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Gene: NPIPB4 |
Gene summary for NPIPB4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPIPB4 | Gene ID | 440345 |
| Gene name | nuclear pore complex interacting protein family member B4 | |
| Gene Alias | 61E3.4 | |
| Cytomap | 16p12.2 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | NA |
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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 |
| 440345 | NPIPB4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.37e-27 | 7.41e-01 | 0.0155 |
| 440345 | NPIPB4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.05e-31 | 1.35e+00 | -0.1808 |
| 440345 | NPIPB4 | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.23e-19 | 1.53e+00 | 0.0216 |
| 440345 | NPIPB4 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.10e-41 | 1.54e+00 | -0.0811 |
| 440345 | NPIPB4 | HTA11_78_2000001011 | Human | Colorectum | AD | 4.21e-31 | 1.35e+00 | -0.1088 |
| 440345 | NPIPB4 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.68e-84 | 1.98e+00 | -0.1954 |
| 440345 | NPIPB4 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.35e-16 | 1.50e+00 | -0.2602 |
| 440345 | NPIPB4 | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.25e-09 | 1.10e+00 | -0.2196 |
| 440345 | NPIPB4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.43e-28 | 1.16e+00 | -0.1207 |
| 440345 | NPIPB4 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.48e-27 | 1.09e+00 | -0.1526 |
| 440345 | NPIPB4 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.14e-62 | 1.54e+00 | -0.1464 |
| 440345 | NPIPB4 | HTA11_866_2000001011 | Human | Colorectum | AD | 5.27e-72 | 1.69e+00 | -0.1001 |
| 440345 | NPIPB4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.85e-47 | 1.62e+00 | -0.059 |
| 440345 | NPIPB4 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.17e-08 | 9.41e-01 | -0.1706 |
| 440345 | NPIPB4 | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.86e-02 | 5.10e-01 | -0.2061 |
| 440345 | NPIPB4 | HTA11_5216_2000001011 | Human | Colorectum | SER | 6.68e-12 | 1.13e+00 | -0.1462 |
| 440345 | NPIPB4 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.49e-38 | 1.72e+00 | -0.0842 |
| 440345 | NPIPB4 | HTA11_9341_2000001011 | Human | Colorectum | SER | 4.41e-10 | 1.20e+00 | -0.00410000000000005 |
| 440345 | NPIPB4 | HTA11_7862_2000001011 | Human | Colorectum | AD | 3.27e-10 | 7.88e-01 | -0.0179 |
| 440345 | NPIPB4 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.19e-27 | 8.38e-01 | 0.096 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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 |
| Page: 1 |
| 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 |
| NPIPB4 | SNV | Missense_Mutation | c.139G>C | p.Asp47His | p.D47H | C9JG80 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.96) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| NPIPB4 | SNV | Missense_Mutation | novel | c.295G>A | p.Gly99Arg | p.G99R | C9JG80 | protein_coding | tolerated_low_confidence(0.3) | probably_damaging(0.972) | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NPIPB4 | SNV | Missense_Mutation | novel | c.302N>T | p.Thr101Met | p.T101M | C9JG80 | protein_coding | tolerated_low_confidence(0.12) | benign(0.222) | TCGA-EW-A1PD-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Chemotherapy | docetaxel | SD |
| NPIPB4 | insertion | Frame_Shift_Ins | novel | c.293_294insACCAGGATCTT | p.Asp98GlufsTer25 | p.D98Efs*25 | C9JG80 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NPIPB4 | SNV | Missense_Mutation | novel | c.467N>C | p.Lys156Thr | p.K156T | C9JG80 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.968) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NPIPB4 | SNV | Missense_Mutation | c.249N>T | p.Trp83Cys | p.W83C | C9JG80 | protein_coding | tolerated_low_confidence(0.75) | benign(0.021) | TCGA-JW-A5VH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
| NPIPB4 | SNV | Missense_Mutation | c.392N>T | p.Ser131Phe | p.S131F | C9JG80 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.966) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NPIPB4 | SNV | Missense_Mutation | novel | c.353T>C | p.Leu118Pro | p.L118P | C9JG80 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.96) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NPIPB4 | SNV | Missense_Mutation | novel | c.535G>A | p.Ala179Thr | p.A179T | C9JG80 | protein_coding | tolerated_low_confidence(0.19) | probably_damaging(0.97) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NPIPB4 | SNV | Missense_Mutation | rs758976643 | c.1801N>T | p.Arg601Cys | p.R601C | C9JG80 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.689) | TCGA-AP-A1E1-01 | 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 |
| Page: 1 |
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