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Gene: RRP12 |
Gene summary for RRP12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RRP12 | Gene ID | 23223 |
| Gene name | ribosomal RNA processing 12 homolog | |
| Gene Alias | KIAA0690 | |
| Cytomap | 10q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | B3KMR5 |
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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 |
| 23223 | RRP12 | LZE7T | Human | Esophagus | ESCC | 1.11e-02 | 9.33e-02 | 0.0667 |
| 23223 | RRP12 | LZE8T | Human | Esophagus | ESCC | 1.41e-02 | 1.31e-01 | 0.067 |
| 23223 | RRP12 | LZE22T | Human | Esophagus | ESCC | 6.03e-03 | 1.78e-01 | 0.068 |
| 23223 | RRP12 | LZE24T | Human | Esophagus | ESCC | 6.34e-07 | 3.19e-01 | 0.0596 |
| 23223 | RRP12 | P2T-E | Human | Esophagus | ESCC | 2.57e-16 | 2.86e-01 | 0.1177 |
| 23223 | RRP12 | P4T-E | Human | Esophagus | ESCC | 2.13e-11 | 1.77e-01 | 0.1323 |
| 23223 | RRP12 | P5T-E | Human | Esophagus | ESCC | 6.69e-27 | 6.08e-01 | 0.1327 |
| 23223 | RRP12 | P8T-E | Human | Esophagus | ESCC | 3.73e-10 | 2.33e-01 | 0.0889 |
| 23223 | RRP12 | P9T-E | Human | Esophagus | ESCC | 5.52e-16 | 1.64e-01 | 0.1131 |
| 23223 | RRP12 | P11T-E | Human | Esophagus | ESCC | 1.85e-05 | 5.83e-01 | 0.1426 |
| 23223 | RRP12 | P12T-E | Human | Esophagus | ESCC | 2.09e-03 | 1.91e-01 | 0.1122 |
| 23223 | RRP12 | P15T-E | Human | Esophagus | ESCC | 1.58e-10 | 1.56e-01 | 0.1149 |
| 23223 | RRP12 | P16T-E | Human | Esophagus | ESCC | 2.13e-15 | 2.32e-01 | 0.1153 |
| 23223 | RRP12 | P17T-E | Human | Esophagus | ESCC | 9.07e-05 | 1.52e-01 | 0.1278 |
| 23223 | RRP12 | P20T-E | Human | Esophagus | ESCC | 5.89e-17 | 4.45e-01 | 0.1124 |
| 23223 | RRP12 | P21T-E | Human | Esophagus | ESCC | 1.47e-19 | 4.01e-01 | 0.1617 |
| 23223 | RRP12 | P22T-E | Human | Esophagus | ESCC | 6.79e-04 | 5.92e-02 | 0.1236 |
| 23223 | RRP12 | P23T-E | Human | Esophagus | ESCC | 2.23e-20 | 4.13e-01 | 0.108 |
| 23223 | RRP12 | P24T-E | Human | Esophagus | ESCC | 2.71e-13 | 1.21e-01 | 0.1287 |
| 23223 | RRP12 | P26T-E | Human | Esophagus | ESCC | 4.65e-24 | 4.40e-01 | 0.1276 |
| Page: 1 2 3 4 |
| 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 |
| ∗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: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: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 |
| GO:00344709 | Oral cavity | OSCC | ncRNA processing | 263/7305 | 395/18723 | 4.38e-29 | 2.78e-26 | 263 |
| GO:001607210 | Oral cavity | OSCC | rRNA metabolic process | 176/7305 | 236/18723 | 6.51e-29 | 3.24e-26 | 176 |
| GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
| GO:0022613110 | Oral cavity | LP | ribonucleoprotein complex biogenesis | 259/4623 | 463/18723 | 7.20e-48 | 2.25e-44 | 259 |
| GO:0042254110 | Oral cavity | LP | ribosome biogenesis | 173/4623 | 299/18723 | 8.97e-35 | 1.41e-31 | 173 |
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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 |
| ∗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 |
| RRP12 | SNV | Missense_Mutation | rs202239906 | c.1846N>A | p.Asp616Asn | p.D616N | Q5JTH9 | protein_coding | tolerated(0.09) | benign(0.404) | TCGA-A2-A0YJ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD |
| RRP12 | SNV | Missense_Mutation | novel | c.278N>A | p.Gly93Asp | p.G93D | Q5JTH9 | protein_coding | tolerated(0.16) | benign(0.247) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RRP12 | SNV | Missense_Mutation | novel | c.3163G>C | p.Glu1055Gln | p.E1055Q | Q5JTH9 | protein_coding | tolerated(0.33) | benign(0.001) | TCGA-AN-A04D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RRP12 | SNV | Missense_Mutation | novel | c.302N>G | p.Asp101Gly | p.D101G | Q5JTH9 | protein_coding | deleterious(0.01) | possibly_damaging(0.735) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| RRP12 | SNV | Missense_Mutation | rs367633522 | c.217N>A | p.Glu73Lys | p.E73K | Q5JTH9 | protein_coding | tolerated(0.34) | benign(0.021) | TCGA-C8-A8HP-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| RRP12 | SNV | Missense_Mutation | novel | c.1279N>A | p.Pro427Thr | p.P427T | Q5JTH9 | protein_coding | tolerated(0.11) | benign(0.007) | TCGA-EW-A3E8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD |
| RRP12 | insertion | In_Frame_Ins | novel | c.2629_2630insAGTTTAAAGGTAAAT | p.Ala877delinsGluPheLysGlyLysSer | p.A877delinsEFKGKS | Q5JTH9 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| RRP12 | insertion | Nonsense_Mutation | novel | c.303_304insCCAAATTAATCTTAATAATGT | p.Asp101_Cys102insProAsnTerSerTerTerCys | p.D101_C102insPN*S**C | Q5JTH9 | protein_coding | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| RRP12 | deletion | Frame_Shift_Del | novel | c.2496delC | p.Lys833ArgfsTer5 | p.K833Rfs*5 | Q5JTH9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RRP12 | deletion | Frame_Shift_Del | novel | c.2088delG | p.Tyr697MetfsTer33 | p.Y697Mfs*33 | Q5JTH9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | 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 |
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