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Gene: NEDD9 |
Gene summary for NEDD9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NEDD9 | Gene ID | 4739 |
| Gene name | neural precursor cell expressed, developmentally down-regulated 9 | |
| Gene Alias | CAS-L | |
| Cytomap | 6p24.2 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A024QZV9 |
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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 |
| 4739 | NEDD9 | AEH-subject1 | Human | Endometrium | AEH | 2.15e-13 | 4.33e-01 | -0.3059 |
| 4739 | NEDD9 | AEH-subject2 | Human | Endometrium | AEH | 1.67e-03 | 3.03e-01 | -0.2525 |
| 4739 | NEDD9 | AEH-subject3 | Human | Endometrium | AEH | 1.08e-07 | 3.79e-01 | -0.2576 |
| 4739 | NEDD9 | AEH-subject4 | Human | Endometrium | AEH | 4.46e-12 | 5.59e-01 | -0.2657 |
| 4739 | NEDD9 | AEH-subject5 | Human | Endometrium | AEH | 7.40e-33 | 8.64e-01 | -0.2953 |
| 4739 | NEDD9 | EEC-subject1 | Human | Endometrium | EEC | 3.84e-10 | 4.91e-01 | -0.2682 |
| 4739 | NEDD9 | EEC-subject2 | Human | Endometrium | EEC | 1.35e-02 | 2.77e-01 | -0.2607 |
| 4739 | NEDD9 | EEC-subject3 | Human | Endometrium | EEC | 5.54e-04 | 2.46e-01 | -0.2525 |
| 4739 | NEDD9 | EEC-subject4 | Human | Endometrium | EEC | 9.96e-14 | 4.85e-01 | -0.2571 |
| 4739 | NEDD9 | EEC-subject5 | Human | Endometrium | EEC | 7.17e-12 | 4.51e-01 | -0.249 |
| 4739 | NEDD9 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 4.31e-02 | -4.17e-03 | -0.1869 |
| 4739 | NEDD9 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 1.33e-03 | 1.05e-02 | -0.1875 |
| 4739 | NEDD9 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 5.00e-04 | 1.69e-02 | -0.1883 |
| 4739 | NEDD9 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 2.99e-03 | 4.34e-02 | -0.1934 |
| 4739 | NEDD9 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.83e-10 | 2.83e-01 | -0.1917 |
| 4739 | NEDD9 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 2.26e-08 | 1.91e-01 | -0.1916 |
| 4739 | NEDD9 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 4.38e-05 | 3.16e-01 | -0.1269 |
| 4739 | NEDD9 | LZE4T | Human | Esophagus | ESCC | 1.11e-13 | 9.13e-01 | 0.0811 |
| 4739 | NEDD9 | LZE7T | Human | Esophagus | ESCC | 9.41e-11 | 1.56e+00 | 0.0667 |
| 4739 | NEDD9 | LZE24T | Human | Esophagus | ESCC | 8.45e-11 | 1.13e+00 | 0.0596 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:001081015 | Endometrium | AEH | regulation of cell-substrate adhesion | 64/2100 | 221/18723 | 3.85e-13 | 9.62e-11 | 64 |
| GO:002260415 | Endometrium | AEH | regulation of cell morphogenesis | 79/2100 | 309/18723 | 1.04e-12 | 2.24e-10 | 79 |
| GO:00315899 | Endometrium | AEH | cell-substrate adhesion | 87/2100 | 363/18723 | 3.51e-12 | 5.70e-10 | 87 |
| GO:190002410 | Endometrium | AEH | regulation of substrate adhesion-dependent cell spreading | 27/2100 | 57/18723 | 9.07e-12 | 1.43e-09 | 27 |
| GO:000701516 | Endometrium | AEH | actin filament organization | 98/2100 | 442/18723 | 1.99e-11 | 2.98e-09 | 98 |
| GO:004578516 | Endometrium | AEH | positive regulation of cell adhesion | 96/2100 | 437/18723 | 5.50e-11 | 7.18e-09 | 96 |
| GO:190002610 | Endometrium | AEH | positive regulation of substrate adhesion-dependent cell spreading | 20/2100 | 41/18723 | 2.36e-09 | 1.89e-07 | 20 |
| GO:001081116 | Endometrium | AEH | positive regulation of cell-substrate adhesion | 38/2100 | 123/18723 | 3.08e-09 | 2.26e-07 | 38 |
| GO:001076910 | Endometrium | AEH | regulation of cell morphogenesis involved in differentiation | 31/2100 | 96/18723 | 2.70e-08 | 1.56e-06 | 31 |
| GO:003444610 | Endometrium | AEH | substrate adhesion-dependent cell spreading | 33/2100 | 108/18723 | 4.45e-08 | 2.43e-06 | 33 |
| GO:00072296 | Endometrium | AEH | integrin-mediated signaling pathway | 32/2100 | 107/18723 | 1.24e-07 | 5.80e-06 | 32 |
| GO:00315329 | Endometrium | AEH | actin cytoskeleton reorganization | 32/2100 | 107/18723 | 1.24e-07 | 5.80e-06 | 32 |
| GO:005101716 | Endometrium | AEH | actin filament bundle assembly | 39/2100 | 157/18723 | 1.21e-06 | 3.91e-05 | 39 |
| GO:006157216 | Endometrium | AEH | actin filament bundle organization | 39/2100 | 161/18723 | 2.36e-06 | 6.86e-05 | 39 |
| GO:00107709 | Endometrium | AEH | positive regulation of cell morphogenesis involved in differentiation | 24/2100 | 79/18723 | 3.33e-06 | 9.03e-05 | 24 |
| GO:00430878 | Endometrium | AEH | regulation of GTPase activity | 66/2100 | 348/18723 | 1.26e-05 | 2.77e-04 | 66 |
| GO:00107207 | Endometrium | AEH | positive regulation of cell development | 57/2100 | 298/18723 | 3.72e-05 | 6.49e-04 | 57 |
| GO:003367414 | Endometrium | AEH | positive regulation of kinase activity | 78/2100 | 467/18723 | 2.03e-04 | 2.54e-03 | 78 |
| GO:00435477 | Endometrium | AEH | positive regulation of GTPase activity | 48/2100 | 255/18723 | 2.18e-04 | 2.67e-03 | 48 |
| GO:00458609 | Endometrium | AEH | positive regulation of protein kinase activity | 66/2100 | 386/18723 | 3.14e-04 | 3.53e-03 | 66 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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. |
| 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 |
| NEDD9 | SNV | Missense_Mutation | c.417N>C | p.Gln139His | p.Q139H | Q14511 | protein_coding | tolerated(0.17) | benign(0.04) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| NEDD9 | SNV | Missense_Mutation | c.932G>A | p.Gly311Asp | p.G311D | Q14511 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | |
| NEDD9 | SNV | Missense_Mutation | rs759739278 | c.74N>A | p.Arg25His | p.R25H | Q14511 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| NEDD9 | SNV | Missense_Mutation | rs748033858 | c.499N>A | p.Glu167Lys | p.E167K | Q14511 | protein_coding | deleterious(0.03) | possibly_damaging(0.736) | TCGA-BH-A0BT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| NEDD9 | SNV | Missense_Mutation | rs200047696 | c.967N>A | p.Val323Ile | p.V323I | Q14511 | protein_coding | tolerated(0.69) | benign(0.003) | TCGA-BH-A1ET-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NEDD9 | SNV | Missense_Mutation | c.1080N>G | p.Asp360Glu | p.D360E | Q14511 | protein_coding | tolerated(0.41) | possibly_damaging(0.622) | TCGA-D8-A1JG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| NEDD9 | SNV | Missense_Mutation | c.1879N>T | p.Asp627Tyr | p.D627Y | Q14511 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-D8-A27F-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| NEDD9 | SNV | Missense_Mutation | c.1157N>T | p.Ser386Phe | p.S386F | Q14511 | protein_coding | deleterious(0.02) | benign(0.406) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NEDD9 | SNV | Missense_Mutation | novel | c.2378N>A | p.Ala793Glu | p.A793E | Q14511 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-D8-A3Z5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NEDD9 | SNV | Missense_Mutation | rs3734401 | c.1730N>T | p.Thr577Met | p.T577M | Q14511 | protein_coding | tolerated(0.06) | benign(0.115) | TCGA-E9-A1RH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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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