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Gene: KDM7A |
Gene summary for KDM7A |
Gene summary. |
Gene information | Species | Human | Gene symbol | KDM7A | Gene ID | 80853 |
Gene name | lysine demethylase 7A | |
Gene Alias | JHDM1D | |
Cytomap | 7q34 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q6ZMT4 |
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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 |
80853 | KDM7A | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.65e-10 | -5.09e-01 | 0.0155 |
80853 | KDM7A | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.42e-02 | -6.58e-01 | 0.0216 |
80853 | KDM7A | HTA11_347_2000001011 | Human | Colorectum | AD | 1.25e-08 | 5.43e-01 | -0.1954 |
80853 | KDM7A | HTA11_866_3004761011 | Human | Colorectum | AD | 8.56e-04 | -4.58e-01 | 0.096 |
80853 | KDM7A | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.47e-03 | -5.29e-01 | 0.0528 |
80853 | KDM7A | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.89e-12 | 8.31e-01 | 0.281 |
80853 | KDM7A | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.17e-02 | -3.26e-01 | 0.3859 |
80853 | KDM7A | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.15e-10 | -4.57e-01 | 0.3005 |
80853 | KDM7A | F007 | Human | Colorectum | FAP | 6.72e-03 | 1.24e-01 | 0.1176 |
80853 | KDM7A | A002-C-010 | Human | Colorectum | FAP | 2.48e-02 | -3.04e-02 | 0.242 |
80853 | KDM7A | A001-C-207 | Human | Colorectum | FAP | 4.09e-03 | 9.80e-02 | 0.1278 |
80853 | KDM7A | A015-C-203 | Human | Colorectum | FAP | 1.38e-32 | -5.32e-02 | -0.1294 |
80853 | KDM7A | A015-C-204 | Human | Colorectum | FAP | 3.79e-04 | 1.96e-02 | -0.0228 |
80853 | KDM7A | A014-C-040 | Human | Colorectum | FAP | 7.14e-04 | -2.30e-01 | -0.1184 |
80853 | KDM7A | A002-C-201 | Human | Colorectum | FAP | 3.45e-14 | -7.56e-02 | 0.0324 |
80853 | KDM7A | A002-C-203 | Human | Colorectum | FAP | 6.02e-11 | 2.52e-01 | 0.2786 |
80853 | KDM7A | A001-C-119 | Human | Colorectum | FAP | 3.56e-08 | -5.36e-03 | -0.1557 |
80853 | KDM7A | A001-C-108 | Human | Colorectum | FAP | 1.55e-24 | 2.62e-01 | -0.0272 |
80853 | KDM7A | A002-C-205 | Human | Colorectum | FAP | 2.54e-30 | 1.66e-01 | -0.1236 |
80853 | KDM7A | A001-C-104 | Human | Colorectum | FAP | 3.87e-11 | 2.54e-01 | 0.0184 |
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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:0070988 | Liver | NAFLD | demethylation | 16/1882 | 73/18723 | 2.09e-03 | 2.06e-02 | 16 |
GO:001657011 | Liver | Cirrhotic | histone modification | 154/4634 | 463/18723 | 1.92e-05 | 2.57e-04 | 154 |
GO:003090111 | Liver | Cirrhotic | midbrain development | 35/4634 | 90/18723 | 2.06e-03 | 1.28e-02 | 35 |
GO:001657021 | Liver | HCC | histone modification | 283/7958 | 463/18723 | 2.68e-16 | 2.33e-14 | 283 |
GO:003090121 | Liver | HCC | midbrain development | 54/7958 | 90/18723 | 6.04e-04 | 3.79e-03 | 54 |
GO:00165704 | Lung | IAC | histone modification | 93/2061 | 463/18723 | 5.41e-09 | 8.03e-07 | 93 |
GO:00165771 | Lung | IAC | histone demethylation | 11/2061 | 31/18723 | 2.91e-04 | 4.72e-03 | 11 |
GO:00700761 | Lung | IAC | histone lysine demethylation | 10/2061 | 28/18723 | 5.17e-04 | 7.37e-03 | 10 |
GO:00064821 | Lung | IAC | protein demethylation | 11/2061 | 33/18723 | 5.41e-04 | 7.57e-03 | 11 |
GO:00082141 | Lung | IAC | protein dealkylation | 11/2061 | 33/18723 | 5.41e-04 | 7.57e-03 | 11 |
GO:00709881 | Lung | IAC | demethylation | 18/2061 | 73/18723 | 7.56e-04 | 9.82e-03 | 18 |
GO:001657012 | Lung | AIS | histone modification | 81/1849 | 463/18723 | 2.30e-07 | 2.16e-05 | 81 |
GO:003090114 | Prostate | BPH | midbrain development | 36/3107 | 90/18723 | 1.02e-07 | 2.49e-06 | 36 |
GO:00165706 | Prostate | BPH | histone modification | 120/3107 | 463/18723 | 1.73e-07 | 3.89e-06 | 120 |
GO:00165772 | Prostate | BPH | histone demethylation | 13/3107 | 31/18723 | 7.48e-04 | 4.95e-03 | 13 |
GO:00700762 | Prostate | BPH | histone lysine demethylation | 12/3107 | 28/18723 | 9.43e-04 | 5.95e-03 | 12 |
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:001657013 | Prostate | Tumor | histone modification | 126/3246 | 463/18723 | 5.51e-08 | 1.65e-06 | 126 |
GO:003090115 | Prostate | Tumor | midbrain development | 36/3246 | 90/18723 | 3.15e-07 | 7.14e-06 | 36 |
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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 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
KDM7A | CD8TEXP | Breast | Precancer | TMEM204,GLO1,THADA, etc. | 4.58e-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. |
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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 |
KDM7A | SNV | Missense_Mutation | c.1553A>G | p.Asn518Ser | p.N518S | Q6ZMT4 | protein_coding | tolerated(1) | benign(0) | TCGA-A2-A04T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
KDM7A | SNV | Missense_Mutation | c.1652N>G | p.Ser551Cys | p.S551C | Q6ZMT4 | protein_coding | deleterious(0.03) | possibly_damaging(0.628) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
KDM7A | SNV | Missense_Mutation | novel | c.1831A>G | p.Arg611Gly | p.R611G | Q6ZMT4 | protein_coding | tolerated(0.13) | benign(0) | TCGA-D8-A1JL-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
KDM7A | insertion | In_Frame_Ins | novel | c.2459_2460insAACATATGGCACACTCAAGGACAG | p.Asp820delinsGluThrTyrGlyThrLeuLysAspSer | p.D820delinsETYGTLKDS | Q6ZMT4 | protein_coding | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
KDM7A | deletion | Frame_Shift_Del | c.914delA | p.Lys305SerfsTer17 | p.K305Sfs*17 | Q6ZMT4 | protein_coding | TCGA-E9-A1NE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | |||
KDM7A | SNV | Missense_Mutation | novel | c.787A>G | p.Lys263Glu | p.K263E | Q6ZMT4 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
KDM7A | SNV | Missense_Mutation | c.1369G>C | p.Asp457His | p.D457H | Q6ZMT4 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-EK-A2RA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
KDM7A | SNV | Missense_Mutation | rs758963637 | c.2548N>A | p.Gly850Ser | p.G850S | Q6ZMT4 | protein_coding | tolerated(0.29) | benign(0.003) | TCGA-VS-A950-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
KDM7A | SNV | Missense_Mutation | novel | c.997N>C | p.Asp333His | p.D333H | Q6ZMT4 | protein_coding | deleterious(0) | probably_damaging(0.943) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
KDM7A | SNV | Missense_Mutation | c.2755G>A | p.Ala919Thr | p.A919T | Q6ZMT4 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A6-2683-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | irinotecan | PD |
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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 |
80853 | KDM7A | ENZYME | inhibitor | 178103604 |
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