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Gene: NTF4 |
Gene summary for NTF4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NTF4 | Gene ID | 4909 |
| Gene name | neurotrophin 4 | |
| Gene Alias | GLC10 | |
| Cytomap | 19q13.33 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A024QZE4 |
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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 |
| 4909 | NTF4 | P2T-E | Human | Esophagus | ESCC | 1.29e-22 | 3.65e-01 | 0.1177 |
| 4909 | NTF4 | P4T-E | Human | Esophagus | ESCC | 4.66e-07 | 2.03e-01 | 0.1323 |
| 4909 | NTF4 | P5T-E | Human | Esophagus | ESCC | 1.94e-04 | 3.35e-02 | 0.1327 |
| 4909 | NTF4 | P8T-E | Human | Esophagus | ESCC | 5.93e-16 | 4.02e-01 | 0.0889 |
| 4909 | NTF4 | P9T-E | Human | Esophagus | ESCC | 3.07e-05 | 1.09e-01 | 0.1131 |
| 4909 | NTF4 | P10T-E | Human | Esophagus | ESCC | 2.12e-27 | 5.89e-01 | 0.116 |
| 4909 | NTF4 | P11T-E | Human | Esophagus | ESCC | 2.49e-05 | 2.96e-01 | 0.1426 |
| 4909 | NTF4 | P12T-E | Human | Esophagus | ESCC | 2.53e-09 | 2.05e-01 | 0.1122 |
| 4909 | NTF4 | P15T-E | Human | Esophagus | ESCC | 1.88e-08 | 2.26e-01 | 0.1149 |
| 4909 | NTF4 | P16T-E | Human | Esophagus | ESCC | 1.10e-07 | 1.50e-01 | 0.1153 |
| 4909 | NTF4 | P21T-E | Human | Esophagus | ESCC | 1.34e-12 | 2.28e-01 | 0.1617 |
| 4909 | NTF4 | P22T-E | Human | Esophagus | ESCC | 3.91e-22 | 4.19e-01 | 0.1236 |
| 4909 | NTF4 | P24T-E | Human | Esophagus | ESCC | 8.57e-06 | 1.27e-01 | 0.1287 |
| 4909 | NTF4 | P26T-E | Human | Esophagus | ESCC | 4.23e-31 | 6.06e-01 | 0.1276 |
| 4909 | NTF4 | P27T-E | Human | Esophagus | ESCC | 1.27e-06 | 1.32e-01 | 0.1055 |
| 4909 | NTF4 | P30T-E | Human | Esophagus | ESCC | 1.02e-10 | 3.30e-01 | 0.137 |
| 4909 | NTF4 | P31T-E | Human | Esophagus | ESCC | 4.99e-17 | 2.38e-01 | 0.1251 |
| 4909 | NTF4 | P32T-E | Human | Esophagus | ESCC | 1.03e-03 | 6.11e-02 | 0.1666 |
| 4909 | NTF4 | P36T-E | Human | Esophagus | ESCC | 3.55e-04 | 2.11e-01 | 0.1187 |
| 4909 | NTF4 | P37T-E | Human | Esophagus | ESCC | 9.10e-03 | 8.20e-02 | 0.1371 |
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| 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 |
| ∗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:0070997111 | Esophagus | ESCC | neuron death | 216/8552 | 361/18723 | 3.49e-08 | 6.45e-07 | 216 |
| GO:000854410 | Esophagus | ESCC | epidermis development | 193/8552 | 324/18723 | 2.87e-07 | 4.19e-06 | 193 |
| GO:00182099 | Esophagus | ESCC | peptidyl-serine modification | 196/8552 | 338/18723 | 3.07e-06 | 3.47e-05 | 196 |
| GO:0051402110 | Esophagus | ESCC | neuron apoptotic process | 148/8552 | 246/18723 | 3.08e-06 | 3.47e-05 | 148 |
| GO:001810515 | Esophagus | ESCC | peptidyl-serine phosphorylation | 184/8552 | 315/18723 | 3.22e-06 | 3.61e-05 | 184 |
| GO:1901214111 | Esophagus | ESCC | regulation of neuron death | 186/8552 | 319/18723 | 3.35e-06 | 3.73e-05 | 186 |
| GO:199009017 | Esophagus | ESCC | cellular response to nerve growth factor stimulus | 38/8552 | 53/18723 | 1.10e-04 | 7.69e-04 | 38 |
| GO:199008916 | Esophagus | ESCC | response to nerve growth factor | 39/8552 | 56/18723 | 2.44e-04 | 1.51e-03 | 39 |
| GO:004352317 | Esophagus | ESCC | regulation of neuron apoptotic process | 122/8552 | 212/18723 | 3.21e-04 | 1.90e-03 | 122 |
| GO:190121516 | Esophagus | ESCC | negative regulation of neuron death | 115/8552 | 208/18723 | 3.24e-03 | 1.34e-02 | 115 |
| GO:00331355 | Esophagus | ESCC | regulation of peptidyl-serine phosphorylation | 81/8552 | 144/18723 | 6.79e-03 | 2.48e-02 | 81 |
| GO:00331383 | Esophagus | ESCC | positive regulation of peptidyl-serine phosphorylation | 61/8552 | 108/18723 | 1.54e-02 | 4.96e-02 | 61 |
| GO:007099720 | Oral cavity | OSCC | neuron death | 202/7305 | 361/18723 | 3.75e-11 | 1.23e-09 | 202 |
| GO:190121420 | Oral cavity | OSCC | regulation of neuron death | 174/7305 | 319/18723 | 1.09e-08 | 2.23e-07 | 174 |
| GO:00085449 | Oral cavity | OSCC | epidermis development | 171/7305 | 324/18723 | 2.89e-07 | 4.43e-06 | 171 |
| GO:005140217 | Oral cavity | OSCC | neuron apoptotic process | 134/7305 | 246/18723 | 5.65e-07 | 8.19e-06 | 134 |
| GO:00182098 | Oral cavity | OSCC | peptidyl-serine modification | 175/7305 | 338/18723 | 1.09e-06 | 1.46e-05 | 175 |
| GO:001810510 | Oral cavity | OSCC | peptidyl-serine phosphorylation | 164/7305 | 315/18723 | 1.51e-06 | 1.99e-05 | 164 |
| GO:004352310 | Oral cavity | OSCC | regulation of neuron apoptotic process | 111/7305 | 212/18723 | 5.12e-05 | 4.27e-04 | 111 |
| GO:199009014 | Oral cavity | OSCC | cellular response to nerve growth factor stimulus | 35/7305 | 53/18723 | 6.14e-05 | 5.02e-04 | 35 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0472225 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa04722111 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0472220 | Oral cavity | OSCC | Neurotrophin signaling pathway | 74/3704 | 119/8465 | 3.55e-05 | 1.49e-04 | 7.58e-05 | 74 |
| hsa0401014 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa041516 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
| hsa04722110 | Oral cavity | OSCC | Neurotrophin signaling pathway | 74/3704 | 119/8465 | 3.55e-05 | 1.49e-04 | 7.58e-05 | 74 |
| hsa0401015 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa0415113 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
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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 |
| NTF4 | NTRK2 | NTF5_NTRK2 | NT | Esophagus | ESCC |
| NTF4 | NTRK2 | NTF5_NTRK2 | NT | HNSCC | Precancer |
| 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 |
| NTF4 | SNV | Missense_Mutation | novel | c.572N>T | p.Arg191Leu | p.R191L | P34130 | protein_coding | deleterious(0) | probably_damaging(0.97) | TCGA-A7-A6VV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| NTF4 | SNV | Missense_Mutation | novel | c.505G>C | p.Glu169Gln | p.E169Q | P34130 | protein_coding | tolerated(0.69) | benign(0.108) | TCGA-XX-A89A-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NTF4 | SNV | Missense_Mutation | novel | c.33C>G | p.Ile11Met | p.I11M | P34130 | protein_coding | deleterious_low_confidence(0.01) | benign(0.037) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NTF4 | SNV | Missense_Mutation | rs377553005 | c.340N>T | p.Arg114Cys | p.R114C | P34130 | protein_coding | deleterious(0) | possibly_damaging(0.904) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NTF4 | SNV | Missense_Mutation | rs200675509 | c.625N>T | p.Arg209Trp | p.R209W | P34130 | protein_coding | deleterious(0) | benign(0.144) | TCGA-A5-A2K3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
| NTF4 | SNV | Missense_Mutation | novel | c.436G>A | p.Ala146Thr | p.A146T | P34130 | protein_coding | tolerated_low_confidence(0.21) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NTF4 | SNV | Missense_Mutation | rs750511722 | c.328G>A | p.Ala110Thr | p.A110T | P34130 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NTF4 | SNV | Missense_Mutation | novel | c.434A>C | p.Asn145Thr | p.N145T | P34130 | protein_coding | tolerated(0.27) | benign(0.003) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| NTF4 | SNV | Missense_Mutation | c.581N>A | p.Arg194Gln | p.R194Q | P34130 | protein_coding | tolerated(0.13) | probably_damaging(1) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| NTF4 | SNV | Missense_Mutation | c.623N>T | p.Gly208Val | p.G208V | P34130 | protein_coding | deleterious(0.01) | probably_damaging(0.991) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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 |
| 4909 | NTF4 | GROWTH FACTOR | BDNF | 7552337 |
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