| 23030 | KDM4B | GSM4909312 | Human | Breast | IDC | 4.48e-04 | 1.95e-01 | 0.1552 |
| 23030 | KDM4B | GSM4909319 | Human | Breast | IDC | 7.64e-09 | -1.77e-02 | 0.1563 |
| 23030 | KDM4B | P3 | Human | Breast | IDC | 1.32e-03 | 5.71e-01 | 0.1542 |
| 23030 | KDM4B | DCIS2 | Human | Breast | DCIS | 2.91e-24 | 9.61e-02 | 0.0085 |
| 23030 | KDM4B | AEH-subject1 | Human | Endometrium | AEH | 2.52e-23 | 6.10e-01 | -0.3059 |
| 23030 | KDM4B | AEH-subject2 | Human | Endometrium | AEH | 9.75e-11 | 4.12e-01 | -0.2525 |
| 23030 | KDM4B | AEH-subject3 | Human | Endometrium | AEH | 4.17e-19 | 5.51e-01 | -0.2576 |
| 23030 | KDM4B | AEH-subject4 | Human | Endometrium | AEH | 7.05e-07 | 3.90e-01 | -0.2657 |
| 23030 | KDM4B | EEC-subject1 | Human | Endometrium | EEC | 6.70e-20 | 5.46e-01 | -0.2682 |
| 23030 | KDM4B | EEC-subject2 | Human | Endometrium | EEC | 2.76e-13 | 4.69e-01 | -0.2607 |
| 23030 | KDM4B | EEC-subject3 | Human | Endometrium | EEC | 8.26e-06 | 1.85e-01 | -0.2525 |
| 23030 | KDM4B | EEC-subject4 | Human | Endometrium | EEC | 1.61e-10 | 4.34e-01 | -0.2571 |
| 23030 | KDM4B | EEC-subject5 | Human | Endometrium | EEC | 1.41e-08 | 3.71e-01 | -0.249 |
| 23030 | KDM4B | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.32e-10 | 1.37e-03 | -0.1869 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:00063258 | Endometrium | AEH | chromatin organization | 64/2100 | 409/18723 | 3.69e-03 | 2.52e-02 | 64 |
| GO:000632513 | Endometrium | EEC | chromatin organization | 65/2168 | 409/18723 | 4.98e-03 | 3.14e-02 | 65 |
| GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
| GO:00064824 | Esophagus | ESCC | protein demethylation | 24/8552 | 33/18723 | 1.50e-03 | 7.06e-03 | 24 |
| GO:00082144 | Esophagus | ESCC | protein dealkylation | 24/8552 | 33/18723 | 1.50e-03 | 7.06e-03 | 24 |
| GO:00165773 | Esophagus | ESCC | histone demethylation | 22/8552 | 31/18723 | 3.90e-03 | 1.58e-02 | 22 |
| GO:00700763 | Esophagus | ESCC | histone lysine demethylation | 20/8552 | 28/18723 | 5.23e-03 | 1.97e-02 | 20 |
| GO:00165703 | Liver | NAFLD | histone modification | 90/1882 | 463/18723 | 5.74e-10 | 1.28e-07 | 90 |
| GO:00063255 | Liver | NAFLD | chromatin organization | 64/1882 | 409/18723 | 2.31e-04 | 3.89e-03 | 64 |
| GO:0070076 | Liver | NAFLD | histone lysine demethylation | 10/1882 | 28/18723 | 2.46e-04 | 4.09e-03 | 10 |
| GO:0016577 | Liver | NAFLD | histone demethylation | 10/1882 | 31/18723 | 6.28e-04 | 8.21e-03 | 10 |
| GO:0006482 | Liver | NAFLD | protein demethylation | 10/1882 | 33/18723 | 1.09e-03 | 1.27e-02 | 10 |
| GO:0008214 | Liver | NAFLD | protein dealkylation | 10/1882 | 33/18723 | 1.09e-03 | 1.27e-02 | 10 |
| GO:0070988 | Liver | NAFLD | demethylation | 16/1882 | 73/18723 | 2.09e-03 | 2.06e-02 | 16 |
| GO:001657021 | Liver | HCC | histone modification | 283/7958 | 463/18723 | 2.68e-16 | 2.33e-14 | 283 |
| GO:000632511 | Liver | HCC | chromatin organization | 206/7958 | 409/18723 | 7.23e-04 | 4.41e-03 | 206 |
| GO:001657010 | Thyroid | PTC | histone modification | 235/5968 | 463/18723 | 1.17e-17 | 1.15e-15 | 235 |
| GO:000632520 | Thyroid | PTC | chromatin organization | 183/5968 | 409/18723 | 2.55e-08 | 5.70e-07 | 183 |
| GO:00063385 | Thyroid | PTC | chromatin remodeling | 106/5968 | 255/18723 | 6.56e-04 | 4.13e-03 | 106 |
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| 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 |
| KDM4B | BN | Breast | ADJ | IGHD,MAML3,GNL1, etc. | 1.95e-01 |  |
| KDM4B | BN | Breast | DCIS | IGHD,MAML3,GNL1, etc. | 3.93e-01 |  |
| KDM4B | BN | Breast | Healthy | IGHD,MAML3,GNL1, etc. | 5.90e-02 |  |
| KDM4B | BN | Breast | IDC | IGHD,MAML3,GNL1, etc. | 2.15e-01 |  |
| KDM4B | BN | Breast | Precancer | IGHD,MAML3,GNL1, etc. | 1.05e-01 |  |
| KDM4B | INCAF | Colorectum | Healthy | C11orf80,LRRK1,ANKRD49, etc. | 1.19e-01 |  |
| KDM4B | HEP | Liver | Cirrhotic | FAM160A1,BMI1,MAP3K4, etc. | 5.95e-01 |  |
| KDM4B | STM | Liver | NAFLD | FAM160A1,BMI1,MAP3K4, etc. | 1.49e-02 |  |
| KDM4B | BN | Prostate | ADJ | ZNF490,HBS1L,TNFRSF13C, etc. | 3.05e-02 |  |
| KDM4B | CD8TEFF | Prostate | ADJ | ZNF490,HBS1L,TNFRSF13C, etc. | 3.79e-02 | |
| ∗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 2 |
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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 |
| KDM4B | SNV | Missense_Mutation | rs766027488 | c.2248N>A | p.Gly750Ser | p.G750S | protein_coding | tolerated(0.25) | possibly_damaging(0.566) | TCGA-A7-A13H-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | PD | |
| KDM4B | SNV | Missense_Mutation | rs759969080 | c.1991N>T | p.Ala664Val | p.A664V | protein_coding | tolerated(0.24) | benign(0.001) | TCGA-AC-A62X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| KDM4B | SNV | Missense_Mutation | c.1867N>A | p.Pro623Thr | p.P623T | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0BP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| KDM4B | SNV | Missense_Mutation | rs757254378 | c.196N>A | p.Val66Met | p.V66M | protein_coding | tolerated(0.42) | benign(0.021) | TCGA-LD-A74U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | taxotere | SD | |
| KDM4B | SNV | Missense_Mutation | novel | c.1958N>T | p.Arg653Met | p.R653M | protein_coding | deleterious(0) | possibly_damaging(0.642) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| KDM4B | SNV | Missense_Mutation | c.2240N>G | p.Ser747Cys | p.S747C | protein_coding | tolerated(0.07) | probably_damaging(0.947) | TCGA-DS-A0VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| KDM4B | SNV | Missense_Mutation | c.2058C>G | p.Ile686Met | p.I686M | protein_coding | deleterious(0) | possibly_damaging(0.576) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| KDM4B | SNV | Missense_Mutation | rs770149637 | c.1255N>A | p.Glu419Lys | p.E419K | protein_coding | tolerated(0.26) | benign(0.364) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| KDM4B | SNV | Missense_Mutation | c.584N>A | p.Leu195Gln | p.L195Q | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-LP-A5U2-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| KDM4B | SNV | Missense_Mutation | c.3031G>C | p.Glu1011Gln | p.E1011Q | protein_coding | tolerated(0.07) | benign(0.117) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| 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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