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Gene: SPDYA |
Gene summary for SPDYA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SPDYA | Gene ID | 245711 |
| Gene name | speedy/RINGO cell cycle regulator family member A | |
| Gene Alias | RINGO3 | |
| Cytomap | 2p23.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q5MJ70 |
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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 |
| 245711 | SPDYA | AEH-subject1 | Human | Endometrium | AEH | 2.33e-15 | 3.57e-01 | -0.3059 |
| 245711 | SPDYA | AEH-subject2 | Human | Endometrium | AEH | 1.68e-10 | 3.62e-01 | -0.2525 |
| 245711 | SPDYA | AEH-subject3 | Human | Endometrium | AEH | 1.97e-14 | 3.92e-01 | -0.2576 |
| 245711 | SPDYA | AEH-subject4 | Human | Endometrium | AEH | 9.07e-06 | 2.73e-01 | -0.2657 |
| 245711 | SPDYA | AEH-subject5 | Human | Endometrium | AEH | 2.32e-51 | 1.04e+00 | -0.2953 |
| 245711 | SPDYA | EEC-subject1 | Human | Endometrium | EEC | 6.32e-13 | 3.77e-01 | -0.2682 |
| 245711 | SPDYA | EEC-subject2 | Human | Endometrium | EEC | 2.71e-06 | 2.26e-01 | -0.2607 |
| 245711 | SPDYA | EEC-subject3 | Human | Endometrium | EEC | 1.79e-06 | 2.48e-01 | -0.2525 |
| 245711 | SPDYA | EEC-subject4 | Human | Endometrium | EEC | 4.33e-26 | 6.53e-01 | -0.2571 |
| 245711 | SPDYA | EEC-subject5 | Human | Endometrium | EEC | 3.25e-13 | 3.29e-01 | -0.249 |
| 245711 | SPDYA | RNA-P17T-P17T-2 | Human | Lung | IAC | 2.13e-03 | 5.23e-01 | 0.3371 |
| 245711 | SPDYA | RNA-P17T-P17T-4 | Human | Lung | IAC | 1.48e-03 | 5.31e-01 | 0.343 |
| 245711 | SPDYA | RNA-P17T-P17T-6 | Human | Lung | IAC | 1.48e-03 | 4.87e-01 | 0.3385 |
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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:003367414 | Endometrium | AEH | positive regulation of kinase activity | 78/2100 | 467/18723 | 2.03e-04 | 2.54e-03 | 78 |
| GO:00457877 | Endometrium | AEH | positive regulation of cell cycle | 56/2100 | 313/18723 | 2.73e-04 | 3.14e-03 | 56 |
| GO:00458609 | Endometrium | AEH | positive regulation of protein kinase activity | 66/2100 | 386/18723 | 3.14e-04 | 3.53e-03 | 66 |
| GO:00719008 | Endometrium | AEH | regulation of protein serine/threonine kinase activity | 61/2100 | 359/18723 | 6.11e-04 | 5.98e-03 | 61 |
| GO:00719026 | Endometrium | AEH | positive regulation of protein serine/threonine kinase activity | 37/2100 | 200/18723 | 1.50e-03 | 1.24e-02 | 37 |
| GO:00447726 | Endometrium | AEH | mitotic cell cycle phase transition | 67/2100 | 424/18723 | 2.37e-03 | 1.78e-02 | 67 |
| GO:003367415 | Endometrium | EEC | positive regulation of kinase activity | 83/2168 | 467/18723 | 4.32e-05 | 7.10e-04 | 83 |
| GO:004578713 | Endometrium | EEC | positive regulation of cell cycle | 59/2168 | 313/18723 | 1.04e-04 | 1.44e-03 | 59 |
| GO:004586014 | Endometrium | EEC | positive regulation of protein kinase activity | 69/2168 | 386/18723 | 1.55e-04 | 1.96e-03 | 69 |
| GO:007190212 | Endometrium | EEC | positive regulation of protein serine/threonine kinase activity | 39/2168 | 200/18723 | 7.39e-04 | 7.01e-03 | 39 |
| GO:007190013 | Endometrium | EEC | regulation of protein serine/threonine kinase activity | 62/2168 | 359/18723 | 8.17e-04 | 7.61e-03 | 62 |
| GO:004477213 | Endometrium | EEC | mitotic cell cycle phase transition | 71/2168 | 424/18723 | 8.68e-04 | 7.97e-03 | 71 |
| GO:00447723 | Lung | IAC | mitotic cell cycle phase transition | 85/2061 | 424/18723 | 2.69e-08 | 3.20e-06 | 85 |
| GO:00719006 | Lung | IAC | regulation of protein serine/threonine kinase activity | 71/2061 | 359/18723 | 6.33e-07 | 3.72e-05 | 71 |
| GO:00458607 | Lung | IAC | positive regulation of protein kinase activity | 72/2061 | 386/18723 | 4.89e-06 | 1.96e-04 | 72 |
| GO:00719024 | Lung | IAC | positive regulation of protein serine/threonine kinase activity | 44/2061 | 200/18723 | 5.16e-06 | 2.04e-04 | 44 |
| GO:00000823 | Lung | IAC | G1/S transition of mitotic cell cycle | 46/2061 | 214/18723 | 6.13e-06 | 2.29e-04 | 46 |
| GO:00336748 | Lung | IAC | positive regulation of kinase activity | 83/2061 | 467/18723 | 6.76e-06 | 2.45e-04 | 83 |
| GO:00448433 | Lung | IAC | cell cycle G1/S phase transition | 49/2061 | 241/18723 | 1.54e-05 | 4.49e-04 | 49 |
| GO:00457875 | Lung | IAC | positive regulation of cell cycle | 56/2061 | 313/18723 | 1.69e-04 | 3.01e-03 | 56 |
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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 |
| SPDYA | SNV | Missense_Mutation | c.844N>C | p.Ser282Pro | p.S282P | Q5MJ70 | protein_coding | tolerated_low_confidence(0.14) | benign(0) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SPDYA | SNV | Missense_Mutation | rs771698422 | c.427G>A | p.Glu143Lys | p.E143K | Q5MJ70 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SPDYA | SNV | Missense_Mutation | rs753354043 | c.926N>T | p.Thr309Ile | p.T309I | Q5MJ70 | protein_coding | tolerated_low_confidence(0.1) | benign(0.444) | TCGA-AA-A02Y-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| SPDYA | SNV | Missense_Mutation | c.362T>C | p.Ile121Thr | p.I121T | Q5MJ70 | protein_coding | tolerated(0.36) | benign(0.053) | TCGA-D5-6927-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| SPDYA | SNV | Missense_Mutation | c.559N>A | p.Ala187Thr | p.A187T | Q5MJ70 | protein_coding | deleterious(0.01) | possibly_damaging(0.479) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SPDYA | SNV | Missense_Mutation | novel | c.88N>C | p.Lys30Gln | p.K30Q | Q5MJ70 | protein_coding | tolerated(0.07) | possibly_damaging(0.723) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| SPDYA | SNV | Missense_Mutation | novel | c.253N>T | p.Asp85Tyr | p.D85Y | Q5MJ70 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SPDYA | SNV | Missense_Mutation | rs749368877 | c.173G>A | p.Arg58His | p.R58H | Q5MJ70 | protein_coding | tolerated(0.56) | benign(0.01) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SPDYA | SNV | Missense_Mutation | c.539N>A | p.Arg180Gln | p.R180Q | Q5MJ70 | protein_coding | tolerated(0.19) | possibly_damaging(0.521) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SPDYA | SNV | Missense_Mutation | c.241N>A | p.Asp81Asn | p.D81N | Q5MJ70 | protein_coding | tolerated(0.13) | benign(0.062) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | 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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