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Gene: RRP1 |
Gene summary for RRP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RRP1 | Gene ID | 8568 |
| Gene name | ribosomal RNA processing 1 | |
| Gene Alias | D21S2056E | |
| Cytomap | 21q22.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | P56182 |
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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 |
| 8568 | RRP1 | LZE2T | Human | Esophagus | ESCC | 6.82e-03 | 2.10e-01 | 0.082 |
| 8568 | RRP1 | LZE5T | Human | Esophagus | ESCC | 4.65e-05 | 1.53e-01 | 0.0514 |
| 8568 | RRP1 | LZE7T | Human | Esophagus | ESCC | 8.87e-14 | 4.22e-01 | 0.0667 |
| 8568 | RRP1 | LZE8T | Human | Esophagus | ESCC | 1.54e-10 | 2.39e-01 | 0.067 |
| 8568 | RRP1 | LZE20T | Human | Esophagus | ESCC | 5.48e-11 | 1.31e-01 | 0.0662 |
| 8568 | RRP1 | LZE22D1 | Human | Esophagus | HGIN | 2.29e-03 | 6.43e-02 | 0.0595 |
| 8568 | RRP1 | LZE24T | Human | Esophagus | ESCC | 8.01e-26 | 6.53e-01 | 0.0596 |
| 8568 | RRP1 | LZE6T | Human | Esophagus | ESCC | 3.53e-04 | 8.97e-02 | 0.0845 |
| 8568 | RRP1 | P1T-E | Human | Esophagus | ESCC | 2.50e-11 | 3.49e-01 | 0.0875 |
| 8568 | RRP1 | P2T-E | Human | Esophagus | ESCC | 2.11e-22 | 4.87e-01 | 0.1177 |
| 8568 | RRP1 | P4T-E | Human | Esophagus | ESCC | 2.41e-17 | 4.82e-01 | 0.1323 |
| 8568 | RRP1 | P5T-E | Human | Esophagus | ESCC | 2.25e-21 | 4.93e-01 | 0.1327 |
| 8568 | RRP1 | P8T-E | Human | Esophagus | ESCC | 4.70e-09 | 1.44e-01 | 0.0889 |
| 8568 | RRP1 | P9T-E | Human | Esophagus | ESCC | 1.24e-10 | 2.46e-01 | 0.1131 |
| 8568 | RRP1 | P10T-E | Human | Esophagus | ESCC | 4.54e-23 | 5.16e-01 | 0.116 |
| 8568 | RRP1 | P11T-E | Human | Esophagus | ESCC | 2.47e-05 | 3.67e-01 | 0.1426 |
| 8568 | RRP1 | P12T-E | Human | Esophagus | ESCC | 4.81e-20 | 4.41e-01 | 0.1122 |
| 8568 | RRP1 | P15T-E | Human | Esophagus | ESCC | 1.66e-15 | 2.12e-01 | 0.1149 |
| 8568 | RRP1 | P16T-E | Human | Esophagus | ESCC | 5.27e-23 | 4.79e-01 | 0.1153 |
| 8568 | RRP1 | P17T-E | Human | Esophagus | ESCC | 4.69e-13 | 5.35e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 |
| 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:001607224 | Skin | cSCC | rRNA metabolic process | 158/4864 | 236/18723 | 4.06e-40 | 2.83e-37 | 158 |
| GO:003447017 | Skin | cSCC | ncRNA processing | 215/4864 | 395/18723 | 6.83e-34 | 4.28e-31 | 215 |
| GO:001603229 | Skin | cSCC | viral process | 211/4864 | 415/18723 | 7.04e-28 | 2.76e-25 | 211 |
| GO:003466013 | Skin | cSCC | ncRNA metabolic process | 234/4864 | 485/18723 | 1.37e-26 | 4.77e-24 | 234 |
| GO:004348429 | Skin | cSCC | regulation of RNA splicing | 97/4864 | 148/18723 | 4.66e-24 | 1.08e-21 | 97 |
| GO:004227328 | Skin | cSCC | ribosomal large subunit biogenesis | 57/4864 | 72/18723 | 4.90e-21 | 8.53e-19 | 57 |
| GO:000961522 | Skin | cSCC | response to virus | 152/4864 | 367/18723 | 5.88e-11 | 2.75e-09 | 152 |
| GO:004440328 | Skin | cSCC | biological process involved in symbiotic interaction | 126/4864 | 290/18723 | 6.39e-11 | 2.97e-09 | 126 |
| GO:000047022 | Skin | cSCC | maturation of LSU-rRNA | 22/4864 | 28/18723 | 8.75e-09 | 2.76e-07 | 22 |
| GO:001908019 | Skin | cSCC | viral gene expression | 50/4864 | 94/18723 | 1.68e-08 | 5.04e-07 | 50 |
| GO:00004604 | Skin | cSCC | maturation of 5.8S rRNA | 25/4864 | 35/18723 | 2.34e-08 | 6.68e-07 | 25 |
| GO:005181715 | Skin | cSCC | modulation of process of other organism involved in symbiotic interaction | 38/4864 | 81/18723 | 3.88e-05 | 4.17e-04 | 38 |
| GO:005185116 | Skin | cSCC | modulation by host of symbiont process | 29/4864 | 60/18723 | 1.62e-04 | 1.42e-03 | 29 |
| GO:005134627 | Skin | cSCC | negative regulation of hydrolase activity | 130/4864 | 379/18723 | 1.74e-04 | 1.49e-03 | 130 |
| GO:003582115 | Skin | cSCC | modulation of process of other organism | 43/4864 | 106/18723 | 7.14e-04 | 5.03e-03 | 43 |
| GO:005170216 | Skin | cSCC | biological process involved in interaction with symbiont | 39/4864 | 94/18723 | 7.37e-04 | 5.15e-03 | 39 |
| GO:001908313 | Skin | cSCC | viral transcription | 23/4864 | 50/18723 | 1.75e-03 | 1.06e-02 | 23 |
| GO:009858622 | Skin | cSCC | cellular response to virus | 34/4864 | 84/18723 | 2.56e-03 | 1.45e-02 | 34 |
| GO:004392312 | Skin | cSCC | positive regulation by host of viral transcription | 9/4864 | 16/18723 | 9.73e-03 | 4.31e-02 | 9 |
| GO:0022613113 | Thyroid | PTC | ribonucleoprotein complex biogenesis | 292/5968 | 463/18723 | 3.24e-44 | 2.05e-40 | 292 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| RRP1 | SNV | Missense_Mutation | novel | c.272N>T | p.Ala91Val | p.A91V | P56182 | protein_coding | deleterious(0.02) | benign(0.255) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RRP1 | SNV | Missense_Mutation | c.1091N>C | p.Gln364Pro | p.Q364P | P56182 | protein_coding | tolerated(0.28) | benign(0.006) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RRP1 | SNV | Missense_Mutation | c.353N>G | p.Phe118Cys | p.F118C | P56182 | protein_coding | deleterious(0) | possibly_damaging(0.905) | TCGA-BH-A0HY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | taxotere | CR | |
| RRP1 | SNV | Missense_Mutation | c.677N>T | p.Pro226Leu | p.P226L | P56182 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E2-A15G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RRP1 | SNV | Missense_Mutation | rs376330937 | c.985N>T | p.Arg329Trp | p.R329W | P56182 | protein_coding | deleterious(0) | probably_damaging(0.913) | TCGA-E2-A1BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| RRP1 | insertion | Nonsense_Mutation | novel | c.1073_1074insCGCGTGGCGGATGGAACTGGCATAGGTTATCG | p.Gln358HisfsTer9 | p.Q358Hfs*9 | P56182 | protein_coding | TCGA-A2-A0EX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RRP1 | SNV | Missense_Mutation | c.601G>T | p.Ala201Ser | p.A201S | P56182 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RRP1 | SNV | Missense_Mutation | novel | c.1305G>C | p.Arg435Ser | p.R435S | P56182 | protein_coding | deleterious_low_confidence(0.03) | benign(0.143) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RRP1 | SNV | Missense_Mutation | rs367993051 | c.382N>A | p.Glu128Lys | p.E128K | P56182 | protein_coding | deleterious(0.01) | possibly_damaging(0.833) | TCGA-Q1-A6DW-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| RRP1 | SNV | Missense_Mutation | novel | c.974N>G | p.Tyr325Cys | p.Y325C | P56182 | protein_coding | tolerated(0.16) | probably_damaging(0.998) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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