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Gene: KDM5A |
Gene summary for KDM5A |
Gene summary. |
Gene information | Species | Human | Gene symbol | KDM5A | Gene ID | 5927 |
Gene name | lysine demethylase 5A | |
Gene Alias | RBBP-2 | |
Cytomap | 12p13.33 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P29375 |
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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 |
5927 | KDM5A | CA_HPV_1 | Human | Cervix | CC | 6.57e-04 | -4.03e-02 | 0.0264 |
5927 | KDM5A | CCI_2 | Human | Cervix | CC | 1.05e-02 | 7.11e-01 | 0.5249 |
5927 | KDM5A | CCI_3 | Human | Cervix | CC | 7.68e-10 | 1.00e+00 | 0.516 |
5927 | KDM5A | L1 | Human | Cervix | CC | 1.60e-05 | -3.24e-01 | 0.0802 |
5927 | KDM5A | LZE2T | Human | Esophagus | ESCC | 2.35e-07 | 7.27e-01 | 0.082 |
5927 | KDM5A | LZE4T | Human | Esophagus | ESCC | 3.15e-14 | 3.95e-01 | 0.0811 |
5927 | KDM5A | LZE7T | Human | Esophagus | ESCC | 2.61e-07 | 7.25e-01 | 0.0667 |
5927 | KDM5A | LZE8T | Human | Esophagus | ESCC | 3.38e-13 | 5.93e-01 | 0.067 |
5927 | KDM5A | LZE20T | Human | Esophagus | ESCC | 1.00e-04 | 3.68e-01 | 0.0662 |
5927 | KDM5A | LZE22T | Human | Esophagus | ESCC | 1.23e-02 | 2.99e-01 | 0.068 |
5927 | KDM5A | LZE24T | Human | Esophagus | ESCC | 3.92e-09 | 4.73e-01 | 0.0596 |
5927 | KDM5A | LZE21T | Human | Esophagus | ESCC | 3.23e-05 | 3.43e-01 | 0.0655 |
5927 | KDM5A | P1T-E | Human | Esophagus | ESCC | 7.68e-08 | 7.55e-01 | 0.0875 |
5927 | KDM5A | P2T-E | Human | Esophagus | ESCC | 1.53e-54 | 1.08e+00 | 0.1177 |
5927 | KDM5A | P4T-E | Human | Esophagus | ESCC | 3.96e-37 | 1.04e+00 | 0.1323 |
5927 | KDM5A | P5T-E | Human | Esophagus | ESCC | 1.70e-22 | 3.51e-01 | 0.1327 |
5927 | KDM5A | P8T-E | Human | Esophagus | ESCC | 5.30e-30 | 6.96e-01 | 0.0889 |
5927 | KDM5A | P9T-E | Human | Esophagus | ESCC | 2.44e-08 | 2.24e-01 | 0.1131 |
5927 | KDM5A | P10T-E | Human | Esophagus | ESCC | 6.36e-35 | 7.71e-01 | 0.116 |
5927 | KDM5A | P11T-E | Human | Esophagus | ESCC | 1.62e-12 | 5.50e-01 | 0.1426 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00513469 | Cervix | CC | negative regulation of hydrolase activity | 81/2311 | 379/18723 | 4.27e-07 | 1.67e-05 | 81 |
GO:00614588 | Cervix | CC | reproductive system development | 87/2311 | 427/18723 | 1.37e-06 | 4.55e-05 | 87 |
GO:00486088 | Cervix | CC | reproductive structure development | 86/2311 | 424/18723 | 1.90e-06 | 5.97e-05 | 86 |
GO:00485118 | Cervix | CC | rhythmic process | 65/2311 | 298/18723 | 2.79e-06 | 8.04e-05 | 65 |
GO:00510904 | Cervix | CC | regulation of DNA-binding transcription factor activity | 87/2311 | 440/18723 | 4.85e-06 | 1.22e-04 | 87 |
GO:00063257 | Cervix | CC | chromatin organization | 78/2311 | 409/18723 | 5.40e-05 | 8.02e-04 | 78 |
GO:00076238 | Cervix | CC | circadian rhythm | 46/2311 | 210/18723 | 6.76e-05 | 9.60e-04 | 46 |
GO:00165705 | Cervix | CC | histone modification | 84/2311 | 463/18723 | 1.70e-04 | 2.01e-03 | 84 |
GO:00310565 | Cervix | CC | regulation of histone modification | 33/2311 | 152/18723 | 7.97e-04 | 7.00e-03 | 33 |
GO:00329226 | Cervix | CC | circadian regulation of gene expression | 18/2311 | 68/18723 | 1.18e-03 | 9.56e-03 | 18 |
GO:00063381 | Cervix | CC | chromatin remodeling | 45/2311 | 255/18723 | 8.33e-03 | 4.30e-02 | 45 |
GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
GO:003105614 | Esophagus | ESCC | regulation of histone modification | 106/8552 | 152/18723 | 1.52e-09 | 3.55e-08 | 106 |
GO:000632517 | Esophagus | ESCC | chromatin organization | 240/8552 | 409/18723 | 6.52e-08 | 1.14e-06 | 240 |
GO:00356015 | Esophagus | ESCC | protein deacylation | 79/8552 | 112/18723 | 8.30e-08 | 1.42e-06 | 79 |
GO:0061458110 | Esophagus | ESCC | reproductive system development | 247/8552 | 427/18723 | 2.24e-07 | 3.42e-06 | 247 |
GO:004860818 | Esophagus | ESCC | reproductive structure development | 245/8552 | 424/18723 | 2.82e-07 | 4.14e-06 | 245 |
GO:00987325 | Esophagus | ESCC | macromolecule deacylation | 80/8552 | 116/18723 | 3.19e-07 | 4.50e-06 | 80 |
GO:00165754 | Esophagus | ESCC | histone deacetylation | 60/8552 | 82/18723 | 3.85e-07 | 5.32e-06 | 60 |
GO:00510908 | Esophagus | ESCC | regulation of DNA-binding transcription factor activity | 252/8552 | 440/18723 | 5.22e-07 | 6.97e-06 | 252 |
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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 |
∗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 |
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 |
KDM5A | SNV | Missense_Mutation | c.4604N>T | p.Lys1535Met | p.K1535M | P29375 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
KDM5A | SNV | Missense_Mutation | c.3710C>T | p.Pro1237Leu | p.P1237L | P29375 | protein_coding | tolerated(0.15) | probably_damaging(0.986) | TCGA-AA-A029-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
KDM5A | SNV | Missense_Mutation | novel | c.1808N>A | p.Arg603Gln | p.R603Q | P29375 | protein_coding | deleterious(0) | possibly_damaging(0.517) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
KDM5A | SNV | Missense_Mutation | novel | c.946N>T | p.Asp316Tyr | p.D316Y | P29375 | protein_coding | deleterious(0) | possibly_damaging(0.57) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
KDM5A | SNV | Missense_Mutation | rs769454180 | c.1943N>A | p.Arg648Gln | p.R648Q | P29375 | protein_coding | tolerated(0.15) | benign(0.03) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
KDM5A | SNV | Missense_Mutation | c.4130A>T | p.Glu1377Val | p.E1377V | P29375 | protein_coding | deleterious(0.02) | probably_damaging(0.987) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
KDM5A | SNV | Missense_Mutation | c.692G>A | p.Ser231Asn | p.S231N | P29375 | protein_coding | tolerated(0.38) | benign(0) | TCGA-CK-5913-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
KDM5A | SNV | Missense_Mutation | novel | c.1222N>A | p.Glu408Lys | p.E408K | P29375 | protein_coding | deleterious(0) | benign(0.258) | TCGA-D5-6923-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
KDM5A | SNV | Missense_Mutation | rs759172420 | c.4170N>A | p.Met1390Ile | p.M1390I | P29375 | protein_coding | tolerated_low_confidence(0.09) | possibly_damaging(0.838) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
KDM5A | SNV | Missense_Mutation | c.3715N>T | p.Arg1239Trp | p.R1239W | P29375 | protein_coding | deleterious(0) | possibly_damaging(0.832) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
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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 |
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | BDBM50158803 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | US9714230, 46 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | 1190312-92-5 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | US10022354, Example 152 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | AKOS020330481 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | BDBM50158794 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | inhibitor | 178103606 | ||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | US10174026, Example 2 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | US10022354, Example 151 | |||
5927 | KDM5A | CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR | US10174026, Example 99 |
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