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Gene: NDE1 |
Gene summary for NDE1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NDE1 | Gene ID | 54820 |
| Gene name | nudE neurodevelopment protein 1 | |
| Gene Alias | HOM-TES-87 | |
| Cytomap | 16p13.11 | |
| Gene Type | protein-coding | GO ID | GO:0000132 | UniProtAcc | Q9NXR1 |
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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 |
| 54820 | NDE1 | LZE4T | Human | Esophagus | ESCC | 3.65e-18 | 5.88e-01 | 0.0811 |
| 54820 | NDE1 | LZE7T | Human | Esophagus | ESCC | 9.10e-10 | 5.21e-01 | 0.0667 |
| 54820 | NDE1 | LZE8T | Human | Esophagus | ESCC | 4.60e-06 | 4.50e-01 | 0.067 |
| 54820 | NDE1 | LZE20T | Human | Esophagus | ESCC | 3.85e-05 | 3.04e-01 | 0.0662 |
| 54820 | NDE1 | LZE21D1 | Human | Esophagus | HGIN | 8.37e-04 | 6.46e-01 | 0.0632 |
| 54820 | NDE1 | LZE22T | Human | Esophagus | ESCC | 1.49e-06 | 7.98e-01 | 0.068 |
| 54820 | NDE1 | LZE24T | Human | Esophagus | ESCC | 4.47e-11 | 2.98e-01 | 0.0596 |
| 54820 | NDE1 | LZE21T | Human | Esophagus | ESCC | 3.42e-07 | 5.46e-01 | 0.0655 |
| 54820 | NDE1 | LZE6T | Human | Esophagus | ESCC | 7.46e-03 | 3.26e-01 | 0.0845 |
| 54820 | NDE1 | P1T-E | Human | Esophagus | ESCC | 2.19e-24 | 1.25e+00 | 0.0875 |
| 54820 | NDE1 | P2T-E | Human | Esophagus | ESCC | 2.14e-73 | 1.34e+00 | 0.1177 |
| 54820 | NDE1 | P4T-E | Human | Esophagus | ESCC | 3.41e-20 | 4.72e-01 | 0.1323 |
| 54820 | NDE1 | P5T-E | Human | Esophagus | ESCC | 1.44e-23 | 6.03e-01 | 0.1327 |
| 54820 | NDE1 | P8T-E | Human | Esophagus | ESCC | 2.56e-19 | 5.20e-01 | 0.0889 |
| 54820 | NDE1 | P9T-E | Human | Esophagus | ESCC | 1.54e-13 | 3.50e-01 | 0.1131 |
| 54820 | NDE1 | P10T-E | Human | Esophagus | ESCC | 6.28e-20 | 4.92e-01 | 0.116 |
| 54820 | NDE1 | P11T-E | Human | Esophagus | ESCC | 2.30e-27 | 1.07e+00 | 0.1426 |
| 54820 | NDE1 | P12T-E | Human | Esophagus | ESCC | 9.45e-44 | 9.57e-01 | 0.1122 |
| 54820 | NDE1 | P15T-E | Human | Esophagus | ESCC | 1.75e-26 | 5.88e-01 | 0.1149 |
| 54820 | NDE1 | P16T-E | Human | Esophagus | ESCC | 5.45e-34 | 6.85e-01 | 0.1153 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:005165616 | Esophagus | HGIN | establishment of organelle localization | 90/2587 | 390/18723 | 4.27e-07 | 1.94e-05 | 90 |
| GO:005125826 | Esophagus | HGIN | protein polymerization | 66/2587 | 297/18723 | 4.96e-05 | 1.19e-03 | 66 |
| GO:00500003 | Esophagus | HGIN | chromosome localization | 24/2587 | 82/18723 | 2.07e-04 | 3.82e-03 | 24 |
| GO:003070517 | Esophagus | HGIN | cytoskeleton-dependent intracellular transport | 45/2587 | 195/18723 | 3.07e-04 | 5.15e-03 | 45 |
| GO:01400146 | Esophagus | HGIN | mitotic nuclear division | 61/2587 | 287/18723 | 3.38e-04 | 5.55e-03 | 61 |
| GO:00070593 | Esophagus | HGIN | chromosome segregation | 71/2587 | 346/18723 | 3.47e-04 | 5.62e-03 | 71 |
| GO:19028507 | Esophagus | HGIN | microtubule cytoskeleton organization involved in mitosis | 36/2587 | 147/18723 | 3.61e-04 | 5.68e-03 | 36 |
| GO:00513033 | Esophagus | HGIN | establishment of chromosome localization | 23/2587 | 80/18723 | 3.71e-04 | 5.77e-03 | 23 |
| GO:00109707 | Esophagus | HGIN | transport along microtubule | 35/2587 | 155/18723 | 2.01e-03 | 2.12e-02 | 35 |
| GO:005165010 | Esophagus | HGIN | establishment of vesicle localization | 35/2587 | 161/18723 | 3.89e-03 | 3.54e-02 | 35 |
| GO:005164810 | Esophagus | HGIN | vesicle localization | 37/2587 | 177/18723 | 6.03e-03 | 4.87e-02 | 37 |
| GO:014001414 | Esophagus | ESCC | mitotic nuclear division | 218/8552 | 287/18723 | 6.17e-26 | 1.78e-23 | 218 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
| GO:190285015 | Esophagus | ESCC | microtubule cytoskeleton organization involved in mitosis | 116/8552 | 147/18723 | 1.25e-16 | 9.91e-15 | 116 |
| GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:005130311 | Esophagus | ESCC | establishment of chromosome localization | 67/8552 | 80/18723 | 1.92e-12 | 8.09e-11 | 67 |
| GO:005000011 | Esophagus | ESCC | chromosome localization | 68/8552 | 82/18723 | 3.37e-12 | 1.32e-10 | 68 |
| GO:00002802 | Esophagus | ESCC | nuclear division | 270/8552 | 439/18723 | 1.17e-11 | 4.24e-10 | 270 |
| GO:005165016 | Esophagus | ESCC | establishment of vesicle localization | 114/8552 | 161/18723 | 8.20e-11 | 2.53e-09 | 114 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 |
| NDE1 | SNV | Missense_Mutation | novel | c.313G>T | p.Ala105Ser | p.A105S | Q9NXR1 | protein_coding | tolerated(0.11) | benign(0.111) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDE1 | SNV | Missense_Mutation | rs766080443 | c.439G>A | p.Glu147Lys | p.E147K | Q9NXR1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NDE1 | SNV | Missense_Mutation | rs886051724 | c.632C>T | p.Ser211Phe | p.S211F | Q9NXR1 | protein_coding | deleterious(0.04) | possibly_damaging(0.817) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD |
| NDE1 | insertion | Frame_Shift_Ins | novel | c.467_468insCAGCATCTTATTTAATCCTCATGACAGCC | p.Asp157SerfsTer23 | p.D157Sfs*23 | Q9NXR1 | protein_coding | TCGA-BH-A0B1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | SD | ||
| NDE1 | SNV | Missense_Mutation | rs201587506 | c.302N>T | p.Ala101Val | p.A101V | Q9NXR1 | protein_coding | deleterious(0.01) | benign(0.197) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NDE1 | SNV | Missense_Mutation | c.893N>C | p.Arg298Thr | p.R298T | Q9NXR1 | protein_coding | tolerated(0.22) | benign(0.175) | TCGA-EX-A3L1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NDE1 | SNV | Missense_Mutation | rs140540712 | c.718N>G | p.Thr240Ala | p.T240A | Q9NXR1 | protein_coding | tolerated(0.5) | benign(0) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NDE1 | SNV | Missense_Mutation | c.748N>T | p.Arg250Trp | p.R250W | Q9NXR1 | protein_coding | deleterious(0.05) | possibly_damaging(0.876) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NDE1 | SNV | Missense_Mutation | novel | c.775N>A | p.Asp259Asn | p.D259N | Q9NXR1 | protein_coding | deleterious(0.02) | probably_damaging(0.996) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| NDE1 | SNV | Missense_Mutation | rs765611446 | c.199G>A | p.Glu67Lys | p.E67K | Q9NXR1 | protein_coding | tolerated(0.27) | benign(0.041) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 |
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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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