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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00070207 | Thyroid | PTC | microtubule nucleation | 18/5968 | 35/18723 | 1.26e-02 | 4.90e-02 | 18 |
GO:014001416 | Thyroid | ATC | mitotic nuclear division | 171/6293 | 287/18723 | 1.13e-19 | 1.66e-17 | 171 |
GO:005165625 | Thyroid | ATC | establishment of organelle localization | 206/6293 | 390/18723 | 2.62e-15 | 1.84e-13 | 206 |
GO:190285017 | Thyroid | ATC | microtubule cytoskeleton organization involved in mitosis | 95/6293 | 147/18723 | 1.29e-14 | 7.62e-13 | 95 |
GO:000705913 | Thyroid | ATC | chromosome segregation | 183/6293 | 346/18723 | 8.03e-14 | 4.23e-12 | 183 |
GO:005125829 | Thyroid | ATC | protein polymerization | 159/6293 | 297/18723 | 9.33e-13 | 3.96e-11 | 159 |
GO:000716329 | Thyroid | ATC | establishment or maintenance of cell polarity | 122/6293 | 218/18723 | 8.46e-12 | 3.16e-10 | 122 |
GO:004828512 | Thyroid | ATC | organelle fission | 229/6293 | 488/18723 | 4.79e-10 | 1.29e-08 | 229 |
GO:000028011 | Thyroid | ATC | nuclear division | 207/6293 | 439/18723 | 1.98e-09 | 4.80e-08 | 207 |
GO:003070532 | Thyroid | ATC | cytoskeleton-dependent intracellular transport | 105/6293 | 195/18723 | 4.31e-09 | 9.70e-08 | 105 |
GO:0051650110 | Thyroid | ATC | establishment of vesicle localization | 87/6293 | 161/18723 | 7.16e-08 | 1.25e-06 | 87 |
GO:0030010111 | Thyroid | ATC | establishment of cell polarity | 79/6293 | 143/18723 | 8.08e-08 | 1.40e-06 | 79 |
GO:001097022 | Thyroid | ATC | transport along microtubule | 83/6293 | 155/18723 | 2.38e-07 | 3.70e-06 | 83 |
GO:005164818 | Thyroid | ATC | vesicle localization | 91/6293 | 177/18723 | 7.21e-07 | 9.64e-06 | 91 |
GO:005000013 | Thyroid | ATC | chromosome localization | 49/6293 | 82/18723 | 1.07e-06 | 1.39e-05 | 49 |
GO:005130312 | Thyroid | ATC | establishment of chromosome localization | 47/6293 | 80/18723 | 3.44e-06 | 3.86e-05 | 47 |
GO:007238413 | Thyroid | ATC | organelle transport along microtubule | 48/6293 | 85/18723 | 1.23e-05 | 1.18e-04 | 48 |
GO:006184216 | Thyroid | ATC | microtubule organizing center localization | 23/6293 | 33/18723 | 2.45e-05 | 2.14e-04 | 23 |
GO:009911112 | Thyroid | ATC | microtubule-based transport | 91/6293 | 190/18723 | 2.97e-05 | 2.48e-04 | 91 |
GO:003090015 | Thyroid | ATC | forebrain development | 164/6293 | 379/18723 | 4.85e-05 | 3.87e-04 | 164 |
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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 |
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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. |
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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 |
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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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