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Gene: RRP7A |
Gene summary for RRP7A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RRP7A | Gene ID | 27341 |
| Gene name | ribosomal RNA processing 7 homolog A | |
| Gene Alias | BK126B4.3 | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000028 | UniProtAcc | Q9Y3A4 |
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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 |
| 27341 | RRP7A | P104T-E | Human | Esophagus | ESCC | 7.42e-06 | 9.98e-01 | 0.0931 |
| 27341 | RRP7A | P107T-E | Human | Esophagus | ESCC | 2.77e-56 | 1.36e+00 | 0.171 |
| 27341 | RRP7A | P126T-E | Human | Esophagus | ESCC | 1.24e-12 | 9.31e-01 | 0.1125 |
| 27341 | RRP7A | P127T-E | Human | Esophagus | ESCC | 3.55e-07 | 1.88e-01 | 0.0826 |
| 27341 | RRP7A | P128T-E | Human | Esophagus | ESCC | 1.18e-43 | 1.60e+00 | 0.1241 |
| 27341 | RRP7A | P130T-E | Human | Esophagus | ESCC | 8.19e-102 | 1.89e+00 | 0.1676 |
| 27341 | RRP7A | HCC1_Meng | Human | Liver | HCC | 4.59e-83 | 2.40e-01 | 0.0246 |
| 27341 | RRP7A | HCC2_Meng | Human | Liver | HCC | 1.70e-21 | 2.19e-02 | 0.0107 |
| 27341 | RRP7A | cirrhotic2 | Human | Liver | Cirrhotic | 1.10e-04 | 9.66e-02 | 0.0201 |
| 27341 | RRP7A | cirrhotic3 | Human | Liver | Cirrhotic | 2.48e-05 | 4.71e-02 | 0.0215 |
| 27341 | RRP7A | HCC1 | Human | Liver | HCC | 9.34e-18 | 4.48e+00 | 0.5336 |
| 27341 | RRP7A | HCC2 | Human | Liver | HCC | 6.18e-25 | 4.03e+00 | 0.5341 |
| 27341 | RRP7A | HCC5 | Human | Liver | HCC | 1.16e-13 | 1.91e+00 | 0.4932 |
| 27341 | RRP7A | Pt13.b | Human | Liver | HCC | 1.29e-15 | 1.29e-01 | 0.0251 |
| 27341 | RRP7A | Pt14.a | Human | Liver | HCC | 5.41e-06 | 3.15e-01 | 0.0169 |
| 27341 | RRP7A | Pt14.b | Human | Liver | HCC | 5.74e-06 | 2.16e-01 | 0.018 |
| 27341 | RRP7A | S014 | Human | Liver | HCC | 5.11e-31 | 1.31e+00 | 0.2254 |
| 27341 | RRP7A | S015 | Human | Liver | HCC | 3.15e-26 | 1.43e+00 | 0.2375 |
| 27341 | RRP7A | S016 | Human | Liver | HCC | 1.18e-35 | 1.32e+00 | 0.2243 |
| 27341 | RRP7A | S027 | Human | Liver | HCC | 3.32e-05 | 7.44e-01 | 0.2446 |
| Page: 1 2 3 4 5 6 7 |
| 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: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:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
| GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
| GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
| GO:000170119 | Esophagus | ESCC | in utero embryonic development | 243/8552 | 367/18723 | 1.00e-15 | 6.86e-14 | 243 |
| GO:0042255111 | Esophagus | ESCC | ribosome assembly | 50/8552 | 61/18723 | 5.66e-09 | 1.17e-07 | 50 |
| GO:000182412 | Esophagus | ESCC | blastocyst development | 73/8552 | 106/18723 | 1.13e-06 | 1.40e-05 | 73 |
| GO:00018253 | Esophagus | ESCC | blastocyst formation | 29/8552 | 38/18723 | 1.18e-04 | 8.13e-04 | 29 |
| GO:0000028111 | Esophagus | ESCC | ribosomal small subunit assembly | 16/8552 | 19/18723 | 6.45e-04 | 3.43e-03 | 16 |
| 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:007182612 | Liver | Cirrhotic | ribonucleoprotein complex subunit organization | 115/4634 | 227/18723 | 2.67e-17 | 3.63e-15 | 115 |
| GO:002261812 | Liver | Cirrhotic | ribonucleoprotein complex assembly | 112/4634 | 220/18723 | 4.35e-17 | 5.81e-15 | 112 |
| 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 |
| RRP7A | SNV | Missense_Mutation | novel | c.766C>A | p.Gln256Lys | p.Q256K | Q9Y3A4 | protein_coding | deleterious(0) | benign(0.076) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| RRP7A | SNV | Missense_Mutation | c.325N>T | p.His109Tyr | p.H109Y | Q9Y3A4 | protein_coding | tolerated(0.07) | benign(0.035) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| RRP7A | insertion | Nonsense_Mutation | novel | c.115_116insGAGCCAGGCATGATGGCATGTGTGGGTAGTCC | p.Tyr39Ter | p.Y39* | Q9Y3A4 | protein_coding | TCGA-BH-A0H9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| RRP7A | SNV | Missense_Mutation | novel | c.773N>A | p.Arg258His | p.R258H | Q9Y3A4 | protein_coding | deleterious(0.01) | possibly_damaging(0.611) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RRP7A | SNV | Missense_Mutation | rs141279637 | c.691N>T | p.Arg231Trp | p.R231W | Q9Y3A4 | protein_coding | deleterious(0.01) | probably_damaging(0.912) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| RRP7A | SNV | Missense_Mutation | c.649C>T | p.Arg217Trp | p.R217W | Q9Y3A4 | protein_coding | deleterious(0.03) | probably_damaging(0.991) | TCGA-AZ-4308-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Targeted Molecular therapy | avastin | CR | |
| RRP7A | SNV | Missense_Mutation | rs761382571 | c.772N>T | p.Arg258Cys | p.R258C | Q9Y3A4 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-AX-A2HA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RRP7A | SNV | Missense_Mutation | rs142219748 | c.230N>A | p.Arg77His | p.R77H | Q9Y3A4 | protein_coding | deleterious(0.01) | benign(0.391) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RRP7A | SNV | Missense_Mutation | novel | c.321N>G | p.Phe107Leu | p.F107L | Q9Y3A4 | protein_coding | tolerated(0.12) | benign(0.005) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RRP7A | SNV | Missense_Mutation | rs187868023 | c.698N>A | p.Arg233His | p.R233H | Q9Y3A4 | protein_coding | deleterious(0.01) | benign(0.249) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | 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 |
| 27341 | RRP7A | NA | methylphenidate | METHYLPHENIDATE | 29382897 |
| Page: 1 |
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