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Gene: RTN4 |
Gene summary for RTN4 |
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Gene information | Species | Human | Gene symbol | RTN4 | Gene ID | 57142 |
Gene name | reticulon 4 | |
Gene Alias | ASY | |
Cytomap | 2p16.1 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9NQC3 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
57142 | RTN4 | GSM4909282 | Human | Breast | IDC | 8.74e-05 | 2.28e-01 | -0.0288 |
57142 | RTN4 | GSM4909286 | Human | Breast | IDC | 3.74e-18 | -4.73e-01 | 0.1081 |
57142 | RTN4 | GSM4909291 | Human | Breast | IDC | 2.10e-09 | -5.84e-01 | 0.1753 |
57142 | RTN4 | GSM4909294 | Human | Breast | IDC | 1.64e-16 | -4.07e-01 | 0.2022 |
57142 | RTN4 | GSM4909296 | Human | Breast | IDC | 1.71e-23 | -5.88e-01 | 0.1524 |
57142 | RTN4 | GSM4909297 | Human | Breast | IDC | 2.30e-31 | -6.23e-01 | 0.1517 |
57142 | RTN4 | GSM4909298 | Human | Breast | IDC | 2.91e-08 | -3.06e-01 | 0.1551 |
57142 | RTN4 | GSM4909301 | Human | Breast | IDC | 1.58e-06 | -3.75e-01 | 0.1577 |
57142 | RTN4 | GSM4909302 | Human | Breast | IDC | 3.57e-14 | -5.61e-01 | 0.1545 |
57142 | RTN4 | GSM4909308 | Human | Breast | IDC | 2.13e-06 | 2.69e-01 | 0.158 |
57142 | RTN4 | GSM4909309 | Human | Breast | IDC | 4.42e-10 | -5.16e-01 | 0.0483 |
57142 | RTN4 | GSM4909311 | Human | Breast | IDC | 8.17e-58 | -8.40e-01 | 0.1534 |
57142 | RTN4 | GSM4909312 | Human | Breast | IDC | 8.12e-16 | -3.53e-01 | 0.1552 |
57142 | RTN4 | GSM4909315 | Human | Breast | IDC | 1.70e-03 | -2.17e-01 | 0.21 |
57142 | RTN4 | GSM4909318 | Human | Breast | IDC | 1.69e-04 | -6.32e-01 | 0.2031 |
57142 | RTN4 | GSM4909319 | Human | Breast | IDC | 2.26e-61 | -7.34e-01 | 0.1563 |
57142 | RTN4 | GSM4909320 | Human | Breast | IDC | 1.58e-13 | -7.17e-01 | 0.1575 |
57142 | RTN4 | GSM4909321 | Human | Breast | IDC | 9.94e-19 | -2.80e-01 | 0.1559 |
57142 | RTN4 | brca1 | Human | Breast | Precancer | 2.77e-11 | 3.28e-01 | -0.0338 |
57142 | RTN4 | brca2 | Human | Breast | Precancer | 1.20e-02 | 1.91e-01 | -0.024 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00508219 | Breast | Precancer | protein stabilization | 29/1080 | 191/18723 | 1.67e-06 | 6.08e-05 | 29 |
GO:00316479 | Breast | Precancer | regulation of protein stability | 38/1080 | 298/18723 | 3.73e-06 | 1.19e-04 | 38 |
GO:00487329 | Breast | Precancer | gland development | 49/1080 | 436/18723 | 6.11e-06 | 1.73e-04 | 49 |
GO:00709725 | Breast | Precancer | protein localization to endoplasmic reticulum | 15/1080 | 74/18723 | 1.74e-05 | 4.17e-04 | 15 |
GO:00106348 | Breast | Precancer | positive regulation of epithelial cell migration | 25/1080 | 176/18723 | 2.75e-05 | 6.21e-04 | 25 |
GO:00106319 | Breast | Precancer | epithelial cell migration | 40/1080 | 357/18723 | 4.57e-05 | 9.71e-04 | 40 |
GO:00901329 | Breast | Precancer | epithelium migration | 40/1080 | 360/18723 | 5.51e-05 | 1.14e-03 | 40 |
GO:00506736 | Breast | Precancer | epithelial cell proliferation | 46/1080 | 437/18723 | 6.02e-05 | 1.23e-03 | 46 |
GO:00335983 | Breast | Precancer | mammary gland epithelial cell proliferation | 8/1080 | 26/18723 | 7.33e-05 | 1.44e-03 | 8 |
GO:00901309 | Breast | Precancer | tissue migration | 40/1080 | 365/18723 | 7.48e-05 | 1.47e-03 | 40 |
GO:00106329 | Breast | Precancer | regulation of epithelial cell migration | 33/1080 | 292/18723 | 1.74e-04 | 2.86e-03 | 33 |
GO:00506786 | Breast | Precancer | regulation of epithelial cell proliferation | 40/1080 | 381/18723 | 1.88e-04 | 3.03e-03 | 40 |
GO:00016678 | Breast | Precancer | ameboidal-type cell migration | 47/1080 | 475/18723 | 2.19e-04 | 3.35e-03 | 47 |
GO:00420633 | Breast | Precancer | gliogenesis | 33/1080 | 301/18723 | 3.06e-04 | 4.40e-03 | 33 |
GO:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
GO:19038299 | Breast | Precancer | positive regulation of cellular protein localization | 30/1080 | 276/18723 | 6.48e-04 | 7.99e-03 | 30 |
GO:00506793 | Breast | Precancer | positive regulation of epithelial cell proliferation | 24/1080 | 207/18723 | 8.88e-04 | 1.02e-02 | 24 |
GO:00018373 | Breast | Precancer | epithelial to mesenchymal transition | 19/1080 | 157/18723 | 1.78e-03 | 1.75e-02 | 19 |
GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
GO:00017017 | Breast | Precancer | in utero embryonic development | 35/1080 | 367/18723 | 2.47e-03 | 2.27e-02 | 35 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
hsa0501033 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
hsa0501043 | Breast | DCIS | Alzheimer disease | 105/846 | 384/8465 | 3.23e-23 | 1.49e-21 | 1.10e-21 | 105 |
hsa0501053 | Breast | DCIS | Alzheimer disease | 105/846 | 384/8465 | 3.23e-23 | 1.49e-21 | 1.10e-21 | 105 |
hsa0501018 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
hsa0501019 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
hsa0501044 | Cervix | N_HPV | Alzheimer disease | 41/349 | 384/8465 | 1.50e-08 | 3.13e-07 | 2.45e-07 | 41 |
hsa0501054 | Cervix | N_HPV | Alzheimer disease | 41/349 | 384/8465 | 1.50e-08 | 3.13e-07 | 2.45e-07 | 41 |
hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050104 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa050105 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa050108 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
hsa050109 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
hsa0501020 | Endometrium | AEH | Alzheimer disease | 124/1197 | 384/8465 | 1.20e-20 | 3.91e-19 | 2.86e-19 | 124 |
hsa05010110 | Endometrium | AEH | Alzheimer disease | 124/1197 | 384/8465 | 1.20e-20 | 3.91e-19 | 2.86e-19 | 124 |
hsa0501025 | Endometrium | EEC | Alzheimer disease | 126/1237 | 384/8465 | 2.25e-20 | 7.40e-19 | 5.52e-19 | 126 |
hsa0501035 | Endometrium | EEC | Alzheimer disease | 126/1237 | 384/8465 | 2.25e-20 | 7.40e-19 | 5.52e-19 | 126 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
RTN4 | insertion | Frame_Shift_Ins | novel | c.2903_2904insGGAATGTTCCC | p.Lys969GlufsTer10 | p.K969Efs*10 | Q9NQC3 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RTN4 | insertion | Frame_Shift_Ins | novel | c.2561_2562insTT | p.Arg854SerfsTer2 | p.R854Sfs*2 | Q9NQC3 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RTN4 | insertion | Frame_Shift_Ins | novel | c.2007dupA | p.Val670SerfsTer9 | p.V670Sfs*9 | Q9NQC3 | protein_coding | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
RTN4 | SNV | Missense_Mutation | novel | c.631N>A | p.Glu211Lys | p.E211K | Q9NQC3 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
RTN4 | SNV | Missense_Mutation | novel | c.3284N>A | p.Ala1095Asp | p.A1095D | Q9NQC3 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
RTN4 | SNV | Missense_Mutation | c.2027N>C | p.Glu676Ala | p.E676A | Q9NQC3 | protein_coding | tolerated(0.48) | benign(0.217) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RTN4 | SNV | Missense_Mutation | novel | c.2377C>T | p.Pro793Ser | p.P793S | Q9NQC3 | protein_coding | tolerated(0.19) | benign(0.005) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
RTN4 | SNV | Missense_Mutation | novel | c.2165N>T | p.Ala722Val | p.A722V | Q9NQC3 | protein_coding | tolerated(0.05) | possibly_damaging(0.824) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RTN4 | SNV | Missense_Mutation | c.2405N>A | p.Ser802Tyr | p.S802Y | Q9NQC3 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
RTN4 | SNV | Missense_Mutation | novel | c.1731N>T | p.Met577Ile | p.M577I | Q9NQC3 | protein_coding | tolerated(1) | benign(0.003) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
57142 | RTN4 | DRUGGABLE GENOME | HYPERBARIC OXYGEN | 12951059 | ||
57142 | RTN4 | DRUGGABLE GENOME | inhibitor | CHEMBL2108679 | OZANEZUMAB | |
57142 | RTN4 | DRUGGABLE GENOME | ATI-355 | ATINUMAB | 22544872 | |
57142 | RTN4 | DRUGGABLE GENOME | ANTISENSE OLIGONUCLEOTIDES | 14574981 | ||
57142 | RTN4 | DRUGGABLE GENOME | antibody | 249565934 | OZANEZUMAB |
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