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Gene: CDKL5 |
Gene summary for CDKL5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDKL5 | Gene ID | 6792 |
| Gene name | cyclin dependent kinase like 5 | |
| Gene Alias | CFAP247 | |
| Cytomap | Xp22.13 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O76039 |
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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 |
| 6792 | CDKL5 | RNA-P23T2-P23T2-1 | Human | Lung | MIAC | 2.00e-02 | 8.28e-01 | -0.037 |
| 6792 | CDKL5 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.14e-08 | 5.41e-01 | -0.2116 |
| 6792 | CDKL5 | RNA-P25T1-P25T1-3 | Human | Lung | AIS | 3.34e-03 | 5.94e-01 | -0.2107 |
| 6792 | CDKL5 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 2.32e-02 | 2.03e-01 | -0.0166 |
| 6792 | CDKL5 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 3.09e-09 | 3.38e-01 | -0.013 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:00226048 | Lung | IAC | regulation of cell morphogenesis | 74/2061 | 309/18723 | 6.31e-11 | 1.70e-08 | 74 |
| GO:00163586 | Lung | IAC | dendrite development | 55/2061 | 243/18723 | 1.35e-07 | 1.18e-05 | 55 |
| GO:00467776 | Lung | IAC | protein autophosphorylation | 51/2061 | 227/18723 | 4.85e-07 | 3.10e-05 | 51 |
| GO:00605605 | Lung | IAC | developmental growth involved in morphogenesis | 52/2061 | 234/18723 | 5.39e-07 | 3.32e-05 | 52 |
| GO:00160496 | Lung | IAC | cell growth | 89/2061 | 482/18723 | 6.10e-07 | 3.67e-05 | 89 |
| GO:00109756 | Lung | IAC | regulation of neuron projection development | 82/2061 | 445/18723 | 1.82e-06 | 8.78e-05 | 82 |
| GO:00430876 | Lung | IAC | regulation of GTPase activity | 67/2061 | 348/18723 | 3.43e-06 | 1.44e-04 | 67 |
| GO:00485885 | Lung | IAC | developmental cell growth | 49/2061 | 234/18723 | 6.67e-06 | 2.43e-04 | 49 |
| GO:00488134 | Lung | IAC | dendrite morphogenesis | 34/2061 | 146/18723 | 1.68e-05 | 4.79e-04 | 34 |
| GO:00486755 | Lung | IAC | axon extension | 29/2061 | 120/18723 | 3.29e-05 | 8.29e-04 | 29 |
| GO:19901384 | Lung | IAC | neuron projection extension | 37/2061 | 172/18723 | 4.69e-05 | 1.08e-03 | 37 |
| GO:00609964 | Lung | IAC | dendritic spine development | 25/2061 | 99/18723 | 5.18e-05 | 1.18e-03 | 25 |
| GO:01200327 | Lung | IAC | regulation of plasma membrane bounded cell projection assembly | 39/2061 | 186/18723 | 5.41e-05 | 1.21e-03 | 39 |
| GO:00604916 | Lung | IAC | regulation of cell projection assembly | 39/2061 | 188/18723 | 6.92e-05 | 1.47e-03 | 39 |
| GO:00313466 | Lung | IAC | positive regulation of cell projection organization | 63/2061 | 353/18723 | 7.37e-05 | 1.55e-03 | 63 |
| GO:00457735 | Lung | IAC | positive regulation of axon extension | 14/2061 | 42/18723 | 9.77e-05 | 1.93e-03 | 14 |
| GO:00459276 | Lung | IAC | positive regulation of growth | 49/2061 | 259/18723 | 1.06e-04 | 2.05e-03 | 49 |
| GO:00615646 | Lung | IAC | axon development | 78/2061 | 467/18723 | 1.12e-04 | 2.15e-03 | 78 |
| GO:00486385 | Lung | IAC | regulation of developmental growth | 59/2061 | 330/18723 | 1.17e-04 | 2.22e-03 | 59 |
| GO:00074096 | Lung | IAC | axonogenesis | 71/2061 | 418/18723 | 1.33e-04 | 2.48e-03 | 71 |
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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 |
| ∗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 |
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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 |
| CDKL5 | SNV | Missense_Mutation | c.481N>A | p.Ser161Thr | p.S161T | O76039 | protein_coding | tolerated_low_confidence(0.08) | benign(0.372) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| CDKL5 | SNV | Missense_Mutation | c.3025N>T | p.His1009Tyr | p.H1009Y | O76039 | protein_coding | deleterious_low_confidence(0) | benign(0.003) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CDKL5 | SNV | Missense_Mutation | novel | c.530A>G | p.Tyr177Cys | p.Y177C | O76039 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CDKL5 | SNV | Missense_Mutation | c.2244N>A | p.Asn748Lys | p.N748K | O76039 | protein_coding | tolerated_low_confidence(0.07) | benign(0.417) | TCGA-AR-A0TS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| CDKL5 | SNV | Missense_Mutation | novel | c.2741N>C | p.Arg914Thr | p.R914T | O76039 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CDKL5 | SNV | Missense_Mutation | c.2803N>C | p.Tyr935His | p.Y935H | O76039 | protein_coding | deleterious_low_confidence(0.02) | benign(0) | TCGA-B6-A400-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| CDKL5 | SNV | Missense_Mutation | novel | c.2971N>G | p.Gln991Glu | p.Q991E | O76039 | protein_coding | deleterious_low_confidence(0) | benign(0.003) | TCGA-BH-A5IZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| CDKL5 | SNV | Missense_Mutation | novel | c.1438N>T | p.Pro480Ser | p.P480S | O76039 | protein_coding | tolerated_low_confidence(0.48) | benign(0.056) | TCGA-D8-A3Z5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CDKL5 | SNV | Missense_Mutation | rs122460159 | c.119N>T | p.Ala40Val | p.A40V | O76039 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-LD-A7W5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD |
| CDKL5 | insertion | Frame_Shift_Ins | novel | c.345_346insTT | p.Ile116LeufsTer5 | p.I116Lfs*5 | O76039 | protein_coding | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=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 |
| Page: 1 |
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