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Gene: NUP88 |
Gene summary for NUP88 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NUP88 | Gene ID | 4927 |
| Gene name | nucleoporin 88 | |
| Gene Alias | FADS4 | |
| Cytomap | 17p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000054 | UniProtAcc | B4DP20 |
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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 |
| 4927 | NUP88 | LZE4T | Human | Esophagus | ESCC | 3.55e-09 | 1.50e-01 | 0.0811 |
| 4927 | NUP88 | LZE7T | Human | Esophagus | ESCC | 6.39e-03 | 9.33e-02 | 0.0667 |
| 4927 | NUP88 | LZE8T | Human | Esophagus | ESCC | 3.97e-03 | 9.85e-02 | 0.067 |
| 4927 | NUP88 | LZE24T | Human | Esophagus | ESCC | 1.27e-09 | 2.65e-01 | 0.0596 |
| 4927 | NUP88 | P1T-E | Human | Esophagus | ESCC | 8.22e-06 | 1.57e-01 | 0.0875 |
| 4927 | NUP88 | P2T-E | Human | Esophagus | ESCC | 3.15e-09 | 2.57e-01 | 0.1177 |
| 4927 | NUP88 | P4T-E | Human | Esophagus | ESCC | 1.14e-10 | 3.63e-01 | 0.1323 |
| 4927 | NUP88 | P5T-E | Human | Esophagus | ESCC | 7.14e-07 | 1.23e-01 | 0.1327 |
| 4927 | NUP88 | P8T-E | Human | Esophagus | ESCC | 2.19e-06 | 1.89e-01 | 0.0889 |
| 4927 | NUP88 | P9T-E | Human | Esophagus | ESCC | 5.52e-07 | 1.94e-01 | 0.1131 |
| 4927 | NUP88 | P10T-E | Human | Esophagus | ESCC | 4.07e-11 | 7.79e-02 | 0.116 |
| 4927 | NUP88 | P12T-E | Human | Esophagus | ESCC | 8.74e-21 | 2.96e-01 | 0.1122 |
| 4927 | NUP88 | P15T-E | Human | Esophagus | ESCC | 6.46e-05 | 1.50e-01 | 0.1149 |
| 4927 | NUP88 | P16T-E | Human | Esophagus | ESCC | 3.98e-20 | 3.26e-01 | 0.1153 |
| 4927 | NUP88 | P17T-E | Human | Esophagus | ESCC | 4.50e-05 | 2.13e-01 | 0.1278 |
| 4927 | NUP88 | P20T-E | Human | Esophagus | ESCC | 6.53e-11 | 2.12e-01 | 0.1124 |
| 4927 | NUP88 | P21T-E | Human | Esophagus | ESCC | 6.17e-15 | 3.15e-01 | 0.1617 |
| 4927 | NUP88 | P22T-E | Human | Esophagus | ESCC | 5.58e-11 | 2.48e-01 | 0.1236 |
| 4927 | NUP88 | P23T-E | Human | Esophagus | ESCC | 2.14e-12 | 3.95e-01 | 0.108 |
| 4927 | NUP88 | P24T-E | Human | Esophagus | ESCC | 1.68e-11 | 2.47e-01 | 0.1287 |
| Page: 1 2 3 4 |
| 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 | ||
| 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 |
| ∗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:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| GO:0006913110 | Esophagus | ESCC | nucleocytoplasmic transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0051169110 | Esophagus | ESCC | nuclear transport | 230/8552 | 301/18723 | 6.04e-28 | 2.02e-25 | 230 |
| GO:0006403110 | Esophagus | ESCC | RNA localization | 166/8552 | 201/18723 | 1.95e-27 | 6.18e-25 | 166 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:003450418 | Esophagus | ESCC | protein localization to nucleus | 211/8552 | 290/18723 | 4.06e-21 | 6.60e-19 | 211 |
| GO:005123617 | Esophagus | ESCC | establishment of RNA localization | 134/8552 | 166/18723 | 1.23e-20 | 1.81e-18 | 134 |
| GO:0051168110 | Esophagus | ESCC | nuclear export | 126/8552 | 154/18723 | 1.88e-20 | 2.65e-18 | 126 |
| GO:005102815 | Esophagus | ESCC | mRNA transport | 110/8552 | 130/18723 | 2.76e-20 | 3.80e-18 | 110 |
| GO:005065717 | Esophagus | ESCC | nucleic acid transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:005065817 | Esophagus | ESCC | RNA transport | 131/8552 | 163/18723 | 6.94e-20 | 8.46e-18 | 131 |
| GO:001593117 | Esophagus | ESCC | nucleobase-containing compound transport | 162/8552 | 222/18723 | 9.87e-17 | 7.93e-15 | 162 |
| GO:001703818 | Esophagus | ESCC | protein import | 149/8552 | 206/18723 | 5.90e-15 | 3.31e-13 | 149 |
| GO:007116612 | Esophagus | ESCC | ribonucleoprotein complex localization | 66/8552 | 77/18723 | 2.94e-13 | 1.38e-11 | 66 |
| GO:007142612 | Esophagus | ESCC | ribonucleoprotein complex export from nucleus | 65/8552 | 76/18723 | 5.56e-13 | 2.50e-11 | 65 |
| GO:000640512 | Esophagus | ESCC | RNA export from nucleus | 68/8552 | 84/18723 | 2.99e-11 | 1.01e-09 | 68 |
| GO:00064064 | Esophagus | ESCC | mRNA export from nucleus | 51/8552 | 59/18723 | 7.98e-11 | 2.47e-09 | 51 |
| GO:00714274 | Esophagus | ESCC | mRNA-containing ribonucleoprotein complex export from nucleus | 51/8552 | 59/18723 | 7.98e-11 | 2.47e-09 | 51 |
| 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 |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa0501428 | Oral cavity | OSCC | Amyotrophic lateral sclerosis | 246/3704 | 364/8465 | 6.65e-21 | 1.11e-18 | 5.67e-19 | 246 |
| hsa030136 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
| hsa05014112 | Oral cavity | OSCC | Amyotrophic lateral sclerosis | 246/3704 | 364/8465 | 6.65e-21 | 1.11e-18 | 5.67e-19 | 246 |
| hsa0301311 | Oral cavity | OSCC | Nucleocytoplasmic transport | 82/3704 | 108/8465 | 7.93e-12 | 1.33e-10 | 6.77e-11 | 82 |
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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 |
| NUP88 | SNV | Missense_Mutation | c.112N>A | p.Glu38Lys | p.E38K | Q99567 | protein_coding | tolerated(0.44) | benign(0.001) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| NUP88 | insertion | In_Frame_Ins | novel | c.1672_1673insTGGTAG | p.Pro558delinsLeuValAla | p.P558delinsLVA | Q99567 | protein_coding | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NUP88 | insertion | Frame_Shift_Ins | novel | c.1671_1672insGG | p.Pro558GlyfsTer46 | p.P558Gfs*46 | Q99567 | protein_coding | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NUP88 | insertion | Frame_Shift_Ins | novel | c.92_93insTGAATATTCAATAAAAATACTAGTGACGGATGAGTGCTCTGGA | p.Lys32GlufsTer23 | p.K32Efs*23 | Q99567 | protein_coding | TCGA-B6-A0RE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NUP88 | SNV | Missense_Mutation | c.1879G>A | p.Glu627Lys | p.E627K | Q99567 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| NUP88 | SNV | Missense_Mutation | novel | c.511N>G | p.Leu171Val | p.L171V | Q99567 | protein_coding | tolerated(0.64) | benign(0.015) | TCGA-GH-A9DA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NUP88 | SNV | Missense_Mutation | novel | c.1936A>C | p.Ser646Arg | p.S646R | Q99567 | protein_coding | tolerated(0.47) | benign(0.025) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NUP88 | SNV | Missense_Mutation | c.1456N>G | p.Thr486Ala | p.T486A | Q99567 | protein_coding | tolerated(0.21) | benign(0.003) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NUP88 | SNV | Missense_Mutation | novel | c.98N>G | p.Asn33Ser | p.N33S | Q99567 | protein_coding | tolerated(0.72) | benign(0.003) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NUP88 | SNV | Missense_Mutation | c.151C>T | p.Pro51Ser | p.P51S | Q99567 | protein_coding | tolerated_low_confidence(0.29) | benign(0.001) | TCGA-D5-6930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 |
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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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