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Gene: KDM4B |
Gene summary for KDM4B |
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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 |
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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 |
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∗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 |
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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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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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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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∗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 |
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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 | novel | c.3179G>A | p.Arg1060His | p.R1060H | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-CR-7380-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | unknown | PD | |
KDM4B | SNV | Missense_Mutation | novel | c.329N>A | p.Pro110Gln | p.P110Q | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-CR-7402-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD | |
KDM4B | SNV | Missense_Mutation | novel | c.1666C>A | p.Gln556Lys | p.Q556K | protein_coding | tolerated(0.46) | benign(0.005) | TCGA-CV-6953-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
KDM4B | SNV | Missense_Mutation | novel | c.178N>C | p.Tyr60His | p.Y60H | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
KDM4B | SNV | Missense_Mutation | novel | c.515N>C | p.Val172Ala | p.V172A | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
KDM4B | SNV | Missense_Mutation | novel | c.521C>T | p.Thr174Met | p.T174M | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-T2-A6WX-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | |
KDM4B | SNV | Missense_Mutation | rs757254378 | c.196G>A | p.Val66Met | p.V66M | protein_coding | tolerated(0.42) | benign(0.021) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD | |
KDM4B | insertion | Frame_Shift_Ins | novel | c.146_147insC | p.Lys52GlufsTer10 | p.K52Efs*10 | protein_coding | TCGA-KK-A59V-01 | Prostate | prostate adenocarcinoma | Male | <65 | 9 | Unknown | Unknown | SD | |||
KDM4B | insertion | Frame_Shift_Ins | novel | c.306_307insA | p.Asn103LysfsTer14 | p.N103Kfs*14 | protein_coding | TCGA-ZG-A9KY-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | SD | |||
KDM4B | SNV | Missense_Mutation | c.571N>A | p.Glu191Lys | p.E191K | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BR-4201-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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