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Gene: RIPK3 |
Gene summary for RIPK3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RIPK3 | Gene ID | 11035 |
| Gene name | receptor interacting serine/threonine kinase 3 | |
| Gene Alias | RIP3 | |
| Cytomap | 14q12 | |
| Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | Q9Y572 |
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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 |
| 11035 | RIPK3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.07e-06 | 3.17e-01 | -0.1808 |
| 11035 | RIPK3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.95e-02 | 1.79e-01 | -0.0811 |
| 11035 | RIPK3 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.21e-06 | 1.98e-01 | -0.1954 |
| 11035 | RIPK3 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.79e-04 | 8.20e-01 | -0.2602 |
| 11035 | RIPK3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.17e-03 | 5.27e-01 | -0.2196 |
| 11035 | RIPK3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.05e-07 | 2.14e-01 | -0.1464 |
| 11035 | RIPK3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.38e-04 | 2.00e-01 | -0.059 |
| 11035 | RIPK3 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.42e-03 | 1.18e-01 | 0.096 |
| 11035 | RIPK3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.17e-02 | 1.84e-01 | 0.281 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer |
| ∗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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0097193 | Colorectum | AD | intrinsic apoptotic signaling pathway | 108/3918 | 288/18723 | 6.25e-11 | 6.41e-09 | 108 |
| GO:2001242 | Colorectum | AD | regulation of intrinsic apoptotic signaling pathway | 67/3918 | 164/18723 | 4.94e-09 | 3.16e-07 | 67 |
| GO:0006979 | Colorectum | AD | response to oxidative stress | 145/3918 | 446/18723 | 5.16e-09 | 3.23e-07 | 145 |
| GO:2001233 | Colorectum | AD | regulation of apoptotic signaling pathway | 119/3918 | 356/18723 | 2.14e-08 | 1.21e-06 | 119 |
| GO:0062197 | Colorectum | AD | cellular response to chemical stress | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| GO:0000302 | Colorectum | AD | response to reactive oxygen species | 78/3918 | 222/18723 | 6.17e-07 | 2.21e-05 | 78 |
| GO:0034599 | Colorectum | AD | cellular response to oxidative stress | 94/3918 | 288/18723 | 2.03e-06 | 6.02e-05 | 94 |
| GO:0048872 | Colorectum | AD | homeostasis of number of cells | 87/3918 | 272/18723 | 1.16e-05 | 2.61e-04 | 87 |
| GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0046777 | Colorectum | AD | protein autophosphorylation | 74/3918 | 227/18723 | 2.48e-05 | 4.76e-04 | 74 |
| GO:0042542 | Colorectum | AD | response to hydrogen peroxide | 52/3918 | 146/18723 | 2.83e-05 | 5.30e-04 | 52 |
| GO:0035303 | Colorectum | AD | regulation of dephosphorylation | 46/3918 | 128/18723 | 6.20e-05 | 1.04e-03 | 46 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0072593 | Colorectum | AD | reactive oxygen species metabolic process | 73/3918 | 239/18723 | 2.79e-04 | 3.42e-03 | 73 |
| GO:2000379 | Colorectum | AD | positive regulation of reactive oxygen species metabolic process | 29/3918 | 76/18723 | 4.31e-04 | 4.82e-03 | 29 |
| GO:0007249 | Colorectum | AD | I-kappaB kinase/NF-kappaB signaling | 82/3918 | 281/18723 | 6.09e-04 | 6.40e-03 | 82 |
| GO:0034614 | Colorectum | AD | cellular response to reactive oxygen species | 50/3918 | 155/18723 | 6.25e-04 | 6.49e-03 | 50 |
| GO:2001235 | Colorectum | AD | positive regulation of apoptotic signaling pathway | 42/3918 | 126/18723 | 7.85e-04 | 7.84e-03 | 42 |
| GO:0045860 | Colorectum | AD | positive regulation of protein kinase activity | 107/3918 | 386/18723 | 8.01e-04 | 7.92e-03 | 107 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05132 | Colorectum | AD | Salmonella infection | 102/2092 | 249/8465 | 7.65e-09 | 1.28e-07 | 8.17e-08 | 102 |
| hsa051321 | Colorectum | AD | Salmonella infection | 102/2092 | 249/8465 | 7.65e-09 | 1.28e-07 | 8.17e-08 | 102 |
| hsa051322 | Colorectum | SER | Salmonella infection | 77/1580 | 249/8465 | 1.56e-06 | 2.35e-05 | 1.71e-05 | 77 |
| hsa04217 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
| hsa051323 | Colorectum | SER | Salmonella infection | 77/1580 | 249/8465 | 1.56e-06 | 2.35e-05 | 1.71e-05 | 77 |
| hsa042171 | Colorectum | SER | Necroptosis | 47/1580 | 159/8465 | 5.21e-04 | 4.44e-03 | 3.22e-03 | 47 |
| hsa051324 | Colorectum | MSS | Salmonella infection | 92/1875 | 249/8465 | 5.23e-08 | 9.74e-07 | 5.97e-07 | 92 |
| hsa051325 | Colorectum | MSS | Salmonella infection | 92/1875 | 249/8465 | 5.23e-08 | 9.74e-07 | 5.97e-07 | 92 |
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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 |
| ∗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 |
| RIPK3 | SNV | Missense_Mutation | rs571257852 | c.136G>A | p.Asp46Asn | p.D46N | Q9Y572 | protein_coding | tolerated(0.09) | benign(0.082) | TCGA-C8-A278-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | SD |
| RIPK3 | SNV | Missense_Mutation | c.709N>A | p.Gln237Lys | p.Q237K | Q9Y572 | protein_coding | tolerated(0.35) | benign(0.037) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| RIPK3 | SNV | Missense_Mutation | novel | c.22N>A | p.Pro8Thr | p.P8T | Q9Y572 | protein_coding | tolerated(0.38) | benign(0.058) | TCGA-D8-A27M-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | methotrexate+5 | SD |
| RIPK3 | insertion | Frame_Shift_Ins | novel | c.1098_1099insGACCCACATTCTTCCCTAC | p.Ser367AspfsTer68 | p.S367Dfs*68 | Q9Y572 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RIPK3 | SNV | Missense_Mutation | rs114413869 | c.716G>A | p.Arg239Gln | p.R239Q | Q9Y572 | protein_coding | deleterious(0.03) | benign(0.259) | TCGA-A6-6140-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | SD |
| RIPK3 | SNV | Missense_Mutation | novel | c.905N>G | p.Lys302Arg | p.K302R | Q9Y572 | protein_coding | tolerated(0.07) | benign(0.103) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| RIPK3 | SNV | Missense_Mutation | c.1224N>A | p.Met408Ile | p.M408I | Q9Y572 | protein_coding | tolerated(0.44) | benign(0.003) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RIPK3 | SNV | Missense_Mutation | c.1172N>T | p.Ser391Leu | p.S391L | Q9Y572 | protein_coding | deleterious(0.01) | possibly_damaging(0.629) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RIPK3 | SNV | Missense_Mutation | c.1225N>T | p.Pro409Ser | p.P409S | Q9Y572 | protein_coding | tolerated(0.14) | possibly_damaging(0.614) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RIPK3 | SNV | Missense_Mutation | c.523N>T | p.Gly175Trp | p.G175W | Q9Y572 | protein_coding | deleterious(0.03) | benign(0.027) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | 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 |
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 384403680 | ||
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 384403666 | ||
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 178102513 | PONATINIB | |
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 381118865 | ||
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 384403668 | ||
| 11035 | RIPK3 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME, TRANSCRIPTION FACTOR | inhibitor | 384403667 |
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