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Gene: IMP3 |
Gene summary for IMP3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | IMP3 | Gene ID | 55272 |
| Gene name | IMP U3 small nucleolar ribonucleoprotein 3 | |
| Gene Alias | BRMS2 | |
| Cytomap | 15q24.2 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q9NV31 |
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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 |
| 55272 | IMP3 | LZE4T | Human | Esophagus | ESCC | 3.54e-19 | 7.34e-01 | 0.0811 |
| 55272 | IMP3 | LZE7T | Human | Esophagus | ESCC | 3.48e-17 | 1.21e+00 | 0.0667 |
| 55272 | IMP3 | LZE8T | Human | Esophagus | ESCC | 1.72e-08 | 4.75e-01 | 0.067 |
| 55272 | IMP3 | LZE20T | Human | Esophagus | ESCC | 2.01e-08 | 3.28e-01 | 0.0662 |
| 55272 | IMP3 | LZE22T | Human | Esophagus | ESCC | 1.56e-04 | 6.43e-01 | 0.068 |
| 55272 | IMP3 | LZE24T | Human | Esophagus | ESCC | 5.53e-16 | 6.28e-01 | 0.0596 |
| 55272 | IMP3 | LZE21T | Human | Esophagus | ESCC | 6.14e-04 | 6.07e-01 | 0.0655 |
| 55272 | IMP3 | LZE6T | Human | Esophagus | ESCC | 1.56e-03 | 3.95e-01 | 0.0845 |
| 55272 | IMP3 | P1T-E | Human | Esophagus | ESCC | 5.65e-15 | 1.20e+00 | 0.0875 |
| 55272 | IMP3 | P2T-E | Human | Esophagus | ESCC | 8.77e-30 | 7.02e-01 | 0.1177 |
| 55272 | IMP3 | P4T-E | Human | Esophagus | ESCC | 2.02e-56 | 1.72e+00 | 0.1323 |
| 55272 | IMP3 | P5T-E | Human | Esophagus | ESCC | 1.93e-20 | 5.13e-01 | 0.1327 |
| 55272 | IMP3 | P8T-E | Human | Esophagus | ESCC | 7.40e-45 | 9.29e-01 | 0.0889 |
| 55272 | IMP3 | P9T-E | Human | Esophagus | ESCC | 7.23e-46 | 1.28e+00 | 0.1131 |
| 55272 | IMP3 | P10T-E | Human | Esophagus | ESCC | 1.28e-62 | 1.20e+00 | 0.116 |
| 55272 | IMP3 | P11T-E | Human | Esophagus | ESCC | 5.06e-19 | 1.12e+00 | 0.1426 |
| 55272 | IMP3 | P12T-E | Human | Esophagus | ESCC | 7.53e-45 | 1.06e+00 | 0.1122 |
| 55272 | IMP3 | P15T-E | Human | Esophagus | ESCC | 2.28e-53 | 1.19e+00 | 0.1149 |
| 55272 | IMP3 | P16T-E | Human | Esophagus | ESCC | 8.87e-54 | 1.31e+00 | 0.1153 |
| 55272 | IMP3 | P17T-E | Human | Esophagus | ESCC | 1.08e-11 | 5.27e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0042176111 | Esophagus | ESCC | regulation of protein catabolic process | 280/8552 | 391/18723 | 8.65e-26 | 2.39e-23 | 280 |
| GO:2001233111 | Esophagus | ESCC | regulation of apoptotic signaling pathway | 256/8552 | 356/18723 | 4.11e-24 | 1.04e-21 | 256 |
| GO:0097191111 | Esophagus | ESCC | extrinsic apoptotic signaling pathway | 159/8552 | 219/18723 | 4.12e-16 | 2.94e-14 | 159 |
| GO:2001236111 | Esophagus | ESCC | regulation of extrinsic apoptotic signaling pathway | 111/8552 | 151/18723 | 2.97e-12 | 1.18e-10 | 111 |
| GO:0009895111 | Esophagus | ESCC | negative regulation of catabolic process | 201/8552 | 320/18723 | 3.88e-10 | 1.05e-08 | 201 |
| GO:2001235110 | Esophagus | ESCC | positive regulation of apoptotic signaling pathway | 92/8552 | 126/18723 | 3.91e-10 | 1.05e-08 | 92 |
| GO:0052547111 | Esophagus | ESCC | regulation of peptidase activity | 275/8552 | 461/18723 | 7.54e-10 | 1.88e-08 | 275 |
| GO:0031330111 | Esophagus | ESCC | negative regulation of cellular catabolic process | 166/8552 | 262/18723 | 5.17e-09 | 1.08e-07 | 166 |
| GO:0052548111 | Esophagus | ESCC | regulation of endopeptidase activity | 253/8552 | 432/18723 | 3.68e-08 | 6.78e-07 | 253 |
| GO:200123817 | Esophagus | ESCC | positive regulation of extrinsic apoptotic signaling pathway | 40/8552 | 48/18723 | 8.03e-08 | 1.39e-06 | 40 |
| GO:0042177111 | Esophagus | ESCC | negative regulation of protein catabolic process | 84/8552 | 121/18723 | 1.03e-07 | 1.69e-06 | 84 |
| GO:000862519 | Esophagus | ESCC | extrinsic apoptotic signaling pathway via death domain receptors | 59/8552 | 82/18723 | 1.23e-06 | 1.52e-05 | 59 |
| GO:0045861111 | Esophagus | ESCC | negative regulation of proteolysis | 195/8552 | 351/18723 | 1.13e-04 | 7.85e-04 | 195 |
| GO:0051346110 | Esophagus | ESCC | negative regulation of hydrolase activity | 208/8552 | 379/18723 | 1.76e-04 | 1.14e-03 | 208 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| IMP3 | SNV | Missense_Mutation | rs746193463 | c.227C>T | p.Ser76Leu | p.S76L | Q9NV31 | protein_coding | deleterious(0.02) | benign(0.242) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| IMP3 | SNV | Missense_Mutation | c.538N>G | p.Phe180Val | p.F180V | Q9NV31 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-AA-A02E-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| IMP3 | SNV | Missense_Mutation | rs200453864 | c.521N>G | p.Asn174Ser | p.N174S | Q9NV31 | protein_coding | deleterious(0.04) | benign(0.063) | TCGA-AG-3594-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| IMP3 | SNV | Missense_Mutation | novel | c.268N>T | p.Pro90Ser | p.P90S | Q9NV31 | protein_coding | tolerated(0.53) | benign(0.015) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| IMP3 | SNV | Missense_Mutation | novel | c.541N>C | p.Asp181His | p.D181H | Q9NV31 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-HD-A4C1-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| IMP3 | insertion | Frame_Shift_Ins | novel | c.456_457insGC | p.Ser153AlafsTer20 | p.S153Afs*20 | Q9NV31 | protein_coding | TCGA-CV-6003-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| IMP3 | SNV | Missense_Mutation | c.540N>A | p.Phe180Leu | p.F180L | Q9NV31 | protein_coding | deleterious(0) | possibly_damaging(0.878) | TCGA-G9-7510-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 8 | Unknown | Unknown | SD |
| Page: 1 |
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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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