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Gene: RIOK1 |
Gene summary for RIOK1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RIOK1 | Gene ID | 83732 |
| Gene name | RIO kinase 1 | |
| Gene Alias | AD034 | |
| Cytomap | 6p24.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9BRS2 |
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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 |
| 83732 | RIOK1 | LZE4T | Human | Esophagus | ESCC | 2.39e-18 | 5.40e-01 | 0.0811 |
| 83732 | RIOK1 | LZE7T | Human | Esophagus | ESCC | 1.73e-05 | 4.31e-01 | 0.0667 |
| 83732 | RIOK1 | LZE8T | Human | Esophagus | ESCC | 2.48e-06 | 2.28e-01 | 0.067 |
| 83732 | RIOK1 | LZE22T | Human | Esophagus | ESCC | 1.95e-04 | 4.89e-01 | 0.068 |
| 83732 | RIOK1 | LZE24T | Human | Esophagus | ESCC | 1.51e-05 | 3.65e-01 | 0.0596 |
| 83732 | RIOK1 | LZE21T | Human | Esophagus | ESCC | 6.38e-06 | 4.84e-01 | 0.0655 |
| 83732 | RIOK1 | P1T-E | Human | Esophagus | ESCC | 9.44e-10 | 4.80e-01 | 0.0875 |
| 83732 | RIOK1 | P2T-E | Human | Esophagus | ESCC | 3.02e-28 | 6.95e-01 | 0.1177 |
| 83732 | RIOK1 | P4T-E | Human | Esophagus | ESCC | 3.00e-29 | 1.01e+00 | 0.1323 |
| 83732 | RIOK1 | P5T-E | Human | Esophagus | ESCC | 7.66e-19 | 2.98e-01 | 0.1327 |
| 83732 | RIOK1 | P8T-E | Human | Esophagus | ESCC | 1.27e-12 | 2.63e-01 | 0.0889 |
| 83732 | RIOK1 | P9T-E | Human | Esophagus | ESCC | 8.36e-21 | 6.19e-01 | 0.1131 |
| 83732 | RIOK1 | P10T-E | Human | Esophagus | ESCC | 3.04e-36 | 8.06e-01 | 0.116 |
| 83732 | RIOK1 | P11T-E | Human | Esophagus | ESCC | 3.27e-19 | 8.81e-01 | 0.1426 |
| 83732 | RIOK1 | P12T-E | Human | Esophagus | ESCC | 4.34e-19 | 4.96e-01 | 0.1122 |
| 83732 | RIOK1 | P15T-E | Human | Esophagus | ESCC | 7.41e-17 | 5.10e-01 | 0.1149 |
| 83732 | RIOK1 | P16T-E | Human | Esophagus | ESCC | 4.45e-33 | 6.99e-01 | 0.1153 |
| 83732 | RIOK1 | P17T-E | Human | Esophagus | ESCC | 2.52e-12 | 7.25e-01 | 0.1278 |
| 83732 | RIOK1 | P20T-E | Human | Esophagus | ESCC | 2.80e-39 | 1.02e+00 | 0.1124 |
| 83732 | RIOK1 | P21T-E | Human | Esophagus | ESCC | 3.12e-26 | 7.15e-01 | 0.1617 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
| GO:00304904 | Esophagus | ESCC | maturation of SSU-rRNA | 45/8552 | 50/18723 | 5.07e-11 | 1.63e-09 | 45 |
| GO:2000234 | Esophagus | ESCC | positive regulation of rRNA processing | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:004227422 | Liver | HCC | ribosomal small subunit biogenesis | 65/7958 | 73/18723 | 1.09e-16 | 9.92e-15 | 65 |
| GO:00304901 | Liver | HCC | maturation of SSU-rRNA | 43/7958 | 50/18723 | 2.35e-10 | 8.04e-09 | 43 |
| GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
| GO:004225420 | Oral cavity | OSCC | ribosome biogenesis | 230/7305 | 299/18723 | 3.22e-41 | 6.80e-38 | 230 |
| GO:000636410 | Oral cavity | OSCC | rRNA processing | 172/7305 | 225/18723 | 1.57e-30 | 1.24e-27 | 172 |
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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 |
| 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 |
| RIOK1 | SNV | Missense_Mutation | c.1491N>A | p.Asp497Glu | p.D497E | Q9BRS2 | protein_coding | tolerated(0.6) | benign(0.003) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| RIOK1 | SNV | Missense_Mutation | c.941N>C | p.Met314Thr | p.M314T | Q9BRS2 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RIOK1 | insertion | Nonsense_Mutation | novel | c.354_355insGTTCATTTACCCCCAAAGTATATAATAAAGAGCTAAGACC | p.Lys119ValfsTer12 | p.K119Vfs*12 | Q9BRS2 | protein_coding | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RIOK1 | SNV | Missense_Mutation | novel | c.1121C>T | p.Ala374Val | p.A374V | Q9BRS2 | protein_coding | deleterious(0.02) | possibly_damaging(0.658) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RIOK1 | SNV | Missense_Mutation | novel | c.1366G>A | p.Ala456Thr | p.A456T | Q9BRS2 | protein_coding | deleterious(0.05) | benign(0.154) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RIOK1 | SNV | Missense_Mutation | rs547473770 | c.658N>T | p.Arg220Trp | p.R220W | Q9BRS2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A7UE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| RIOK1 | SNV | Missense_Mutation | c.1423G>C | p.Asp475His | p.D475H | Q9BRS2 | protein_coding | deleterious(0) | possibly_damaging(0.536) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| RIOK1 | SNV | Missense_Mutation | c.1465C>G | p.Gln489Glu | p.Q489E | Q9BRS2 | protein_coding | tolerated(0.81) | benign(0) | TCGA-EK-A2H0-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RIOK1 | SNV | Missense_Mutation | c.1465N>G | p.Gln489Glu | p.Q489E | Q9BRS2 | protein_coding | tolerated(0.81) | benign(0) | TCGA-ZJ-A8QQ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| RIOK1 | SNV | Missense_Mutation | c.295N>A | p.Asp99Asn | p.D99N | Q9BRS2 | protein_coding | tolerated(0.69) | benign(0) | TCGA-AA-3815-01 | Colorectum | colon adenocarcinoma | 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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