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Gene: RPRD1B |
Gene summary for RPRD1B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPRD1B | Gene ID | 58490 |
| Gene name | regulation of nuclear pre-mRNA domain containing 1B | |
| Gene Alias | C20orf77 | |
| Cytomap | 20q11.23 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9NQG5 |
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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 |
| 58490 | RPRD1B | LZE4T | Human | Esophagus | ESCC | 4.52e-07 | 1.77e-01 | 0.0811 |
| 58490 | RPRD1B | LZE5T | Human | Esophagus | ESCC | 2.40e-04 | 3.31e-01 | 0.0514 |
| 58490 | RPRD1B | LZE20T | Human | Esophagus | ESCC | 4.19e-09 | 1.56e-01 | 0.0662 |
| 58490 | RPRD1B | LZE24T | Human | Esophagus | ESCC | 3.89e-24 | 5.95e-01 | 0.0596 |
| 58490 | RPRD1B | P1T-E | Human | Esophagus | ESCC | 1.22e-03 | 1.75e-01 | 0.0875 |
| 58490 | RPRD1B | P2T-E | Human | Esophagus | ESCC | 4.00e-17 | 3.67e-01 | 0.1177 |
| 58490 | RPRD1B | P4T-E | Human | Esophagus | ESCC | 7.40e-09 | 2.20e-01 | 0.1323 |
| 58490 | RPRD1B | P5T-E | Human | Esophagus | ESCC | 3.08e-15 | 2.19e-01 | 0.1327 |
| 58490 | RPRD1B | P8T-E | Human | Esophagus | ESCC | 2.24e-27 | 6.08e-01 | 0.0889 |
| 58490 | RPRD1B | P9T-E | Human | Esophagus | ESCC | 1.18e-09 | 1.44e-01 | 0.1131 |
| 58490 | RPRD1B | P10T-E | Human | Esophagus | ESCC | 2.83e-28 | 4.61e-01 | 0.116 |
| 58490 | RPRD1B | P11T-E | Human | Esophagus | ESCC | 5.62e-10 | 3.31e-01 | 0.1426 |
| 58490 | RPRD1B | P12T-E | Human | Esophagus | ESCC | 4.47e-23 | 3.68e-01 | 0.1122 |
| 58490 | RPRD1B | P15T-E | Human | Esophagus | ESCC | 1.50e-24 | 4.47e-01 | 0.1149 |
| 58490 | RPRD1B | P16T-E | Human | Esophagus | ESCC | 3.63e-26 | 4.63e-01 | 0.1153 |
| 58490 | RPRD1B | P17T-E | Human | Esophagus | ESCC | 2.19e-04 | 2.75e-01 | 0.1278 |
| 58490 | RPRD1B | P19T-E | Human | Esophagus | ESCC | 1.78e-04 | 2.61e-01 | 0.1662 |
| 58490 | RPRD1B | P20T-E | Human | Esophagus | ESCC | 1.83e-22 | 4.39e-01 | 0.1124 |
| 58490 | RPRD1B | P21T-E | Human | Esophagus | ESCC | 4.92e-23 | 4.15e-01 | 0.1617 |
| 58490 | RPRD1B | P22T-E | Human | Esophagus | ESCC | 3.00e-17 | 2.48e-01 | 0.1236 |
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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 |
| ∗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:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:003112412 | Esophagus | ESCC | mRNA 3'-end processing | 47/8552 | 62/18723 | 1.29e-06 | 1.58e-05 | 47 |
| GO:00311233 | Esophagus | ESCC | RNA 3'-end processing | 76/8552 | 116/18723 | 1.25e-05 | 1.15e-04 | 76 |
| GO:00163115 | Liver | NAFLD | dephosphorylation | 69/1882 | 417/18723 | 2.27e-05 | 6.23e-04 | 69 |
| GO:00064706 | Liver | NAFLD | protein dephosphorylation | 50/1882 | 281/18723 | 4.53e-05 | 1.09e-03 | 50 |
| GO:000647011 | Liver | Cirrhotic | protein dephosphorylation | 96/4634 | 281/18723 | 2.32e-04 | 2.11e-03 | 96 |
| GO:001631111 | Liver | Cirrhotic | dephosphorylation | 130/4634 | 417/18723 | 1.58e-03 | 1.03e-02 | 130 |
| GO:0031123 | Liver | Cirrhotic | RNA 3'-end processing | 42/4634 | 116/18723 | 3.85e-03 | 2.10e-02 | 42 |
| GO:0031124 | Liver | Cirrhotic | mRNA 3'-end processing | 25/4634 | 62/18723 | 4.90e-03 | 2.56e-02 | 25 |
| GO:00311241 | Liver | HCC | mRNA 3'-end processing | 50/7958 | 62/18723 | 8.44e-10 | 2.60e-08 | 50 |
| GO:00311231 | Liver | HCC | RNA 3'-end processing | 81/7958 | 116/18723 | 2.27e-09 | 6.32e-08 | 81 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
| GO:00311242 | Oral cavity | OSCC | mRNA 3'-end processing | 49/7305 | 62/18723 | 1.40e-10 | 4.14e-09 | 49 |
| GO:000647015 | Oral cavity | OSCC | protein dephosphorylation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:00311232 | Oral cavity | OSCC | RNA 3'-end processing | 75/7305 | 116/18723 | 1.93e-08 | 3.79e-07 | 75 |
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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. |
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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 |
| RPRD1B | SNV | Missense_Mutation | c.201N>G | p.Ile67Met | p.I67M | Q9NQG5 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-EW-A1IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | aromasin | SD | |
| RPRD1B | SNV | Missense_Mutation | c.429G>T | p.Lys143Asn | p.K143N | Q9NQG5 | protein_coding | tolerated(0.24) | benign(0.159) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| RPRD1B | SNV | Missense_Mutation | c.49A>T | p.Ser17Cys | p.S17C | Q9NQG5 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-G4-6293-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | fluorouracil | SD | |
| RPRD1B | SNV | Missense_Mutation | c.955N>T | p.Ala319Ser | p.A319S | Q9NQG5 | protein_coding | deleterious(0.04) | possibly_damaging(0.666) | TCGA-AG-3726-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPRD1B | SNV | Missense_Mutation | rs763665562 | c.391N>T | p.Asp131Tyr | p.D131Y | Q9NQG5 | protein_coding | deleterious(0.02) | benign(0.135) | TCGA-AG-A01J-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPRD1B | insertion | Frame_Shift_Ins | novel | c.612_613insC | p.Gln206ProfsTer19 | p.Q206Pfs*19 | Q9NQG5 | protein_coding | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| RPRD1B | SNV | Missense_Mutation | c.727C>T | p.Arg243Cys | p.R243C | Q9NQG5 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPRD1B | SNV | Missense_Mutation | novel | c.263N>A | p.Ala88Asp | p.A88D | Q9NQG5 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| RPRD1B | SNV | Missense_Mutation | rs201881637 | c.751N>T | p.Arg251Cys | p.R251C | Q9NQG5 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPRD1B | SNV | Missense_Mutation | c.737C>T | p.Ala246Val | p.A246V | Q9NQG5 | protein_coding | tolerated(0.06) | probably_damaging(0.962) | TCGA-B5-A0JZ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
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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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