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Gene: RPP40 |
Gene summary for RPP40 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPP40 | Gene ID | 10799 |
| Gene name | ribonuclease P/MRP subunit p40 | |
| Gene Alias | RNASEP1 | |
| Cytomap | 6p25.1 | |
| Gene Type | protein-coding | GO ID | GO:0000447 | UniProtAcc | O75818 |
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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 |
| 10799 | RPP40 | LZE4T | Human | Esophagus | ESCC | 5.79e-05 | 2.21e-01 | 0.0811 |
| 10799 | RPP40 | LZE24T | Human | Esophagus | ESCC | 3.76e-05 | 1.00e-01 | 0.0596 |
| 10799 | RPP40 | P2T-E | Human | Esophagus | ESCC | 6.75e-11 | 1.99e-01 | 0.1177 |
| 10799 | RPP40 | P4T-E | Human | Esophagus | ESCC | 5.31e-09 | 3.14e-01 | 0.1323 |
| 10799 | RPP40 | P5T-E | Human | Esophagus | ESCC | 1.06e-04 | 1.54e-01 | 0.1327 |
| 10799 | RPP40 | P8T-E | Human | Esophagus | ESCC | 1.96e-07 | 3.35e-02 | 0.0889 |
| 10799 | RPP40 | P9T-E | Human | Esophagus | ESCC | 2.03e-19 | 2.10e-01 | 0.1131 |
| 10799 | RPP40 | P10T-E | Human | Esophagus | ESCC | 1.02e-06 | 8.74e-02 | 0.116 |
| 10799 | RPP40 | P11T-E | Human | Esophagus | ESCC | 4.49e-09 | 4.65e-01 | 0.1426 |
| 10799 | RPP40 | P12T-E | Human | Esophagus | ESCC | 8.21e-15 | 2.26e-01 | 0.1122 |
| 10799 | RPP40 | P15T-E | Human | Esophagus | ESCC | 6.61e-10 | 1.42e-01 | 0.1149 |
| 10799 | RPP40 | P16T-E | Human | Esophagus | ESCC | 4.62e-11 | 1.90e-01 | 0.1153 |
| 10799 | RPP40 | P20T-E | Human | Esophagus | ESCC | 8.66e-11 | 2.58e-01 | 0.1124 |
| 10799 | RPP40 | P21T-E | Human | Esophagus | ESCC | 9.93e-16 | 4.44e-01 | 0.1617 |
| 10799 | RPP40 | P22T-E | Human | Esophagus | ESCC | 6.12e-12 | 1.96e-01 | 0.1236 |
| 10799 | RPP40 | P23T-E | Human | Esophagus | ESCC | 6.25e-15 | 3.63e-01 | 0.108 |
| 10799 | RPP40 | P24T-E | Human | Esophagus | ESCC | 9.67e-11 | 1.83e-01 | 0.1287 |
| 10799 | RPP40 | P26T-E | Human | Esophagus | ESCC | 1.79e-13 | 2.06e-01 | 0.1276 |
| 10799 | RPP40 | P27T-E | Human | Esophagus | ESCC | 7.59e-10 | 2.01e-01 | 0.1055 |
| 10799 | RPP40 | P28T-E | Human | Esophagus | ESCC | 6.89e-20 | 3.45e-01 | 0.1149 |
| 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:000046211 | Oral cavity | LP | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 22/4623 | 37/18723 | 7.11e-06 | 1.37e-04 | 22 |
| GO:00903051 | Oral cavity | LP | nucleic acid phosphodiester bond hydrolysis | 92/4623 | 261/18723 | 8.07e-05 | 1.04e-03 | 92 |
| GO:00004661 | Oral cavity | LP | maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 14/4623 | 24/18723 | 4.52e-04 | 4.30e-03 | 14 |
| GO:00009661 | Oral cavity | LP | RNA 5'-end processing | 13/4623 | 23/18723 | 1.09e-03 | 9.03e-03 | 13 |
| GO:00991161 | Oral cavity | LP | tRNA 5'-end processing | 10/4623 | 16/18723 | 1.48e-03 | 1.16e-02 | 10 |
| GO:00344711 | Oral cavity | LP | ncRNA 5'-end processing | 12/4623 | 21/18723 | 1.49e-03 | 1.17e-02 | 12 |
| GO:00004781 | Oral cavity | LP | endonucleolytic cleavage involved in rRNA processing | 9/4623 | 15/18723 | 3.82e-03 | 2.48e-02 | 9 |
| GO:00004791 | Oral cavity | LP | endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 9/4623 | 15/18723 | 3.82e-03 | 2.48e-02 | 9 |
| GO:00016821 | Oral cavity | LP | tRNA 5'-leader removal | 8/4623 | 13/18723 | 5.19e-03 | 3.19e-02 | 8 |
| GO:00905021 | Oral cavity | LP | RNA phosphodiester bond hydrolysis, endonucleolytic | 31/4623 | 82/18723 | 5.66e-03 | 3.41e-02 | 31 |
| GO:00080331 | Oral cavity | LP | tRNA processing | 44/4623 | 127/18723 | 7.50e-03 | 4.15e-02 | 44 |
| GO:002261329 | Skin | cSCC | ribonucleoprotein complex biogenesis | 302/4864 | 463/18723 | 5.13e-72 | 3.22e-68 | 302 |
| GO:004225428 | Skin | cSCC | ribosome biogenesis | 206/4864 | 299/18723 | 3.33e-55 | 1.04e-51 | 206 |
| GO:000636424 | Skin | cSCC | rRNA processing | 156/4864 | 225/18723 | 1.42e-42 | 1.48e-39 | 156 |
| 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:003466013 | Skin | cSCC | ncRNA metabolic process | 234/4864 | 485/18723 | 1.37e-26 | 4.77e-24 | 234 |
| GO:004227429 | Skin | cSCC | ribosomal small subunit biogenesis | 59/4864 | 73/18723 | 1.39e-22 | 2.90e-20 | 59 |
| GO:003049012 | Skin | cSCC | maturation of SSU-rRNA | 39/4864 | 50/18723 | 2.04e-14 | 1.40e-12 | 39 |
| GO:000046212 | Skin | cSCC | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 26/4864 | 37/18723 | 2.11e-08 | 6.08e-07 | 26 |
| Page: 1 2 3 4 5 6 |
| 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 |
| RPP40 | SNV | Missense_Mutation | c.351N>T | p.Leu117Phe | p.L117F | O75818 | protein_coding | tolerated(0.08) | probably_damaging(0.992) | TCGA-AN-A0XU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPP40 | SNV | Missense_Mutation | c.780N>G | p.Phe260Leu | p.F260L | O75818 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPP40 | SNV | Missense_Mutation | rs147319010 | c.754N>A | p.Asp252Asn | p.D252N | O75818 | protein_coding | tolerated(0.35) | benign(0.005) | TCGA-D8-A1Y1-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | PD |
| RPP40 | SNV | Missense_Mutation | c.142G>C | p.Glu48Gln | p.E48Q | O75818 | protein_coding | deleterious(0.02) | probably_damaging(0.963) | TCGA-E9-A1R4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| RPP40 | SNV | Missense_Mutation | c.805N>T | p.Pro269Ser | p.P269S | O75818 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPP40 | SNV | Missense_Mutation | rs575359259 | c.995G>A | p.Arg332Gln | p.R332Q | O75818 | protein_coding | tolerated(0.38) | benign(0.001) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| RPP40 | SNV | Missense_Mutation | c.476N>A | p.Ser159Tyr | p.S159Y | O75818 | protein_coding | deleterious(0.02) | possibly_damaging(0.889) | TCGA-CA-6719-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RPP40 | deletion | Frame_Shift_Del | c.980delA | p.Asn327MetfsTer16 | p.N327Mfs*16 | O75818 | protein_coding | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| RPP40 | insertion | Frame_Shift_Ins | novel | c.980dupA | p.Asn327LysfsTer2 | p.N327Kfs*2 | O75818 | protein_coding | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RPP40 | SNV | Missense_Mutation | c.538N>A | p.Leu180Ile | p.L180I | O75818 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | 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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