|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: RPP30 |
Gene summary for RPP30 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPP30 | Gene ID | 10556 |
| Gene name | ribonuclease P/MRP subunit p30 | |
| Gene Alias | TSG15 | |
| Cytomap | 10q23.31 | |
| Gene Type | protein-coding | GO ID | GO:0000966 | UniProtAcc | P78346 |
Top |
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 |
| 10556 | RPP30 | LZE4T | Human | Esophagus | ESCC | 7.16e-08 | 2.58e-01 | 0.0811 |
| 10556 | RPP30 | LZE7T | Human | Esophagus | ESCC | 4.31e-02 | 1.53e-01 | 0.0667 |
| 10556 | RPP30 | LZE8T | Human | Esophagus | ESCC | 1.76e-04 | 2.31e-01 | 0.067 |
| 10556 | RPP30 | LZE20T | Human | Esophagus | ESCC | 1.60e-02 | 6.87e-02 | 0.0662 |
| 10556 | RPP30 | LZE22T | Human | Esophagus | ESCC | 3.76e-02 | 3.70e-01 | 0.068 |
| 10556 | RPP30 | LZE24T | Human | Esophagus | ESCC | 1.19e-15 | 4.11e-01 | 0.0596 |
| 10556 | RPP30 | LZE6T | Human | Esophagus | ESCC | 1.49e-06 | 3.28e-01 | 0.0845 |
| 10556 | RPP30 | P2T-E | Human | Esophagus | ESCC | 3.61e-20 | 3.84e-01 | 0.1177 |
| 10556 | RPP30 | P4T-E | Human | Esophagus | ESCC | 4.61e-28 | 7.46e-01 | 0.1323 |
| 10556 | RPP30 | P5T-E | Human | Esophagus | ESCC | 1.26e-26 | 5.98e-01 | 0.1327 |
| 10556 | RPP30 | P8T-E | Human | Esophagus | ESCC | 3.91e-16 | 3.42e-01 | 0.0889 |
| 10556 | RPP30 | P9T-E | Human | Esophagus | ESCC | 2.55e-09 | 2.01e-01 | 0.1131 |
| 10556 | RPP30 | P10T-E | Human | Esophagus | ESCC | 1.07e-09 | 1.51e-01 | 0.116 |
| 10556 | RPP30 | P11T-E | Human | Esophagus | ESCC | 5.54e-11 | 4.78e-01 | 0.1426 |
| 10556 | RPP30 | P12T-E | Human | Esophagus | ESCC | 1.45e-27 | 5.85e-01 | 0.1122 |
| 10556 | RPP30 | P15T-E | Human | Esophagus | ESCC | 3.14e-20 | 4.87e-01 | 0.1149 |
| 10556 | RPP30 | P16T-E | Human | Esophagus | ESCC | 8.58e-30 | 5.00e-01 | 0.1153 |
| 10556 | RPP30 | P17T-E | Human | Esophagus | ESCC | 1.62e-06 | 4.39e-01 | 0.1278 |
| 10556 | RPP30 | P19T-E | Human | Esophagus | ESCC | 9.93e-06 | 5.53e-01 | 0.1662 |
| 10556 | RPP30 | P20T-E | Human | Esophagus | ESCC | 3.02e-08 | 5.71e-02 | 0.1124 |
| 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. |
Top |
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:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00080333 | Esophagus | ESCC | tRNA processing | 92/8552 | 127/18723 | 7.83e-10 | 1.93e-08 | 92 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:00344713 | Esophagus | ESCC | ncRNA 5'-end processing | 18/8552 | 21/18723 | 1.81e-04 | 1.16e-03 | 18 |
| GO:00009663 | Esophagus | ESCC | RNA 5'-end processing | 19/8552 | 23/18723 | 3.12e-04 | 1.85e-03 | 19 |
| GO:00991163 | Esophagus | ESCC | tRNA 5'-end processing | 14/8552 | 16/18723 | 6.78e-04 | 3.56e-03 | 14 |
| GO:00016823 | Esophagus | ESCC | tRNA 5'-leader removal | 11/8552 | 13/18723 | 4.76e-03 | 1.85e-02 | 11 |
| GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:004225412 | Liver | Cirrhotic | ribosome biogenesis | 154/4634 | 299/18723 | 1.18e-23 | 6.72e-21 | 154 |
| GO:000636412 | Liver | Cirrhotic | rRNA processing | 115/4634 | 225/18723 | 1.12e-17 | 1.64e-15 | 115 |
| GO:00160724 | Liver | Cirrhotic | rRNA metabolic process | 119/4634 | 236/18723 | 1.19e-17 | 1.70e-15 | 119 |
| GO:00344701 | Liver | Cirrhotic | ncRNA processing | 158/4634 | 395/18723 | 1.09e-11 | 6.96e-10 | 158 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| RPP30 | SNV | Missense_Mutation | rs376621947 | c.436A>G | p.Ile146Val | p.I146V | P78346 | protein_coding | deleterious(0.05) | benign(0.022) | TCGA-A8-A08X-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | PD |
| RPP30 | SNV | Missense_Mutation | c.607N>T | p.Val203Leu | p.V203L | P78346 | protein_coding | deleterious(0.03) | benign(0.433) | TCGA-AC-A3YI-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | CR | |
| RPP30 | SNV | Missense_Mutation | c.273A>T | p.Arg91Ser | p.R91S | P78346 | protein_coding | tolerated(0.21) | probably_damaging(0.993) | TCGA-E2-A15M-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| RPP30 | insertion | Frame_Shift_Ins | novel | c.963_964insA | p.Leu322ThrfsTer? | p.L322Tfs*? | P78346 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| RPP30 | SNV | Missense_Mutation | novel | c.758N>T | p.Gly253Val | p.G253V | P78346 | protein_coding | tolerated(0.36) | benign(0) | TCGA-VS-A9UP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| RPP30 | SNV | Missense_Mutation | rs768419490 | c.434N>T | p.Ala145Val | p.A145V | P78346 | protein_coding | deleterious(0.01) | benign(0.341) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPP30 | SNV | Missense_Mutation | rs764936639 | c.607N>A | p.Val203Met | p.V203M | P78346 | protein_coding | deleterious(0) | possibly_damaging(0.883) | TCGA-A5-A0VP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPP30 | SNV | Missense_Mutation | c.22G>A | p.Asp8Asn | p.D8N | P78346 | protein_coding | tolerated(1) | benign(0) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPP30 | SNV | Missense_Mutation | novel | c.563N>A | p.Ser188Tyr | p.S188Y | P78346 | protein_coding | deleterious(0) | benign(0.194) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| RPP30 | SNV | Missense_Mutation | novel | c.290N>T | p.Ala97Val | p.A97V | P78346 | protein_coding | tolerated(0.91) | benign(0.003) | TCGA-AX-A0IZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |