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Gene: UPF3B |
Gene summary for UPF3B |
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Gene information | Species | Human | Gene symbol | UPF3B | Gene ID | 65109 |
Gene name | UPF3B regulator of nonsense mediated mRNA decay | |
Gene Alias | HUPF3B | |
Cytomap | Xq24 | |
Gene Type | protein-coding | GO ID | GO:0000184 | UniProtAcc | Q9BZI7 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
65109 | UPF3B | A015-C-203 | Human | Colorectum | FAP | 7.07e-09 | 5.93e-02 | -0.1294 |
65109 | UPF3B | A002-C-201 | Human | Colorectum | FAP | 2.39e-02 | 7.47e-02 | 0.0324 |
65109 | UPF3B | A001-C-119 | Human | Colorectum | FAP | 7.59e-07 | 5.20e-01 | -0.1557 |
65109 | UPF3B | A001-C-108 | Human | Colorectum | FAP | 1.58e-04 | 5.37e-02 | -0.0272 |
65109 | UPF3B | A002-C-205 | Human | Colorectum | FAP | 3.10e-07 | 1.62e-01 | -0.1236 |
65109 | UPF3B | A015-C-006 | Human | Colorectum | FAP | 3.36e-05 | 2.04e-01 | -0.0994 |
65109 | UPF3B | A002-C-114 | Human | Colorectum | FAP | 2.01e-03 | -8.62e-02 | -0.1561 |
65109 | UPF3B | A015-C-104 | Human | Colorectum | FAP | 1.58e-10 | 5.23e-02 | -0.1899 |
65109 | UPF3B | A001-C-014 | Human | Colorectum | FAP | 3.64e-02 | 9.14e-02 | 0.0135 |
65109 | UPF3B | A002-C-016 | Human | Colorectum | FAP | 9.09e-08 | 7.70e-04 | 0.0521 |
65109 | UPF3B | A001-C-203 | Human | Colorectum | FAP | 4.03e-02 | 1.10e-01 | -0.0481 |
65109 | UPF3B | A002-C-116 | Human | Colorectum | FAP | 6.16e-13 | -6.42e-03 | -0.0452 |
65109 | UPF3B | A014-C-008 | Human | Colorectum | FAP | 1.31e-02 | -4.81e-02 | -0.191 |
65109 | UPF3B | A018-E-020 | Human | Colorectum | FAP | 3.55e-06 | 1.35e-01 | -0.2034 |
65109 | UPF3B | F034 | Human | Colorectum | FAP | 5.82e-08 | 1.67e-01 | -0.0665 |
65109 | UPF3B | LZE2T | Human | Esophagus | ESCC | 4.48e-08 | 8.00e-01 | 0.082 |
65109 | UPF3B | LZE4T | Human | Esophagus | ESCC | 2.02e-05 | 3.19e-01 | 0.0811 |
65109 | UPF3B | LZE7T | Human | Esophagus | ESCC | 2.73e-17 | 1.17e+00 | 0.0667 |
65109 | UPF3B | LZE20T | Human | Esophagus | ESCC | 1.22e-09 | 3.16e-01 | 0.0662 |
65109 | UPF3B | LZE24T | Human | Esophagus | ESCC | 3.13e-37 | 1.14e+00 | 0.0596 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00064024 | Colorectum | FAP | mRNA catabolic process | 68/2622 | 232/18723 | 9.87e-10 | 2.16e-07 | 68 |
GO:00064014 | Colorectum | FAP | RNA catabolic process | 77/2622 | 278/18723 | 1.42e-09 | 2.77e-07 | 77 |
GO:00064174 | Colorectum | FAP | regulation of translation | 111/2622 | 468/18723 | 8.47e-09 | 1.13e-06 | 111 |
GO:00069134 | Colorectum | FAP | nucleocytoplasmic transport | 77/2622 | 301/18723 | 6.15e-08 | 4.54e-06 | 77 |
GO:00511694 | Colorectum | FAP | nuclear transport | 77/2622 | 301/18723 | 6.15e-08 | 4.54e-06 | 77 |
GO:00442704 | Colorectum | FAP | cellular nitrogen compound catabolic process | 101/2622 | 451/18723 | 7.42e-07 | 3.44e-05 | 101 |
GO:00346554 | Colorectum | FAP | nucleobase-containing compound catabolic process | 92/2622 | 407/18723 | 1.50e-06 | 6.49e-05 | 92 |
GO:00467004 | Colorectum | FAP | heterocycle catabolic process | 98/2622 | 445/18723 | 2.36e-06 | 9.21e-05 | 98 |
GO:00194394 | Colorectum | FAP | aromatic compound catabolic process | 100/2622 | 467/18723 | 6.75e-06 | 2.08e-04 | 100 |
GO:00009562 | Colorectum | FAP | nuclear-transcribed mRNA catabolic process | 33/2622 | 112/18723 | 1.69e-05 | 4.35e-04 | 33 |
GO:19013614 | Colorectum | FAP | organic cyclic compound catabolic process | 101/2622 | 495/18723 | 4.87e-05 | 9.93e-04 | 101 |
GO:00064034 | Colorectum | FAP | RNA localization | 47/2622 | 201/18723 | 2.27e-04 | 3.22e-03 | 47 |
GO:00342504 | Colorectum | FAP | positive regulation of cellular amide metabolic process | 39/2622 | 162/18723 | 4.02e-04 | 4.86e-03 | 39 |
GO:00457274 | Colorectum | FAP | positive regulation of translation | 34/2622 | 136/18723 | 4.43e-04 | 5.25e-03 | 34 |
GO:00512364 | Colorectum | FAP | establishment of RNA localization | 39/2622 | 166/18723 | 6.71e-04 | 7.28e-03 | 39 |
GO:00506574 | Colorectum | FAP | nucleic acid transport | 38/2622 | 163/18723 | 9.12e-04 | 9.19e-03 | 38 |
GO:00506584 | Colorectum | FAP | RNA transport | 38/2622 | 163/18723 | 9.12e-04 | 9.19e-03 | 38 |
GO:00001841 | Colorectum | FAP | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 12/2622 | 37/18723 | 3.43e-03 | 2.48e-02 | 12 |
GO:00159314 | Colorectum | FAP | nucleobase-containing compound transport | 45/2622 | 222/18723 | 6.22e-03 | 3.90e-02 | 45 |
GO:0006913110 | Esophagus | ESCC | nucleocytoplasmic transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030152 | Colorectum | FAP | mRNA surveillance pathway | 26/1404 | 97/8465 | 7.11e-03 | 2.64e-02 | 1.60e-02 | 26 |
hsa030153 | Colorectum | FAP | mRNA surveillance pathway | 26/1404 | 97/8465 | 7.11e-03 | 2.64e-02 | 1.60e-02 | 26 |
hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301524 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
hsa0301534 | Esophagus | ESCC | mRNA surveillance pathway | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
hsa030154 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa0301511 | Liver | Cirrhotic | mRNA surveillance pathway | 46/2530 | 97/8465 | 1.92e-04 | 1.30e-03 | 8.03e-04 | 46 |
hsa03013 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
hsa0301521 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030131 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
hsa0301531 | Liver | HCC | mRNA surveillance pathway | 66/4020 | 97/8465 | 3.16e-05 | 1.88e-04 | 1.04e-04 | 66 |
hsa030136 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
hsa030158 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
hsa0301311 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
hsa0301513 | Oral cavity | OSCC | mRNA surveillance pathway | 75/3704 | 97/8465 | 1.30e-11 | 2.01e-10 | 1.02e-10 | 75 |
hsa0301523 | Oral cavity | LP | mRNA surveillance pathway | 50/2418 | 97/8465 | 1.39e-06 | 1.50e-05 | 9.66e-06 | 50 |
hsa030132 | Oral cavity | LP | Nucleocytoplasmic transport | 53/2418 | 108/8465 | 4.68e-06 | 4.10e-05 | 2.64e-05 | 53 |
hsa0301533 | Oral cavity | LP | mRNA surveillance pathway | 50/2418 | 97/8465 | 1.39e-06 | 1.50e-05 | 9.66e-06 | 50 |
hsa030133 | Oral cavity | LP | Nucleocytoplasmic transport | 53/2418 | 108/8465 | 4.68e-06 | 4.10e-05 | 2.64e-05 | 53 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
UPF3B | SNV | Missense_Mutation | c.1302G>C | p.Lys434Asn | p.K434N | Q9BZI7 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-G3-A7M6-01 | Liver | liver hepatocellular carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
UPF3B | insertion | Frame_Shift_Ins | novel | c.738dupT | p.Ile247TyrfsTer19 | p.I247Yfs*19 | Q9BZI7 | protein_coding | TCGA-WQ-AB4B-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | ||
UPF3B | SNV | Missense_Mutation | novel | c.460N>T | p.Ile154Phe | p.I154F | Q9BZI7 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-05-4390-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
UPF3B | SNV | Missense_Mutation | novel | c.1009C>A | p.Pro337Thr | p.P337T | Q9BZI7 | protein_coding | tolerated(0.5) | benign(0.003) | TCGA-50-5931-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
UPF3B | SNV | Missense_Mutation | c.697N>T | p.Arg233Trp | p.R233W | Q9BZI7 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-55-8510-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
UPF3B | SNV | Missense_Mutation | c.452N>G | p.Val151Gly | p.V151G | Q9BZI7 | protein_coding | deleterious(0) | benign(0.277) | TCGA-64-5778-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Targeted Molecular therapy | tarceva | PD | |
UPF3B | SNV | Missense_Mutation | c.897N>T | p.Glu299Asp | p.E299D | Q9BZI7 | protein_coding | tolerated(0.12) | benign(0.005) | TCGA-97-7938-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
UPF3B | SNV | Missense_Mutation | c.373N>A | p.Gln125Lys | p.Q125K | Q9BZI7 | protein_coding | tolerated(1) | possibly_damaging(0.45) | TCGA-22-1012-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
UPF3B | SNV | Missense_Mutation | rs757733776 | c.56N>T | p.Pro19Leu | p.P19L | Q9BZI7 | protein_coding | deleterious(0.01) | benign(0.127) | TCGA-22-5492-01 | Lung | lung squamous cell carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
UPF3B | SNV | Missense_Mutation | novel | c.1019N>G | p.Glu340Gly | p.E340G | Q9BZI7 | protein_coding | tolerated(0.06) | benign(0.08) | TCGA-33-AASL-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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