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Gene: NDFIP2 |
Gene summary for NDFIP2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDFIP2 | Gene ID | 54602 |
| Gene name | Nedd4 family interacting protein 2 | |
| Gene Alias | N4WBP5A | |
| Cytomap | 13q31.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | B4DGY6 |
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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 |
| 54602 | NDFIP2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.47e-15 | -5.82e-01 | 0.0155 |
| 54602 | NDFIP2 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.68e-03 | -3.63e-01 | -0.1088 |
| 54602 | NDFIP2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.57e-04 | -5.26e-01 | -0.1207 |
| 54602 | NDFIP2 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.10e-11 | -4.56e-01 | -0.1464 |
| 54602 | NDFIP2 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.38e-08 | -4.24e-01 | -0.1001 |
| 54602 | NDFIP2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.94e-02 | -3.69e-01 | -0.059 |
| 54602 | NDFIP2 | HTA11_546_2000001011 | Human | Colorectum | AD | 3.60e-02 | -4.80e-01 | -0.0842 |
| 54602 | NDFIP2 | HTA11_866_3004761011 | Human | Colorectum | AD | 3.44e-04 | -4.07e-01 | 0.096 |
| 54602 | NDFIP2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 5.98e-07 | -5.80e-01 | 0.0338 |
| 54602 | NDFIP2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.54e-13 | -5.07e-01 | 0.0674 |
| 54602 | NDFIP2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 6.24e-07 | -6.14e-01 | 0.0588 |
| 54602 | NDFIP2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.43e-12 | -5.17e-01 | 0.3005 |
| 54602 | NDFIP2 | A015-C-203 | Human | Colorectum | FAP | 2.17e-27 | -5.19e-01 | -0.1294 |
| 54602 | NDFIP2 | A015-C-204 | Human | Colorectum | FAP | 8.63e-03 | -2.75e-01 | -0.0228 |
| 54602 | NDFIP2 | A014-C-040 | Human | Colorectum | FAP | 1.73e-03 | -3.10e-01 | -0.1184 |
| 54602 | NDFIP2 | A002-C-201 | Human | Colorectum | FAP | 9.81e-09 | -3.03e-01 | 0.0324 |
| 54602 | NDFIP2 | A001-C-119 | Human | Colorectum | FAP | 1.98e-12 | -5.72e-01 | -0.1557 |
| 54602 | NDFIP2 | A001-C-108 | Human | Colorectum | FAP | 9.69e-17 | -3.94e-01 | -0.0272 |
| 54602 | NDFIP2 | A002-C-205 | Human | Colorectum | FAP | 2.15e-21 | -5.37e-01 | -0.1236 |
| 54602 | NDFIP2 | A001-C-104 | Human | Colorectum | FAP | 6.85e-06 | -2.82e-01 | 0.0184 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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 | ||
| 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:1903320 | Colorectum | AD | regulation of protein modification by small protein conjugation or removal | 86/3918 | 242/18723 | 9.43e-08 | 4.65e-06 | 86 |
| GO:0007034 | Colorectum | AD | vacuolar transport | 60/3918 | 157/18723 | 4.97e-07 | 1.85e-05 | 60 |
| GO:0031396 | Colorectum | AD | regulation of protein ubiquitination | 72/3918 | 210/18723 | 4.50e-06 | 1.21e-04 | 72 |
| GO:0043123 | Colorectum | AD | positive regulation of I-kappaB kinase/NF-kappaB signaling | 60/3918 | 186/18723 | 1.91e-04 | 2.56e-03 | 60 |
| GO:0043122 | Colorectum | AD | regulation of I-kappaB kinase/NF-kappaB signaling | 76/3918 | 249/18723 | 2.17e-04 | 2.85e-03 | 76 |
| GO:0007249 | Colorectum | AD | I-kappaB kinase/NF-kappaB signaling | 82/3918 | 281/18723 | 6.09e-04 | 6.40e-03 | 82 |
| GO:19033202 | Colorectum | MSS | regulation of protein modification by small protein conjugation or removal | 82/3467 | 242/18723 | 7.49e-09 | 4.63e-07 | 82 |
| GO:00313962 | Colorectum | MSS | regulation of protein ubiquitination | 70/3467 | 210/18723 | 1.88e-07 | 8.26e-06 | 70 |
| GO:00070342 | Colorectum | MSS | vacuolar transport | 52/3467 | 157/18723 | 8.25e-06 | 2.07e-04 | 52 |
| GO:00431221 | Colorectum | MSS | regulation of I-kappaB kinase/NF-kappaB signaling | 71/3467 | 249/18723 | 7.12e-05 | 1.21e-03 | 71 |
| GO:00072491 | Colorectum | MSS | I-kappaB kinase/NF-kappaB signaling | 77/3467 | 281/18723 | 1.51e-04 | 2.19e-03 | 77 |
| GO:00431231 | Colorectum | MSS | positive regulation of I-kappaB kinase/NF-kappaB signaling | 55/3467 | 186/18723 | 1.60e-04 | 2.29e-03 | 55 |
| GO:00324091 | Colorectum | MSS | regulation of transporter activity | 78/3467 | 310/18723 | 2.09e-03 | 1.78e-02 | 78 |
| GO:00510511 | Colorectum | MSS | negative regulation of transport | 110/3467 | 470/18723 | 4.20e-03 | 3.04e-02 | 110 |
| GO:19033204 | Colorectum | FAP | regulation of protein modification by small protein conjugation or removal | 61/2622 | 242/18723 | 2.36e-06 | 9.21e-05 | 61 |
| GO:00313964 | Colorectum | FAP | regulation of protein ubiquitination | 50/2622 | 210/18723 | 9.03e-05 | 1.59e-03 | 50 |
| GO:00070343 | Colorectum | FAP | vacuolar transport | 40/2622 | 157/18723 | 9.41e-05 | 1.61e-03 | 40 |
| GO:00324092 | Colorectum | FAP | regulation of transporter activity | 67/2622 | 310/18723 | 1.59e-04 | 2.43e-03 | 67 |
| GO:00431222 | Colorectum | FAP | regulation of I-kappaB kinase/NF-kappaB signaling | 56/2622 | 249/18723 | 1.82e-04 | 2.69e-03 | 56 |
| GO:00510512 | Colorectum | FAP | negative regulation of transport | 91/2622 | 470/18723 | 7.09e-04 | 7.64e-03 | 91 |
| 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 |
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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 |
| NDFIP2 | SNV | Missense_Mutation | c.203N>T | p.Thr68Met | p.T68M | Q9NV92 | protein_coding | deleterious_low_confidence(0) | benign(0.01) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD | |
| NDFIP2 | SNV | Missense_Mutation | c.943N>G | p.Leu315Val | p.L315V | Q9NV92 | protein_coding | tolerated(0.12) | probably_damaging(0.999) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NDFIP2 | SNV | Missense_Mutation | rs754913477 | c.341N>T | p.Asn114Ile | p.N114I | Q9NV92 | protein_coding | deleterious(0.01) | benign(0.11) | TCGA-PL-A8LZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| NDFIP2 | insertion | Frame_Shift_Ins | novel | c.765_766insTTGCTCTGTTGCCC | p.Asn256LeufsTer8 | p.N256Lfs*8 | Q9NV92 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NDFIP2 | SNV | Missense_Mutation | novel | c.872N>A | p.Gly291Glu | p.G291E | Q9NV92 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-VS-A94W-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NDFIP2 | deletion | In_Frame_Del | novel | c.826_828delNNN | p.Ile276del | p.I276del | Q9NV92 | protein_coding | TCGA-BI-A20A-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NDFIP2 | SNV | Missense_Mutation | rs775126701 | c.517N>A | p.Val173Met | p.V173M | Q9NV92 | protein_coding | deleterious(0.01) | probably_damaging(0.961) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NDFIP2 | SNV | Missense_Mutation | c.353N>T | p.Ser118Leu | p.S118L | Q9NV92 | protein_coding | deleterious(0.03) | benign(0) | TCGA-AH-6544-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| NDFIP2 | insertion | In_Frame_Ins | novel | c.829_830insTTATTGTCAGGGTGAGTGTCT | p.Arg280_Phe281insValSerValPheIleValArg | p.R280_F281insVSVFIVR | Q9NV92 | protein_coding | TCGA-F4-6809-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| NDFIP2 | SNV | Missense_Mutation | novel | c.932T>G | p.Phe311Cys | p.F311C | Q9NV92 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-AP-A056-01 | 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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