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Gene: RRP12 |
Gene summary for RRP12 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RRP12 | Gene ID | 23223 |
Gene name | ribosomal RNA processing 12 homolog | |
Gene Alias | KIAA0690 | |
Cytomap | 10q24.1 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | B3KMR5 |
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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 |
23223 | RRP12 | LZE7T | Human | Esophagus | ESCC | 1.11e-02 | 9.33e-02 | 0.0667 |
23223 | RRP12 | LZE8T | Human | Esophagus | ESCC | 1.41e-02 | 1.31e-01 | 0.067 |
23223 | RRP12 | LZE22T | Human | Esophagus | ESCC | 6.03e-03 | 1.78e-01 | 0.068 |
23223 | RRP12 | LZE24T | Human | Esophagus | ESCC | 6.34e-07 | 3.19e-01 | 0.0596 |
23223 | RRP12 | P2T-E | Human | Esophagus | ESCC | 2.57e-16 | 2.86e-01 | 0.1177 |
23223 | RRP12 | P4T-E | Human | Esophagus | ESCC | 2.13e-11 | 1.77e-01 | 0.1323 |
23223 | RRP12 | P5T-E | Human | Esophagus | ESCC | 6.69e-27 | 6.08e-01 | 0.1327 |
23223 | RRP12 | P8T-E | Human | Esophagus | ESCC | 3.73e-10 | 2.33e-01 | 0.0889 |
23223 | RRP12 | P9T-E | Human | Esophagus | ESCC | 5.52e-16 | 1.64e-01 | 0.1131 |
23223 | RRP12 | P11T-E | Human | Esophagus | ESCC | 1.85e-05 | 5.83e-01 | 0.1426 |
23223 | RRP12 | P12T-E | Human | Esophagus | ESCC | 2.09e-03 | 1.91e-01 | 0.1122 |
23223 | RRP12 | P15T-E | Human | Esophagus | ESCC | 1.58e-10 | 1.56e-01 | 0.1149 |
23223 | RRP12 | P16T-E | Human | Esophagus | ESCC | 2.13e-15 | 2.32e-01 | 0.1153 |
23223 | RRP12 | P17T-E | Human | Esophagus | ESCC | 9.07e-05 | 1.52e-01 | 0.1278 |
23223 | RRP12 | P20T-E | Human | Esophagus | ESCC | 5.89e-17 | 4.45e-01 | 0.1124 |
23223 | RRP12 | P21T-E | Human | Esophagus | ESCC | 1.47e-19 | 4.01e-01 | 0.1617 |
23223 | RRP12 | P22T-E | Human | Esophagus | ESCC | 6.79e-04 | 5.92e-02 | 0.1236 |
23223 | RRP12 | P23T-E | Human | Esophagus | ESCC | 2.23e-20 | 4.13e-01 | 0.108 |
23223 | RRP12 | P24T-E | Human | Esophagus | ESCC | 2.71e-13 | 1.21e-01 | 0.1287 |
23223 | RRP12 | P26T-E | Human | Esophagus | ESCC | 4.65e-24 | 4.40e-01 | 0.1276 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
GO:004225420 | Oral cavity | OSCC | ribosome biogenesis | 230/7305 | 299/18723 | 3.22e-41 | 6.80e-38 | 230 |
GO:000636410 | Oral cavity | OSCC | rRNA processing | 172/7305 | 225/18723 | 1.57e-30 | 1.24e-27 | 172 |
GO:00344709 | Oral cavity | OSCC | ncRNA processing | 263/7305 | 395/18723 | 4.38e-29 | 2.78e-26 | 263 |
GO:001607210 | Oral cavity | OSCC | rRNA metabolic process | 176/7305 | 236/18723 | 6.51e-29 | 3.24e-26 | 176 |
GO:00346605 | Oral cavity | OSCC | ncRNA metabolic process | 296/7305 | 485/18723 | 2.94e-23 | 6.65e-21 | 296 |
GO:0022613110 | Oral cavity | LP | ribonucleoprotein complex biogenesis | 259/4623 | 463/18723 | 7.20e-48 | 2.25e-44 | 259 |
GO:0042254110 | Oral cavity | LP | ribosome biogenesis | 173/4623 | 299/18723 | 8.97e-35 | 1.41e-31 | 173 |
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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 |
RRP12 | SNV | Missense_Mutation | novel | c.3272N>T | p.Arg1091Ile | p.R1091I | Q5JTH9 | protein_coding | tolerated(0.06) | benign(0.157) | TCGA-AJ-A8CW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RRP12 | SNV | Missense_Mutation | rs191140594 | c.3883N>T | p.Arg1295Cys | p.R1295C | Q5JTH9 | protein_coding | deleterious(0) | benign(0.38) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RRP12 | SNV | Missense_Mutation | c.3128N>G | p.Lys1043Arg | p.K1043R | Q5JTH9 | protein_coding | tolerated(0.24) | benign(0.03) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
RRP12 | SNV | Missense_Mutation | c.3288N>T | p.Glu1096Asp | p.E1096D | Q5JTH9 | protein_coding | tolerated(0.44) | benign(0.003) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RRP12 | SNV | Missense_Mutation | c.2567N>A | p.Thr856Asn | p.T856N | Q5JTH9 | protein_coding | tolerated(0.06) | benign(0.062) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RRP12 | SNV | Missense_Mutation | novel | c.873G>T | p.Glu291Asp | p.E291D | Q5JTH9 | protein_coding | deleterious(0.02) | possibly_damaging(0.48) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RRP12 | SNV | Missense_Mutation | c.2296G>A | p.Glu766Lys | p.E766K | Q5JTH9 | protein_coding | tolerated(0.13) | benign(0.382) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD | |
RRP12 | SNV | Missense_Mutation | rs560486956 | c.2507G>A | p.Arg836His | p.R836H | Q5JTH9 | protein_coding | deleterious(0.05) | probably_damaging(0.999) | TCGA-AX-A1C9-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RRP12 | SNV | Missense_Mutation | novel | c.85N>A | p.Ala29Thr | p.A29T | Q5JTH9 | protein_coding | tolerated(0.1) | benign(0) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
RRP12 | SNV | Missense_Mutation | rs781271284 | c.2678C>T | p.Ser893Leu | p.S893L | Q5JTH9 | protein_coding | tolerated(0.35) | benign(0.046) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | 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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