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Gene: KDM2B |
Gene summary for KDM2B |
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Gene information | Species | Human | Gene symbol | KDM2B | Gene ID | 84678 |
Gene name | lysine demethylase 2B | |
Gene Alias | CXXC2 | |
Cytomap | 12q24.31 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q8NHM5 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
84678 | KDM2B | LZE7T | Human | Esophagus | ESCC | 4.52e-03 | 1.57e-01 | 0.0667 |
84678 | KDM2B | LZE24T | Human | Esophagus | ESCC | 2.93e-03 | 1.56e-01 | 0.0596 |
84678 | KDM2B | P2T-E | Human | Esophagus | ESCC | 1.48e-41 | 7.82e-01 | 0.1177 |
84678 | KDM2B | P4T-E | Human | Esophagus | ESCC | 1.09e-07 | 2.23e-01 | 0.1323 |
84678 | KDM2B | P5T-E | Human | Esophagus | ESCC | 2.67e-09 | 1.16e-01 | 0.1327 |
84678 | KDM2B | P8T-E | Human | Esophagus | ESCC | 3.20e-18 | 2.35e-01 | 0.0889 |
84678 | KDM2B | P9T-E | Human | Esophagus | ESCC | 1.92e-03 | 7.94e-02 | 0.1131 |
84678 | KDM2B | P10T-E | Human | Esophagus | ESCC | 4.99e-16 | 1.93e-01 | 0.116 |
84678 | KDM2B | P11T-E | Human | Esophagus | ESCC | 2.03e-04 | 2.66e-01 | 0.1426 |
84678 | KDM2B | P12T-E | Human | Esophagus | ESCC | 2.27e-21 | 2.29e-01 | 0.1122 |
84678 | KDM2B | P15T-E | Human | Esophagus | ESCC | 1.89e-08 | 1.85e-01 | 0.1149 |
84678 | KDM2B | P16T-E | Human | Esophagus | ESCC | 7.33e-11 | 2.93e-01 | 0.1153 |
84678 | KDM2B | P20T-E | Human | Esophagus | ESCC | 3.88e-07 | 1.82e-01 | 0.1124 |
84678 | KDM2B | P21T-E | Human | Esophagus | ESCC | 8.32e-21 | 3.51e-01 | 0.1617 |
84678 | KDM2B | P22T-E | Human | Esophagus | ESCC | 9.53e-12 | 1.34e-01 | 0.1236 |
84678 | KDM2B | P23T-E | Human | Esophagus | ESCC | 1.37e-11 | 2.07e-01 | 0.108 |
84678 | KDM2B | P24T-E | Human | Esophagus | ESCC | 2.64e-13 | 7.68e-02 | 0.1287 |
84678 | KDM2B | P26T-E | Human | Esophagus | ESCC | 2.43e-14 | 2.58e-01 | 0.1276 |
84678 | KDM2B | P27T-E | Human | Esophagus | ESCC | 1.02e-21 | 3.20e-01 | 0.1055 |
84678 | KDM2B | P28T-E | Human | Esophagus | ESCC | 1.15e-18 | 2.98e-01 | 0.1149 |
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Tissue | Expression Dynamics | Abbreviation |
Esophagus | ![]() | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias | ||
LGIN: Low-grade intraepithelial neoplasias |
∗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:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
GO:0016049110 | Esophagus | ESCC | cell growth | 289/8552 | 482/18723 | 1.29e-10 | 3.77e-09 | 289 |
GO:000155819 | Esophagus | ESCC | regulation of cell growth | 248/8552 | 414/18723 | 2.97e-09 | 6.45e-08 | 248 |
GO:000184115 | Esophagus | ESCC | neural tube formation | 75/8552 | 102/18723 | 9.68e-09 | 1.95e-07 | 75 |
GO:000184314 | Esophagus | ESCC | neural tube closure | 66/8552 | 88/18723 | 1.98e-08 | 3.82e-07 | 66 |
GO:00065136 | Esophagus | ESCC | protein monoubiquitination | 53/8552 | 67/18723 | 2.11e-08 | 4.03e-07 | 53 |
GO:001657414 | Esophagus | ESCC | histone ubiquitination | 40/8552 | 47/18723 | 2.40e-08 | 4.55e-07 | 40 |
GO:0070997111 | Esophagus | ESCC | neuron death | 216/8552 | 361/18723 | 3.49e-08 | 6.45e-07 | 216 |
GO:001402014 | Esophagus | ESCC | primary neural tube formation | 69/8552 | 94/18723 | 4.22e-08 | 7.76e-07 | 69 |
GO:006060614 | Esophagus | ESCC | tube closure | 66/8552 | 89/18723 | 4.24e-08 | 7.76e-07 | 66 |
GO:00219159 | Esophagus | ESCC | neural tube development | 101/8552 | 152/18723 | 1.78e-07 | 2.79e-06 | 101 |
GO:00163316 | Esophagus | ESCC | morphogenesis of embryonic epithelium | 98/8552 | 147/18723 | 2.12e-07 | 3.27e-06 | 98 |
GO:000183814 | Esophagus | ESCC | embryonic epithelial tube formation | 83/8552 | 121/18723 | 2.78e-07 | 4.08e-06 | 83 |
GO:009872714 | Esophagus | ESCC | maintenance of cell number | 90/8552 | 134/18723 | 3.94e-07 | 5.43e-06 | 90 |
GO:001982714 | Esophagus | ESCC | stem cell population maintenance | 88/8552 | 131/18723 | 5.23e-07 | 6.97e-06 | 88 |
GO:003514815 | Esophagus | ESCC | tube formation | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
GO:0051402110 | Esophagus | ESCC | neuron apoptotic process | 148/8552 | 246/18723 | 3.08e-06 | 3.47e-05 | 148 |
GO:1901214111 | Esophagus | ESCC | regulation of neuron death | 186/8552 | 319/18723 | 3.35e-06 | 3.73e-05 | 186 |
GO:00721759 | Esophagus | ESCC | epithelial tube formation | 86/8552 | 132/18723 | 4.81e-06 | 5.10e-05 | 86 |
GO:003352213 | Esophagus | ESCC | histone H2A ubiquitination | 23/8552 | 26/18723 | 6.82e-06 | 6.90e-05 | 23 |
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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 |
KDM2B | SNV | Missense_Mutation | c.1264N>C | p.Glu422Gln | p.E422Q | Q8NHM5 | protein_coding | tolerated(0.32) | benign(0.382) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
KDM2B | SNV | Missense_Mutation | c.2782G>A | p.Glu928Lys | p.E928K | Q8NHM5 | protein_coding | tolerated_low_confidence(0.08) | benign(0) | TCGA-EK-A2R7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
KDM2B | SNV | Missense_Mutation | c.3949G>A | p.Glu1317Lys | p.E1317K | Q8NHM5 | protein_coding | deleterious(0) | benign(0.007) | TCGA-EK-A3GJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
KDM2B | SNV | Missense_Mutation | novel | c.2461N>A | p.Leu821Ile | p.L821I | Q8NHM5 | protein_coding | tolerated(0.2) | benign(0.157) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
KDM2B | SNV | Missense_Mutation | novel | c.2078N>C | p.Glu693Ala | p.E693A | Q8NHM5 | protein_coding | deleterious(0) | benign(0.297) | TCGA-VS-A950-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
KDM2B | SNV | Missense_Mutation | c.2722N>A | p.Asp908Asn | p.D908N | Q8NHM5 | protein_coding | tolerated_low_confidence(0.09) | benign(0.007) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
KDM2B | SNV | Missense_Mutation | c.1829N>A | p.Arg610Gln | p.R610Q | Q8NHM5 | protein_coding | deleterious(0.01) | benign(0.298) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
KDM2B | SNV | Missense_Mutation | c.290T>C | p.Val97Ala | p.V97A | Q8NHM5 | protein_coding | deleterious(0) | possibly_damaging(0.498) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
KDM2B | SNV | Missense_Mutation | rs782061809 | c.3692N>A | p.Arg1231Gln | p.R1231Q | Q8NHM5 | protein_coding | deleterious(0.05) | possibly_damaging(0.652) | TCGA-AA-3697-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
KDM2B | SNV | Missense_Mutation | c.977N>A | p.Gly326Asp | p.G326D | Q8NHM5 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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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